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Theoretical studies of transmembrane...

Zhang, Jinming.

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Theoretical studies of transmembrane helix association.

Record Type:	Language materials, printed : Monograph/item
Title/Author:	Theoretical studies of transmembrane helix association./
Author:	Zhang, Jinming.
Description:	108 p.
Notes:	Adviser: Themis Lazaridis.
Contained By:	Dissertation Abstracts International69-01B.
Subject:	Biology, Bioinformatics. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3296938
ISBN:	9780549434399

Theoretical studies of transmembrane helix association.
Zhang, Jinming.

Theoretical studies of transmembrane helix association. - 108 p.

Adviser: Themis Lazaridis.

Thesis (Ph.D.)--City University of New York, 2008.

Association of transmembrane (TM) helices plays a key role in the structure and function of membrane proteins. A large number of experimental studies have been devoted to quantifying the interaction between TM helices in detergent micelles and, more recently, in bilayers. However, despite the abundance of experimental data, our understanding of the structural determinants of TM helix association affinity is still limited. In this work a theoretical methodology is first developed for calculating the standard association free energy of TM helices in both micelles and bilayers based on an implicit membrane model (IMM1). This methodology is applied to the TM domain of Glycophorin A (GpA), a human erythrocyte protein. The calculated standard association free energy of GpA in DPC micelles is in good agreement with the experimental value. The translational entropy cost is larger, while the rotational entropy cost is smaller in bilayers than in micelles. The standard association free energy in DMPC bilayers is calculated to be &sim;1.3 kcal/mol more favorable than in DPC micelles, consistent with available experimental data. Finally we investigated the question why association affinities of GpA and bacteriophage M13 major coat protein (MCP) are dramatically different although they both contain the GxxxG motif. The calculated association free energies follow experimental observations: the association affinity of MCP-GpA (MCP mutant with all interfacial residues of MCP substituted for those of GpA) falls between those of GpA15p11 (GpA with 15 residues from the wild type sequence plus 11 flanking residues from the ToxCAT construct) and MCP wild type. MCP and MCP-GpA have the same flanking residues used in the ToxCAT assay as those in GpA15p11, but the position of the flanking residues relative to the GxxxG motif is different. MCP exhibits an equally strong inter-helical interaction in the TM domain. A major reason for the weaker association of MCP in the calculations was the non-interfacial residue Lys40, which in the dimer structure is forced to be buried in the membrane interior. To alleviate the desolvation cost, in MCP and MCP-GpA dimers Lys40 gets deprotonated. A second factor that modulates association affinity is the flanking residues. Thanks to them, GpA15p11 exhibits a much stronger association affinity than GpA29 (GpA with 29 residues all from the wild type sequence). The positioning of the flanking residues is also important, as evidenced by the difference in association affinity between MCP and MCP-GpA on one hand and GpA15p11 on the other. Thus, residues outside the contact interface can exert a significant influence on transmembrane helix association affinity. These theoretical studies enhance our understanding of the molecular mechanisms of TM helix association and could be useful for structure prediction and rational design of TM proteins.

ISBN: 9780549434399Subjects--Topical Terms:

1018415
Biology, Bioinformatics.

Theoretical studies of transmembrane helix association.
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020 $a 9780549434399
035 $a (UMI)AAI3296938
035 $a AAI3296938
040 $a UMI $c UMI
100 1 $a Zhang, Jinming. $3 1263126
245 1 0 $a Theoretical studies of transmembrane helix association.
300 $a 108 p.
500 $a Adviser: Themis Lazaridis.
500 $a Source: Dissertation Abstracts International, Volume: 69-01, Section: B, page: 0309.
502 $a Thesis (Ph.D.)--City University of New York, 2008.
520 $a Association of transmembrane (TM) helices plays a key role in the structure and function of membrane proteins. A large number of experimental studies have been devoted to quantifying the interaction between TM helices in detergent micelles and, more recently, in bilayers. However, despite the abundance of experimental data, our understanding of the structural determinants of TM helix association affinity is still limited. In this work a theoretical methodology is first developed for calculating the standard association free energy of TM helices in both micelles and bilayers based on an implicit membrane model (IMM1). This methodology is applied to the TM domain of Glycophorin A (GpA), a human erythrocyte protein. The calculated standard association free energy of GpA in DPC micelles is in good agreement with the experimental value. The translational entropy cost is larger, while the rotational entropy cost is smaller in bilayers than in micelles. The standard association free energy in DMPC bilayers is calculated to be &sim;1.3 kcal/mol more favorable than in DPC micelles, consistent with available experimental data. Finally we investigated the question why association affinities of GpA and bacteriophage M13 major coat protein (MCP) are dramatically different although they both contain the GxxxG motif. The calculated association free energies follow experimental observations: the association affinity of MCP-GpA (MCP mutant with all interfacial residues of MCP substituted for those of GpA) falls between those of GpA15p11 (GpA with 15 residues from the wild type sequence plus 11 flanking residues from the ToxCAT construct) and MCP wild type. MCP and MCP-GpA have the same flanking residues used in the ToxCAT assay as those in GpA15p11, but the position of the flanking residues relative to the GxxxG motif is different. MCP exhibits an equally strong inter-helical interaction in the TM domain. A major reason for the weaker association of MCP in the calculations was the non-interfacial residue Lys40, which in the dimer structure is forced to be buried in the membrane interior. To alleviate the desolvation cost, in MCP and MCP-GpA dimers Lys40 gets deprotonated. A second factor that modulates association affinity is the flanking residues. Thanks to them, GpA15p11 exhibits a much stronger association affinity than GpA29 (GpA with 29 residues all from the wild type sequence). The positioning of the flanking residues is also important, as evidenced by the difference in association affinity between MCP and MCP-GpA on one hand and GpA15p11 on the other. Thus, residues outside the contact interface can exert a significant influence on transmembrane helix association affinity. These theoretical studies enhance our understanding of the molecular mechanisms of TM helix association and could be useful for structure prediction and rational design of TM proteins.
590 $a School code: 0046.
650 4 $a Biology, Bioinformatics. $3 1018415
650 4 $a Biophysics, General. $3 1019105
650 4 $a Chemistry, Biochemistry. $3 1017722
690 $a 0487
690 $a 0715
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710 2 $a City University of New York. $b Biochemistry. $3 1263127
773 0 $t Dissertation Abstracts International $g 69-01B.
790 $a 0046
790 1 0 $a Green, Michael $e committee member
790 1 0 $a Gunner, Marilyn $e committee member
790 1 0 $a Lazaridis, Themis, $e advisor
790 1 0 $a Murray, Diana $e committee member
790 1 0 $a Naider, Fred $e committee member
790 1 0 $a Ubarretxena-Belandia, Iban $e committee member
791 $a Ph.D.
792 $a 2008
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3296938