Name: sedimentation equilibrium of a small oligomer-forming membrane protein: effect of histidine protonation on pentameric stability
Uploaded: 2015-04-02T15:00:00
Description: Watch this Scientific Journal Video about Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability at JoVE.com

This work has been funded by the National Research Foundation grant NRF-CRP4-2008-02 (J.T.) and Tier 1 grant RG 51/13.

This protocol is based on the following resources, which are to be referred for more details and special considerations3,25-28.
1. Density matching of detergent micelles with 2H2O
Note: The density of the buffer solution needs to be matched to the density of the detergent micelles. Common density-adjusting agents include 2H2O, H218O, 2H218</sup...

<ol>
	<li>Laue, T. M., Stafford, W. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Modern+applications+of+analytical+ultracentrifugation.">Modern applications of analytical ultracentrifugation.</a> Annu. Rev. Biophys. Biomol. Struct. 28, 75-100 (1999).</li><li>Lebowitz, J., Lewis, M. S., Schuck, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Modern+analytical+ultracentrifugation+in+protein+science:+A+tutorial+review.">Modern analytical ultracentrifugation in protein science: A tutorial review.</a> Protein Sci. 11, 2067-2079 (2002).</li><li>Balbo, A., Zhao, H., Brown, P. H., Schuck, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Assembly, Loading, and Alignment of an Analytical Ultracentrifuge Sample Cell. , e1530 (2009).</li><li>Rivas, G., Stafford, W., Minton, A. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Characterization+of+heterologous+protein-protein+interactions+using+analytical+ultracentrifugation.">Characterization of heterologous protein-protein interactions using analytical ultracentrifugation.</a> Methods-a Companion to Methods in Enzymology. 19, 194-212 (1999).</li><li>Howlett, G. J., Minton, A. P., Rivas, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analytical+ultracentrifugation+for+association+and+assembly+the+study+of+protein.">Analytical ultracentrifugation for association and assembly the study of protein.</a> Curr. Opin. Chem. Biol. 10, 430-436 (2006).</li><li>MacGregor, I. K., Anderson, A. L., Laue, T. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fluorescence+detection+for+the+XLI+analytical+ultracentrifuge.">Fluorescence detection for the XLI analytical ultracentrifuge.</a> Biophys. Chem. 108, 165-185 (2004).</li><li>Phizicky, E. M., Fields, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein-Protein+Interactions+-+Methods+for+Detection+and+Analysis.">Protein-Protein Interactions - Methods for Detection and Analysis.</a> Microbiol. Rev. 59, 94-123 (1995).</li><li>Alexandrov, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+facile+method+for+high-throughput+co-expression+of+protein+pairs.">A facile method for high-throughput co-expression of protein pairs.</a> Mol. Cell. Proteomics. 3, 934-938 (2004).</li><li>Nooren, I. M. A., Thornton, J. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structural+characterisation+and+functional+significance+of+transient+protein-protein+interactions.">Structural characterisation and functional significance of transient protein-protein interactions.</a> J. Mol. Biol. 325, 991-1018 (2003).</li><li>Ebel, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sedimentation+velocity+to+characterize+surfactants+and+solubilized+membrane+proteins.">Sedimentation velocity to characterize surfactants and solubilized membrane proteins.</a> Methods. 54, 56-66 (2011).</li><li>Minton, A. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantitative+characterization+of+reversible+macromolecular+associations+via+sedimentation+equilibrium:+an+introduction.">Quantitative characterization of reversible macromolecular associations via sedimentation equilibrium: an introduction.</a> Exp. Mol. Med. 32, 1-5 (2000).</li><li>Dowell, S. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Respiratory+syncytial+virus+is+an+important+cause+of+community-acquired+lower+respiratory+infection+among+hospitalized+adults.">Respiratory syncytial virus is an important cause of community-acquired lower respiratory infection among hospitalized adults.</a> J. Infect. Dis. 174, 456-462 (1996).</li><li>Bukreyev, A., Whitehead, S. S., Murphy, B. R., Collins, P. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Recombinant+respiratory+syncytial+virus+from+which+the+entire+SH+gene+has+been+deleted+grows+efficiently+in+cell+culture+and+exhibits+site-specific+attenuation+in+the+respiratory+tract+of+the+mouse.">Recombinant respiratory syncytial virus from which the entire SH gene has been deleted grows efficiently in cell culture and exhibits site-specific attenuation in the respiratory tract of the mouse.</a> J. Virol. 71, 8973-8982 (1997).</li><li>Fuentes, S., Tran, K. C., Luthra, P., Teng, M. N., He, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Function+of+the+respiratory+syncytial+virus+small+hydrophobic+protein.">Function of the respiratory syncytial virus small hydrophobic protein.</a> J. Virol. 81, 8361-8366 (2007).</li><li>Jin, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Recombinant+respiratory+syncytial+viruses+with+deletions+in+the+NS1,+NS2,+SH,+and+M2-2+genes+are+attenuated+in+vitro+and+in+vivo.">Recombinant respiratory syncytial viruses with deletions in the NS1, NS2, SH, and M2-2 genes are attenuated in vitro and in vivo.</a> Virology. 273, 210-218 (2000).</li><li>Karron, R. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Respiratory+syncytial+virus+(RSV)+SH+and+G+proteins+are+not+essential+for+viral+replication+in+vitro:+clinical+evaluation+and+molecular+characterization+of+a+cold-passaged,+attenuated+RSV+subgroup+B.">Respiratory syncytial virus (RSV) SH and G proteins are not essential for viral replication in vitro: clinical evaluation and molecular characterization of a cold-passaged, attenuated RSV subgroup B.</a> Proc. Nat. Acad. Sci. USA. 94, 13961-13966 (1997).</li><li>Whitehead, S. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Recombinant+respiratory+syncytial+virus+bearing+a+deletion+of+either+the+NS2+or+SH+gene+is+attenuated+in+chimpanzees.">Recombinant respiratory syncytial virus bearing a deletion of either the NS2 or SH gene is attenuated in chimpanzees.</a> J. Virol. 73, 3438-3442 (1999).</li><li>Rixon, H. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+small+hydrophobic+(SH)+protein+accumulates+within+lipid-raft+structures+of+the+Golgi+complex+during+respiratory+syncytial+virus+infection.">The small hydrophobic (SH) protein accumulates within lipid-raft structures of the Golgi complex during respiratory syncytial virus infection.