Local interactions as a structure determinant for protein molecules: II |
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| Affiliation: | 1. Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India;2. Advanced Instrumentation Research Facility (AIRF), Jawaharlal Nehru University, New Delhi 110067, India;1. Department of Genetics & Biotechnology, Bhavan''s Vivekananda College of Science, Humanities and Commerce, Sainikpuri, Secunderabad 500094, Telangana State, India;2. Department of Genetics, Osmania University, Hyderabad 500007, Telangana State, India;3. Division of Biostatistics, National Institute of Nutrition, Hyderabad 500007, Telangana State, India;1. Department of Medicine Solna, Experimental Cardiovascular Research Unit and Departments of Medicine and Neurology, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden;2. Department of Breast and Endocrine Surgery, Akershus University Hospital, Lørenskog, Norway;3. Norwegian System of Compensation for Patient Claimes, Oslo, Norway;4. Norwegian University of Life Sciences, Oslo, Norway;5. Department of Pathology, Akershus University Hospital, Lørenskog, Norway;6. Institute of Clinical Medicine, University of Oslo, Campus Akershus University Hospital, Lørenskog, Oslo, Norway;7. Department of Oncology, Akershus University Hospital, Lørenskog, Norway;1. York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom;2. Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan;3. Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan |
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| Abstract: | Van der Waals interactions between sidechains are indicated to be important in determining the native state of the proteins of known structure by the following observations: - 1.1.|the average radial distribution of polarity increases continuously from the center of the molecule to its periphery.
- 2.2.|nonpolar sidechains tend to occur in clusters.
- 3.3.|the frequencies of long-range nearest-neighbor pairs are markedly non-random; each type of sidechain seeks nearest-neighbors of similar polarity. To investigate how these interactions affect the overall structure of the protein molecule, three simpified models are treated: a sheath-core model composed of independent residues, a modification accounting approximately for the connected nature of the chain, and a model consisting of three concentric spherical phases.
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