2004 Fiscal Year Final Research Report Summary
Prediction of structure and function of protein complexes
| Project/Area Number |
13208010
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| Research Category |
Grant-in-Aid for Scientific Research on Priority Areas
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| Allocation Type | Single-year Grants |
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| Review Section |
Biological Sciences
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| Research Institution | Yokohama City University |
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Principal Investigator |
KIDERA Akinori Yokohama City University, Graduate School of Integrated Sciences, Professor, 大学院総合理学研究科, 教授 (00186280)
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| Co-Investigator(Kenkyū-buntansha) |
IKEGUCHI Mitsunori Yokohama City University, Graduate School of Integrated Sciences, Professor, 大学院総合理学研究科, 助教授 (60261955)
AKIO Kitao University of Tokyo, Insistute of Molecular and Cellular Biosciences, 分子細胞生物研究所, 助教授 (30252422)
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| Project Period (FY) |
2001 – 2004
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| Keywords | protein complex / protein structure / protein function / neutron scattering / probabilistic alignment / linear response theory / molecular dynamics simulation / aquaporin |
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| Research Abstract |
Database analyses of protein structures
(1)Structural classification of all B-proteins: A novel structural classification of all B-proteins is presented from the viewpoint of the ring-shaped structure and the zipper-like contact pattern, based on the fact that 92% and 60% of B proteins have the ring topology and the zippered contact pattern, respectively.
(2)Probabilistic alignment method: We developed a method of generating probabilistic alignments for sequences and structures, by which the correspondence between pairs of residues is evaluated in a probabilistic manner. This method was applied to TIM-barrel and β-trefoil proteins.
Simulation analyses of protein functions
(1)Development of a molecular dynamics program on parallel computer: A partial rigid-body method of molecular dynamics simulations for proteins and membranes is presented. The standard NPT ensemble is extended to the membrane-specific ensembles, the NPAT and NPyT ensembles.
(2)Molecular dynamics simulations of aquaporins: Molecular dynamics simulations were performed for four members of the aquaporin family (AQPl, AQPZ, AQPO, and GlpF) in the explicit membrane environment. The single channel water permeability was evaluated to be GlpF AQPZ > AQPl≫AQPO.
(3)Linear response theory of protein structural change upon ligand binding: A simple formula based on linear response theory is proposed to explain and predict the structural change of proteins upon ligand binding. The results for three protein systems of various sizes are consistent with the observations in the crystal structures.
Experimental analyses of protein dynamics
(1)Development of analysis method for neutron scattering spectra: The origin of the Boson peak in the inelastic neutron scattering was clarified based on the dynamic structural transition of proteins at low temperature.
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