</a> J. Gen. Virol. 85, 1153-1165 (2004).</li><li>Collins, P. L., Mottet, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Membrane+orientation+and+oligomerization+of+the+small+hydrophobic+protein+of+human+respiratory+syncytial+virus.">Membrane orientation and oligomerization of the small hydrophobic protein of human respiratory syncytial virus.</a> J. Gen. Virol. 74, 1445-1450 (1993).</li><li>Collins, P. L., Olmsted, R. A., Johnson, P. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+small+hydrophobic+protein+of+human+respiratory+syncytial+virus:+comparison+between+antigenic+subgroups+A+and+B.">The small hydrophobic protein of human respiratory syncytial virus: comparison between antigenic subgroups A and B.</a> J. Gen. Virol. 71, 1571-1576 (1990).</li><li>Chen, M. D., Vazquez, M., Buonocore, L., Kahn, J. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Conservation+of+the+respiratory+syncytial+virus+SH+gene.">Conservation of the respiratory syncytial virus SH gene.</a> J. Infect. Dis. 182, 1228-1233 (2000).</li><li>Gan, S. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+small+hydrophobic+protein+of+the+human+respiratory+syncytial+virus+forms+pentameric+ion+channels.">The small hydrophobic protein of the human respiratory syncytial virus forms pentameric ion channels.</a> J. Biol. Chem. 287, 24671-24689 (2012).</li><li>Gan, S. W., Ng, L., Xin, L., Gong, X., Torres, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structure+and+ion+channel+activity+of+the+human+respiratory+syncytial+virus+(hRSV)+small+hydrophobic+protein+transmembrane+domain.">Structure and ion channel activity of the human respiratory syncytial virus (hRSV) small hydrophobic protein transmembrane domain.</a> Protein Sci. 17, 813-820 (2008).</li><li>Li, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Inhibition+of+the+Human+Respiratory+Syncytial+Virus+Small+Hydrophobic+Protein+and+Structural+variations+in+a+bicelle+environment.">Inhibition of the Human Respiratory Syncytial Virus Small Hydrophobic Protein and Structural variations in a bicelle environment.</a> J. Virol. 88 (22), 11899-914 (2014).</li><li>Burgess, N. K., Stanley, A. M., Fleming, K. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Determination+of+membrane+protein+molecular+weights+and+association+equilibrium+constants+using+sedimentation+equilibrium+and+sedimentation+velocity.">Determination of membrane protein molecular weights and association equilibrium constants using sedimentation equilibrium and sedimentation velocity.</a> Meth. Cell. Biol. 84, 181-211 (2008).</li><li>Cole, J. L., Lary, J. W., Moody, T. P., Laue, T. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analytical+Ultracentrifugation:+Sedimentation+Velocity+and+Sedimentation+Equilibrium.">Analytical Ultracentrifugation: Sedimentation Velocity and Sedimentation Equilibrium.</a> Meth. Cell. Biol. 84, 143-179 (2008).</li><li>Fleming, K. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Determination+of+membrane+protein+molecular+weight+using+sedimentation+equilibrium+analytical+ultracentrifugation.">Determination of membrane protein molecular weight using sedimentation equilibrium analytical ultracentrifugation.</a> Curr. Protoc. Prot. Sci. 53, 17.12.11-17.12.13 (2008).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> An-50 Ti and An-60 Ti Analytical Rotor, Cells, and Counterbalance. , (2005).</li><li>Mayer, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Studying+membrane+proteins+in+detergent+solution+by+analytical+ultracentrifugation:+Different+methods+for+density+matching.">Studying membrane proteins in detergent solution by analytical ultracentrifugation: Different methods for density matching.</a> Prog. Colloid Polym. Sci. 113, 176-181 (1999).</li><li>Laue, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ch.+20.3.">Ch. 20.3.</a> Current Protocols in Protein Science. 20, 20.23.21-20.23.13 (2001).</li><li>Gan, S. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Small+Hydrophobic+Protein+Of+The+Human+Respiratory+Syncytial+Virus+Forms+Pentameric+Ion+Channels.">The Small Hydrophobic Protein Of The Human Respiratory Syncytial Virus Forms Pentameric Ion Channels.</a> J. Biol. Chem. 287, 24671-24689 (2012).</li><li>Bevington, P. R., Robinson, D. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Data reduction and error analysis for the physical sciences. 336, (1969).</li><li>Schuck, P., Radu, C. G., Ward, E. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sedimentation+equilibrium+analysis+of+recombinant+mouse+FcRn+with+murine+IgG1.">Sedimentation equilibrium analysis of recombinant mouse FcRn with murine IgG1.</a> Molecular Immunology. 36, 1117-1125 (1999).</li><li>Gan, S. W., Vararattanavech, A., Nordin, N., Eshaghi, S., Torres, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+cost-effective+method+for+simultaneous+homo-oligomeric+size+determination+and+monodispersity+conditions+for+membrane+proteins.">A cost-effective method for simultaneous homo-oligomeric size determination and monodispersity conditions for membrane proteins.</a> Anal. Biochem. 416, 100-106 (2011).</li><li>Montserret, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=NMR+structure+and+ion+channel+activity+of+the+p7+protein+from+hepatitis+C+virus).">NMR structure and ion channel activity of the p7 protein from hepatitis C virus).</a> J. Biol. Chem. 285, 31446-31461 (2010).</li><li>Stouffer, A. L., DeGrado, W. F., Lear, J. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analytical+Ultracentrifugation+Studies+of+the+Influenza+M2+Homotetramerization+Equilibrium+in+Detergent+Solutions.">Analytical Ultracentrifugation Studies of the Influenza M2 Homotetramerization Equilibrium in Detergent Solutions.</a> Progr Colloid Polym Sci. 131, 108-115 (2006).</li><li>Sorkin, A., von Zastrow, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Signal+transduction+and+endocytosis:+Close+encounters+of+many+kinds.">Signal transduction and endocytosis: Close encounters of many kinds.</a> Nat. Rev. Mol. Cell Biol. 3, 600-614 (2002).</li><li>Gan, S. W., Ng, L., Lin, X., Gong, X., Torres, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structure+and+ion+channel+activity+of+the+human+respiratory+syncytial+virus+(hRSV)+small+hydrophobic+protein+transmembrane+domain.">Structure and ion channel activity of the human respiratory syncytial virus (hRSV) small hydrophobic protein transmembrane domain.</a> Protein science : a publication of the Protein Society. 17, 813-820 (2008).</li></ol>

