The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
Studies on protein folding, unfolding, and fluctuations by computer simulation. II. A. Three‐dimensional lattice model of lysozyme
Abstract
A three‐dimensional lattice model of protein designed to assimilate lysozyme is introduced. An attractive interaction is assumed to work between preassigned specific pairs of units, when they occupy the nearest‐nighbor lattice points. The behavior of this lattice lysozyme is studied by a Monte Carlo simulation method. Because of the specific interunit interactions,“native state” of the lattice lysozyme is stable at low temperatures. Conformational fluctuations in the native state are observed to occur at both termini and loop regions of the main chain existing on the surface. The process of unfolding and denatured states of this model are discussed. Complete refolding from a denatured state was not observed. However, by starting from partially folded structures, the native conformation could be attained. From these observation it is concluded that, in the process of folding of proteins as simplified in a lattice model, nulceation is a rate‐limiting factor. The artificial character of this model and possible improvement are discussed.
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Cites
Equation of State Calculations by Fast Computing Machines
Metropolis, N., Rosenbluth, A. W., Rosenbluth, M. N., Teller, A. H., & Teller, E. (1953) · The Journal of Chemical Physics · doi:10.1063/1.1699114 · Cited by 37,192
Cited by
Onuchic, J. N., & Wolynes, P. G. (2004) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2004.01.009 · Cited by 1,301
ModBase, a database of annotated comparative protein structure models, and associated resources
Pieper, U., Webb, B. M., Barkan, D. T., Schneidman-Duhovny, D., Schlessinger, A., Braberg, H., Yang, Z., Meng, E. C., Pettersen, E. F., Huang, C. C., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1091 · Cited by 1,071
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
Šponer, J., Bussi, G., Krepl, M., Banáš, P., Bottaro, S., Cunha, R. A., Gil-Ley, A., Pinamonti, G., Poblete, S., Jurečka, P., et al. (2018) · Chemical Reviews · doi:10.1021/acs.chemrev.7b00427 · Cited by 599
Coarse-Graining Methods for Computational Biology
Saunders, M. G., & Voth, G. A. (2013) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-083012-130348 · Cited by 565
Molecular crowding enhances native state stability and refolding rates of globular proteins
Cheung, M. S., Klimov, D., & Thirumalai, D. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409630102 · Cited by 558
Metadata
- Authors
- Ueda, Y., Taketomi, H., & Gō, N.
- Venue
- Biopolymers
- Publisher
- Wiley
- Published
- 1978-06
- Volume
- 17
- Issue
- 6
- Pages
- 1531-1548
- ISSN
- 0006-3525 (ISSN-L)
- 1097-0282
- OpenAlex
- W2160349767
- Cited by
- 266
- References
- 1
- FWCI
- 0.18
- Type
- journal article
- Language
- en
- Open access
- closed
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- Ueda, Y., Taketomi, H., & Gō, N. (1978). Studies on protein folding, unfolding, and fluctuations by computer simulation. II. A. Three‐dimensional lattice model of lysozyme. Biopolymers. https://doi.org/10.1002/bip.1978.360170612
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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