This paper provides an experimental protocol for sample preparation and analysis of oligomerization of a small membrane protein in detergent using equilibrium sedimentation. The protocol described is equally valid &#8211;and simpler- for soluble proteins, as the density matching step is not required. Indeed, the system is constituted by a mixture of detergent and protein. To conduct sedimentation studies, the detergent must be invisible to the gravitational field so that it does not contribute to the particle flotation. ...

Analytical ultracentrifugation1-5 is one of the most important methods to study interactions of macromolecules under physiological conditions, being accessible to both weak and strong interactions. The method is label-free and uses light absorption or interference, and even fluorescence optical systems can be used to access concentration ranges over several orders of magnitude6.
This method is especially useful since most biochemical processes depend on reversible interactions. The stoichiometry and strength of these interactions have to be quantitatively characterized to understand biological processes, and a number of methods exist for this purpose 7,8. However, transient interactions are difficult to study 9.
The choice of a method to characterize macromolecular interactions depends on its static or dynamic nature. In the first case, sedimentation velocity (SV) is used, where the rate of radial transport is measured and complexes are fractionated on the basis of differences in buoyant mass and shape.
In contrast, dynamic associations that are reversible on the time scale of the experiment cannot be physically separated. In this case, self- or hetero-interactions leading to non-covalent interactions are in an equilibrium that depends on the total protein concentration. These dynamic interactions can be studied by both sedimentation equilibrium (SE) and sedimentation velocity (SV) 10. However, the first method is simpler to perform and is described here. In SE, centrifugation is performed at a sufficiently low speed so that an equilibrium is reached between diffusion and sedimentation. At this point, the equilibrium profile of an optical signal (UV-VIS) as a function of radial distance, can be analyzed using pre-set thermodynamic models for associations11.
In the present paper, a sedimentation equilibrium study is presented of the self-association of a viral membrane protein that forms ion channels. Because of its hydrophobicity, the experiment is run in presence of detergent, and in this case the density of solvent has to be matched to that of the detergent. However, the protocol described would identical in the case of a water soluble protein, except that no solvent density matching would be required.
The protein used is encoded in the human respiratory syncytial virus (hRSV), an enveloped pneumovirus in the paramyxoviridae family that causes lower respiratory tract disease in infants, elderly and immunocompromised populations worldwide 12. Up to 64 million reported cases of hRSV infection and 160,000 deaths occur each year.
The hRSV genome transcribes 11 proteins, including the three membrane proteins F, G, and small hydrophobic (SH). SH protein is involved in the pathogenesis of RSV infection. RSV lacking the SH gene (RSV&#916;SH) was viable, caused formation of syncytia and grew as well as the wild-type (WT) virus 13-16. However, RSV&#916;SH virus replicated 10-fold less efficiently than the WT in the upper respiratory tract 15,16. Also, RSV&#916;SH virus was attenuated in in vivo mouse and chimpanzee models 13,17.
The SH protein is a 64 (RSV subgroup A) or 65 (RSV subgroup B) amino acids long type II integral membrane protein that &#160;accumulates mostly at the membranes of the Golgi compartment 18. &#160;SH protein has a single predicted a-helical transmembrane (TM) domain 19 which is highly conserved 20,21. The C- and N-terminal extramembrane domains are oriented lumenally/extracellularly and cytoplasmically, respectively.
Both synthetic TM domain (residues 18-43) and full length SH protein have been shown to form homopentamers in a variety of detergents. The homopentameric form is responsible for channel activity in planar lipid bilayers 22,23. The correct orientation of the TM monomers in the lipid bilayer was first determined using site specific infrared dichroism 23, which showed His-22 to be in a lumenal, close to inter-helical, orientation. The same TM domain orientation was confirmed by NMR studies that reconstructed the pentameric a-helical bundle of the full-length protein in dodecylphosphocholine (DPC) micelles 22. In this &#8216;micelle&#8217; model, a single a- helical TM domain was flanked N-terminally by an a-helix, and C-terminally by an extended b-hairpin. The two protonatable residues of SH protein, His-22 and His-51, are located in the TM domain (lumenally oriented), and at the tip of the extramembrane C-terminal &#946; hairpin (far from the channel pore), respectively. In a bicellar environment, however, the TM &#945;-helix&#160; extends up to His-51, and both His residues are accessible to the lumen of the channel24. The channel structure adopts a &#160;funnel-like architecture 22, where the narrower region (Ser-29 to Cys-45) 22 is lined with hydrophobic side chains (Ile-32, Ile-36, Ile-40 and Leu-44), and Ile-36 defines the narrowest point in the channel lumen. His-22 is located at the largest opening of this funnel, whereas His-51 is at the tip of the smallest opening.
In the present paper, analytical centrifugation in a sedimentation equilibrium mode has been used to determine if His protonation affects the stability of the SH protein pentamer. In this case, SH protein was solubilized in C14-betaine detergent, which has been used previously to show that SH protein forms pentameric oligomers22.

<table border="0" cellpadding="0" cellspacing="0" width="1345">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:632px;">Name of Material/ Equipment</td>
			<td style="width:147px;">Company</td>
			<td style="width:119px;">Catalog Number</td>
			<td style="width:448px;">Comments/Description</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:632px;">3-(N,N-dimethylmyristylammonio)propanesulfonate</td>
			<td style="width:147px;">Sigma</td>
			<td style="width:119px;">T0807</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:632px;">Deuterium oxide 99.8%</td>
			<td style="width:147px;">Cambridge Isotope</td>
			<td style="width:119px;">DLM-4-99.8</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:632px;">An-50 Ti Rotor, Analytical, 8-Place</td>
			<td style="width:147px;">Beckman Coulter</td>
			<td align="right" style="width:119px;">363782</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:632px;">An-60 Ti Rotor, Analytical, 4-Place</td>
			<td style="width:147px;">Beckman Coulter</td>
			<td align="right" style="width:119px;">361964</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:632px;">Cell housing</td>
			<td style="width:147px;">Beckman Coulter</td>
			<td align="right" style="width:119px;">334784</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:632px;">12 mm six-channel centerpiece, epon charcoal-filled</td>
			<td style="width:147px;">Beckman Coulter</td>
			<td align="right" style="width:119px;">331376</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:632px;">Window holder</td>
			<td style="width:147px;">Beckman Coulter</td>
			<td align="right" style="width:119px;">305037</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:632px;">Window gasket</td>
			<td style="width:147px;">Beckman Coulter</td>
			<td align="right" style="width:119px;">327021</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:632px;">Window liner</td>
			<td style="width:147px;">Beckman Coulter</td>
			<td align="right" style="width:119px;">362329</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:632px;">Sapphire window</td>
			<td style="width:147px;">Beckman Coulter</td>
			<td align="right" style="width:119px;">307177</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:632px;">Quartz window</td>
			<td style="width:147px;">Beckman Coulter</td>
			<td align="right" style="width:119px;">301730</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:632px;">Screw-ring washer</td>
			<td style="width:147px;">Beckman Coulter</td>
			<td align="right" style="width:119px;">362328</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:632px;">Screw ring</td>
			<td style="width:147px;">Beckman Coulter</td>
			<td align="right" style="width:119px;">301922</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:632px;">Spinkote</td>
			<td style="width:147px;">Beckman Coulter</td>
			<td align="right" style="width:119px;">306812</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:632px;">Torque stand assembly</td>
			<td style="width:147px;">Beckman Coulter</td>
			<td align="right" style="width:119px;">361318</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:632px;">Counterbalance</td>
			<td style="width:147px;">Beckman Coulter</td>
			<td align="right" style="width:119px;">360219</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:632px;">Cell alignment tool</td>
			<td style="width:147px;">Beckman Coulter</td>
			<td align="right" style="width:119px;">362340</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">SEDNTERP</td>
			<td style="width:147px;"></td>
			<td style="width:119px;"></td>
			<td>http://bitcwiki.sr.unh.edu/index.php/Main_Page</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">HeteroAnalysis&#160;</td>
			<td style="width:147px;"></td>
			<td style="width:119px;"></td>
			<td>http://www.biotech.uconn.edu/auf/?i=aufftp</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">SEDFIT</td>
			<td style="width:147px;"></td>
			<td style="width:119px;"></td>
			<td>http://www.analyticalultracentrifugation 
			.com/sedfit.htm</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">SEDPHAT</td>
			<td style="width:147px;"></td>
			<td style="width:119px;"></td>
			<td>http://www.analyticalultracentrifugation 
			.com/sedphat/default.htm</td>
		</tr>
	</tbody>
</table>

sedimentation equilibrium of a small oligomer-forming membrane protein: effect of histidine protonation on pentameric stability

Analytical ultracentrifugation (AUC) can be used to study reversible interactions between macromolecules over a wide range of interaction strengths and under physiological conditions. This makes AUC a method of choice to quantitatively assess stoichiometry and thermodynamics of homo- and hetero-association that are transient and reversible in biochemical processes. In the modality of sedimentation equilibrium (SE), a balance between diffusion and sedimentation provides a profile as a function of radial distance that depends on a specific association model. Herein, a detailed SE protocol is described to determine the size and monomer-monomer association energy of a small membrane protein oligomer using an analytical ultracentrifuge. AUC-ES is label-free, only based on physical principles, and can be used on both water soluble and membrane proteins. An example is shown of the latter, the small hydrophobic (SH) protein in the human respiratory syncytial virus (hRSV), a 65-amino acid polypeptide with a single &#945;-helical transmembrane (TM) domain that forms pentameric ion channels. NMR-based structural data shows that SH protein has two protonatable His residues in its transmembrane domain that are oriented facing the lumen of the channel. SE experiments have been designed to determine how pH affects association constant and the oligomeric size of SH protein. While the pentameric form was preserved in all cases, its association constant was reduced at low pH. These data are in agreement with a similar pH dependency observed for SH channel activity, consistent with a lumenal orientation of the two His residues in SH protein. The latter may experience electrostatic repulsion and reduced oligomer stability at low pH. In summary, this method is applicable whenever quantitative information on subtle protein-protein association changes in physiological conditions have to be measured.&#160;&#160;

The radial distribution profile of C14SB detergent micelles in 50 mM Tris, 100 mM NaCl pH 7.3 forms a very shallow exponential that could be fitted to a linear model (Figure 7A). The slope of this distribution is inversely correlated to D2O concentration (Figure 7B). The point where the slope is zero, i.e., the matching D2O concentration, was found to be 32.3%.
See Figure 7 Below.
<p class="j...

Watch this Scientific Journal Video about Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability at JoVE.com

Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability

Sedimentation equilibrium (SE) can be used to study protein-protein interactions in a physiological environment. This manuscript describes the use of this technique to determine the effect of pH on the stability of a homo-pentamer formed by the small hydrophobic (SH) protein encoded by the human syncytial respiratory virus (hRSV).

Analytical ultracentrifugation (AUC) can be used to study reversible interactions between macromolecules over a wide range of interaction strengths and ...

sedimentation-equilibrium-small-oligomer-forming-membrane-protein

Research

Education

JoVE Journal

JoVE Core

Chemistry

Acids and Bases

SCIENTISTS IN ACTION

Iridium(III) Luminescent Probe for Detection of the Malarial Protein Biomarker Histidine Rich Protein-II

This work outlines the synthesis of a non-emissive, cyclometalated Ir(III) complex, Ir(ppy)2(H2O)2+ (Ir1), which elicits a rapid, long-lived phosphorescent signal when coordinated to a histidine-containing protein immobilized on the surface of a magnetic particle. Synthesis of Ir1, in high yields,is complete O/N&#160;and involves splitting of the parent cyclometalated Ir(III) chloro-bridged dimer into two equivalents of the solvated complex. To confirm specificity, several amino acids were probed for coordination activity when added to the synthesized probe, and only histidine elicited a signal response. Using BNT-II, a branched peptide mimic of the malarial biomarker Histidine Rich Protein II (pfHRP-II), the iridium probe was validated as a tool for HRP-II detection. Quenching effects were noted in the BNT-II/Ir1 titration when compared to L-Histidine/Ir1, but these were attributed to steric hindrance and triplet state quenching. Biolayer interferometry was used to determine real-time kinetics of interaction of Ir1 with BNT-II. Once the system was optimized, the limit of detection of rcHRP-II using the probe was found to be 12.8 nM in solution. When this protein was immobilized on the surface of a 50 &#181;m magnetic agarose particle, the limit of detection was 14.5 nM. The robust signal response of this inorganic probe, as well as its flexibility of use in solution or immobilized on a surface, can lend itself toward a variety of applications, from diagnostic use to imaging.

IridiumIII Luminescent Probe for Detection of the Malarial Protein Biomarker Histidine Rich Protein-II

Robust detection reagents are of increasing necessity for developing new malaria diagnostic tools. An iridium(III) probe was designed that emits long-lasting luminescent signal in the presence of a histidine-rich malarial protein biomarker. Detection of the protein either in solution or immobilized on a magnetic particle affords flexibility in application.

This work outlines the synthesis of a non-emissive, cyclometalated Ir(III) complex, Ir(ppy)2(H2O)2+ (Ir1), which elicits a rapid, long-lived ...

Dynamic Electrochemical Measurement of Chloride Ions

This protocol describes the dynamic measurement of chloride ions using the transition time of a silver silver chloride (Ag/AgCl) electrode. Silver silver chloride electrode is used extensively for potentiometric measurement of chloride ions concentration in electrolyte. In this measurement, long-term and continuous monitoring is limited due to the inherent drift and the requirement of a stable reference electrode. We utilized the chronopotentiometric approach to minimize drift and avoid the use of a conventional reference electrode. A galvanostatic pulse is applied to an Ag/AgCl electrode which initiates a faradic reaction depleting the Cl&#713; ions near the electrode surface. The transition time, which is the time to completely deplete the ions near the electrode surface, is a function of the ion concentration, given by the Nernst equation. The square root of the transition time is in linear relation to the chloride ion concentration. Drift of the response over two weeks is negligible (59 &#181;M/day) when measuring 1 mM [Cl&#713;]using a current pulse of 10 Am-2. This is a dynamic measurement where the moment of transition time determines the response and thus is independent of the absolute potential. Any metal wire can be used as a pseudo-reference electrode, making this approach feasible for long-term measurement inside concrete structures.

Dynamic measurement of chloride ions is presented. Transition time of an Ag/AgCl electrode, during a chronopotentiometric technique, can give the concentration of chloride ions in electrolyte. This method does not require a stable conventional reference electrode.

This protocol describes the dynamic measurement of chloride ions using the transition time of a silver silver chloride (Ag/AgCl) electrode. Silver silver ...

Site Directed Spin Labeling and EPR Spectroscopic Studies of Pentameric Ligand-Gated Ion Channels

Ion channel gating is a stimulus-driven orchestration of protein motions that leads to transitions between closed, open, and desensitized states. Fundamental to these transitions is the intrinsic flexibility of the protein, which is critically modulated by membrane lipid-composition. To better understand the structural basis of channel function, it is necessary to study protein dynamics in a physiological membrane environment. Electron Paramagnetic Resonance (EPR) spectroscopy is an important tool to characterize conformational transitions between functional states. In comparison to NMR and X-ray crystallography, the information obtained from EPR is intrinsically of lower resolution. However, unlike in other techniques, in EPR there is no upper-limit to the molecular weight of the protein, the sample requirements are significantly lower, and more importantly the protein is not constrained by the crystal lattice forces. Therefore, EPR is uniquely suited for studying large protein complexes and proteins in reconstituted systems. In this article, we will discuss general protocols for site-directed spin labeling and membrane reconstitution using a prokaryotic proton-gated pentameric Ligand-Gated Ion Channel (pLGIC) from Gloeobacter violaceus (GLIC) as an example. A combination of steady-state Continuous Wave (CW) and Pulsed (Double Electron Electron Resonance-DEER) EPR approaches will be described that will enable a complete quantitative characterization of channel dynamics.

This article describes methods for site-directed spin labeling and reconstitution of pentameric ligand-gated channels for Electron Paramagnetic Resonance studies. This protocol can be adapted for any membrane protein. The reconstitution method described here can also be used for patch-clamp measurements of macroscopic and single-channel currents in a defined lipid system.

Ion channel gating is a stimulus-driven orchestration of protein motions that leads to transitions between closed, open, and desensitized states. ...

Original Experimental Approach for Assessing Transport Fuel Stability

The study of fuel oxidation stability is an important issue for the development of future fuels. Diesel and kerosene fuel systems have undergone several technological changes to fulfill environmental and economic requirements. These developments have resulted in increasingly severe operating conditions whose suitability for conventional and alternative fuels needs to be addressed. For example, fatty acid methyl esters (FAMEs) introduced as biodiesel are more prone to oxidation and may lead to deposit formation. Although several methods exist to evaluate fuel stability (induction period, peroxides, acids, and insolubles), no technique allows one to monitor the real-time oxidation mechanism and to measure the formation of oxidation intermediates that may lead to deposit formation. In this article, we developed an advanced oxidation procedure (AOP) based on two existing reactors. This procedure allows the simulation of different oxidation conditions and the monitoring of the oxidation progress by the means of macroscopic parameters, such as total acid number (TAN) and advanced analytical methods like gas chromatography coupled to mass spectrometry (GC-MS) and Fourier Transform Infrared - Attenuated Total Reflection (FTIR-ATR). We successfully applied AOP to gain an in-depth understanding of the oxidation kinetics of a model molecule (methyl oleate) and commercial diesel and biodiesel fuels. These developments represent a key strategy for fuel quality monitoring during logistics and on-board utilization.

Oxidation stability of transport fuels has become a concern for future fuel development. This work presents an original methodology developed by IFP Energies Nouvelles for assessing fuel stability using two different reactors. This methodology was successfully applied to gain an in-depth understanding of the oxidation kinetics and pathways of model molecules and commercial fuels.

The study of fuel oxidation stability is an important issue for the development of future fuels. Diesel and kerosene fuel systems have undergone several ...

Application and Methodology of the Non-destructive 19F Time-domain NMR Technique to Measure the Content in Fluorine-containing Drug Products

Here, we describe a protocol developed by our group that uses low-field fluorine-19 (19F) time-domain (TD) nuclear magnetic resonance (NMR) to measure the average content of fluorinated drugs in their formulated drug product forms: tablets or capsules. This method is specific to fluorinated drugs because it detects only the content of fluorine, avoiding interference from the excipients that lack fluorine. The advantages of measuring the active content of fluorinated drugs using low-field 19F TD-NMR versus high-field 19F solid-state (SS) NMR are the simplicity of the method; the low cost; and the non-destructive nature of the technique, with all samples recoverable in intact forms (e.g., powders, tablets, and capsules), making this technique affordable for any laboratory.
We have tested the method with three fluorinated drug products available on the market - cinacalcet, lansoprazole, and ciprofloxacin - with doses ranging from 15 to 500 mg. The results of the analyses, measured by low-field 19F TD-NMR, supported the reported label claims for the average drug content.
Based on the simplicity and reproducibility of the analysis, we envision this methodology being implemented in any laboratory, including manufacturing plants, as a process analytical technology (PAT) tool in the pharmaceutical industry.

Application and Methodology of the Non-destructive 19F Time-domain NMR Technique to Measure the Content in Fluorine-containing Drug Products

A simple and non-destructive technique that measures the average content of drug substances in formulated drug products containing fluorine using low-field fluorine-19 (19F) time-domain (TD) nuclear magnetic resonance (NMR) is presented here. The technique can be applied to the development and manufacturing of drugs in the pharmaceutical industry.

Here, we describe a protocol developed by our group that uses low-field fluorine-19 (19F) time-domain (TD) nuclear magnetic resonance (NMR) to measure the ...

The Effect of Interfacial Chemical Bonding in TiO2-SiO2 Composites on Their Photocatalytic NOx Abatement Performance

The chemical bonding of particulate photocatalysts to supporting material surfaces is of great importance in engineering more efficient and practical photocatalytic structures. However, the influence of such chemical bonding on the optical and surface properties of the photocatalyst and thus its photocatalytic activity/reaction selectivity behavior has not been systematically studied. In this investigation, TiO2 has been supported on the surface of SiO2 by means of two different methods: (i) by the in situ formation of TiO2 in the presence of sand quartz via a sol-gel method employing tetrabutyl orthotitanium (TBOT); and (ii) by binding the commercial TiO2 powder to quartz on a surface silica gel layer formed from the reaction of quartz with tetraethylorthosilicate (TEOS). For comparison, TiO2 nanoparticles were also deposited on the surfaces of a more reactive SiO2 prepared by a hydrolysis-controlled sol-gel technique as well as through a sol-gel route from TiO2 and SiO2 precursors. The combination of TiO2 and SiO2, through interfacial Ti-O-Si bonds, was confirmed by FTIR spectroscopy and the photocatalytic activities of the obtained composites were tested for photocatalytic degradation of NO according to the ISO standard method (ISO 22197&#8722;1). The electron microscope images of the obtained materials showed that variable photocatalyst coverage of the support surface can successfully be achieved but the photocatalytic activity towards NO removal was found to be affected by the preparation method and the nitrate selectivity is adversely affected by Ti-O-Si bonding.

The Effect of Interfacial Chemical Bonding in TiO2-SiO2 Composites on Their Photocatalytic NOx Abatement Performance

The focus of the present work is to establish means to generate and quantify levels of Ti-O-Si linkages and to correlate these with the photocatalytic properties of the supported TiO2.

The chemical bonding of particulate photocatalysts to supporting material surfaces is of great importance in engineering more efficient and practical ...

The Effect of Charging and Discharging Lithium Iron Phosphate-graphite Cells at Different Temperatures on Degradation

The effect of charging and discharging lithium iron phosphate-graphite cells at different temperatures on their degradation is evaluated systematically. The degradation of the cells is assessed by using 10 charging and discharging temperature permutations ranging from -20 &#176;C to 30 &#176;C. This allows an analysis of the effect of charge and discharge temperatures on aging, and their associations. A total of 100 charge/discharge cycles were carried out. Every 25 cycles a reference cycle was performed to assess the reversible and irreversible capacity degradation. A multi-factor analysis of variance was used, and the experimental results were fitted showing: i) a quadratic relationship between the rate of degradation and the temperature of charge, ii) a linear relationship with the temperature of discharge, and iii) a correlation between the temperature of charge and discharge. It was found that the temperature combination for charging at +30 &#176;C and discharging at -5 &#176;C led to the highest rate of degradation. On the other hand, the cycling in a temperature range from -20 &#176;C to 15 &#176;C (with various combinations of temperatures of charge and discharge), led to a much lower degradation. Additionally, when the temperature of charge is 15 &#176;C, it was found that the degradation rate is nondependent on the temperature of discharge.

This article describes the effect of dissimilar charging/discharging temperatures on the degradation of lithium iron phosphate-graphite pouch cells, aiming at simulating close to real case scenarios. In total, 10 temperature combinations are investigated in the range -20 to 30 &#176;C in order to analyze the impact of temperature on degradation.

The effect of charging and discharging lithium iron phosphate-graphite cells at different temperatures on their degradation is evaluated systematically. ...

The Effect of Ultraviolet Radiation on the Chemical Bath Deposition of Bis(thiourea) Cadmium Chloride Crystals and the Subsequent CdS Obtention

In this work, the effects on the preparation of bis(thiourea) cadmium chloride crystals when illuminated with ultraviolet (UV) light at a wavelength of 367 nm using the chemical bath deposition technique are studied comparatively. Two experiments are performed to make a comparison: one without UV light and the other with the aid of UV light. Both experiments are performed under equal conditions, at a temperature of 343 K and with a pH of 3.2. The precursors used are cadmium chloride (CdCl2) and thiourea [CS(NH2)2], which are dissolved in 50 mL of deionized water with an acidic pH. In this experiment, the interaction of electromagnetic radiation is sought at the moment the chemical reaction is carried out. The results demonstrate the existence of an interaction between the crystals and the UV light; the UV light assistance causes crystal growths in an acicular shape. Also, the final product obtained is cadmium sulfide and shows no evident difference when synthesized with or without the use of UV light.

The Effect of Ultraviolet Radiation on the Chemical Bath Deposition of Bisthiourea Cadmium Chloride Crystals and the Subsequent CdS Obtention

This article presents a protocol for the synthesis of bis(thiourea) cadmium chloride crystals by chemical bath deposition. Two experiments are described: one aided by ultraviolet light compared to one without ultraviolet light.

In this work, the effects on the preparation of bis(thiourea) cadmium chloride crystals when illuminated with ultraviolet (UV) light at a wavelength of ...

Extraction of Lignin with High &#946;-O-4 Content by Mild Ethanol Extraction and Its Effect on the Depolymerization Yield

Lignin valorization strategies are a key factor for achieving more economically competitive biorefineries based on lignocellulosic biomass. Most of the emerging elegant procedures to obtain specific aromatic products rely on the lignin substrate having a high content of the readily cleavable &#946;-O-4 linkage as present in the native lignin structure. This provides a miss-match with typical technical lignins that are highly degraded and therefore are low in &#946;-O-4 linkages. Therefore, the extraction yields, and the quality of the obtained lignin are of utmost importance to access new lignin valorization pathways. In this manuscript, a simple protocol is presented to obtain lignins with high &#946;-O-4 content by relatively mild ethanol extraction that can be applied to different lignocellulose sources. Furthermore, analysis procedures to determine the quality of the lignins are presented together with a depolymerization protocol that yields specific phenolic 2-arylmethyl-1,3-dioxolanes, which can be used to evaluate the obtained lignins. The presented results demonstrate the link between lignin quality and potential for the lignins to be depolymerized into specific monomeric aromatic chemicals. Overall, the extraction and depolymerization demonstrates a trade-off between the lignin extraction yield and the retention of the native aryl-ether structure and thus the potential of the lignin to be used as the substrate for the production of chemicals for higher-value applications.

Here, we present a protocol to perform ethanol extraction of lignin from several biomass sources. The effect of the extraction conditions on the lignin yield and &#946;-O-4 content are presented. Selective depolymerization is performed on the obtained lignins to obtain high aromatic monomer products.

Lignin valorization strategies are a key factor for achieving more economically competitive biorefineries based on lignocellulosic biomass. Most of the ...

Niobium Oxide Films Deposited by Reactive Sputtering: Effect of Oxygen Flow Rate

Reactive sputtering is a versatile technique used to form compact films with excellent homogeneity. In addition, it allows easy control over deposition parameters such as gas flow rate that results in changes on composition and thus in the film required properties. In this report, reactive sputtering is used to deposit niobium oxide films. A niobium target is used as metal source and different oxygen flow rates to deposit niobium oxide films. The oxygen flow rate was changed from 3 to 10 sccm. The films deposited under low oxygen flow rates show higher electrical conductivity and provide better perovskite solar cells when used as electron transport layer.

Here, we present a protocol for niobium oxide films deposition by reactive sputtering with different oxygen flow rates for use as an electron transport layer in perovskite solar cells.

Reactive sputtering is a versatile technique used to form compact films with excellent homogeneity. In addition, it allows easy control over deposition ...