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Monte carlo simulations of protein folding. I. Lattice model and interaction scheme
Abstract
A new hierarchical method for the simulation of the protein folding process and the de novo prediction of protein three‐dimensional structure is proposed. The reduced representation of the protein α‐carbon backbone employs lattice discretizations of increasing geometrical resolution and a single ball representation of side chain rotamers. In particular, coarser and finer lattice backbone descriptions are used. The coarser (finer) lattice represents Cα traces of native proteins with an accuracy of 1.0 (0.7) Å rms. Folding is simulated by means of very fast Monte Carlo lattice dynamics. The potential of mean force, predominantly of statistical origin, contains several novel terms that facilitate the cooperative assembly of secondary structure elements and the cooperative packing of the side chains. Particular contributions to the interaction scheme are discussed in detail. In the accompanying paper (Kolinski, A., Skolnick, J. Monte Carlo simulation of protein folding. II. Application to protein A, ROP, and crambin. Proteins 18:353–366, 1994), the method is applied to three small globular proteins. © 1994 John Wiley & Sons, Inc.
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Cites
Kabsch, W., & Sander, C. (1983) · Biopolymers · doi:10.1002/bip.360221211 · Cited by 15,320
Scaling Concepts in Polymer Physics
de Gennes, P. G., & Witten, T. A. (1980) · Physics Today · doi:10.1063/1.2914118 · Cited by 9,348
The protein data bank: A computer-based archival file for macromolecular structures
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., & Tasumi, M. (1977) · Journal of Molecular Biology · doi:10.1016/s0022-2836(77)80200-3 · Cited by 8,578
A Method to Identify Protein Sequences That Fold into a Known Three-Dimensional Structure
Bowie, J. U., Lüthy, R., & Eisenberg, D. (1991) · Science · doi:10.1126/science.1853201 · Cited by 2,851
An Introduction to Statistical Thermodynamics
Hill, T. L., & Gillis, J. (1961) · Physics Today · doi:10.1063/1.3057470 · Cited by 2,207
Creighton, T. E. (1992) · Cited by 1,583
Are there pathways for protein folding?
Levinthal, C. (1968) · Journal de Chimie Physique · doi:10.1051/jcp/1968650044 · Cited by 1,517
Kuwajima, K. (1989) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.340060202 · Cited by 1,439
Profile analysis: detection of distantly related proteins.
Gribskov, M., McLachlan, A. D., & Eisenberg, D. (1987) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.84.13.4355 · Cited by 1,325
A new approach to protein fold recognition
Jones, D. T., Taylort, W. R., & Thornton, J. M. (1992) · Nature · doi:10.1038/358086a0 · Cited by 1,221
Molecular dynamics simulations in biology
Karplus, M., & Petsko, G. A. (1990) · Nature · doi:10.1038/347631a0 · Cited by 1,152
Introduction to statistical thermodynamics
(1960) · Journal of the Franklin Institute · doi:10.1016/0016-0032(60)90133-2 · Cited by 1,145
Monte Carlo Methods in Statistical Physics
(1986) · Topics in Current Physics · doi:10.1007/978-3-642-82803-4 · Cited by 1,058
Characterization of Polystyrenes of Extremely High Molecular Weights
Appelt, B., & Meyerhoff, G. (1980) · Macromolecules · doi:10.1021/ma60075a033 · Cited by 927
Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics
Brooks, C. L., Karplus, M., Montgomery Pettitt, B., & Austin, R. H. (1990) · Physics Today · doi:10.1063/1.2810459 · Cited by 747
Evidence for a molten globule state as a general intermediate in protein folding
Ptitsyn, O. B., Pain, R. H., Semisotnov, G. V., Zerovnik, E., & Razgulyaev, O. I. (1990) · FEBS Letters · doi:10.1016/0014-5793(90)80143-7 · Cited by 678
Multiple Conformational States of Proteins: A Molecular Dynamics Analysis of Myoglobin
Elber, R., & Karplus, M. (1987) · Science · doi:10.1126/science.3798113 · Cited by 673
Creighton, T. E. (1990) · Biochemical Journal · doi:10.1042/bj2700001 · Cited by 515
Automatic identification of secondary structure in globular proteins
Levitt, M., & Greer, J. (1977) · Journal of Molecular Biology · doi:10.1016/0022-2836(77)90207-8 · Cited by 507
Solvent effects on protein motion and protein effects on solvent motion
Brooks, C. L., & Karplus, M. (1989) · Journal of Molecular Biology · doi:10.1016/0022-2836(89)90093-4 · Cited by 410
An empirical energy function for threading protein sequence through the folding motif
Bryant, S. H., & Lawrence, C. E. (1993) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.340160110 · Cited by 400
Topology fingerprint approach to the inverse protein folding problem
Godzik, A., Kolinski, A., & Skolnick, J. (1992) · Journal of Molecular Biology · doi:10.1016/0022-2836(92)90693-e · Cited by 339
Self-citationSimulations of the Folding of a Globular Protein
Skolnick, J., & Kolinski, A. (1990) · Science · doi:10.1126/science.250.4984.1121 · Cited by 315
Self-citationPiela, L., Kostrowicki, J., & Scheraga, H. A. (1989) · The Journal of Physical Chemistry · doi:10.1021/j100345a090 · Cited by 299
An analysis of incorrectly folded protein models
Novotný, J., Bruccoleri, R., & Karplus, M. (1984) · Journal of Molecular Biology · doi:10.1016/0022-2836(84)90049-4 · Cited by 280
Why do globular proteins fit the limited set of foldin patterns?
Finkelstein, A. V., & Ptitsyn, O. B. (1987) · Progress in Biophysics and Molecular Biology · doi:10.1016/0079-6107(87)90013-7 · Cited by 271
Metal Ion-Dependent Modulation of the Dynamics of a Designed Protein
Handel, T. M., Williams, S. A., & DeGrado, W. F. (1993) · Science · doi:10.1126/science.8346440 · Cited by 252
Sippl, M. J., & Weitckus, S. (1992) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.340130308 · Cited by 235
Kolinski, A., Godzik, A., & Skolnick, J. (1993) · The Journal of Chemical Physics · doi:10.1063/1.464706 · Cited by 193
Self-citationGenerating and testing protein folds
Wodak, S. J., & Rooman, M. J. (1993) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(05)80160-5 · Cited by 152
Monte carlo simulations of protein folding. II. Application to protein A, ROP, and crambin
Koliński, A., & Skolnick, J. (1994) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340180406 · Cited by 143
Self-citationGodzik, A., & Skolnick, J. (1992) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.89.24.12098 · Cited by 137
Self-citationA search for the most stable folds of protein chains
Finkelstein, A. V., & Reva, B. A. (1991) · Nature · doi:10.1038/351497a0 · Cited by 135
Baumgärtner, A. (1984) · Annual Review of Physical Chemistry · doi:10.1146/annurev.pc.35.100184.002223 · Cited by 131
Application of the diffusion equation method for global optimization to oligopeptides
Kostrowicki, J., & Scheraga, H. A. (1992) · The Journal of Physical Chemistry · doi:10.1021/j100197a057 · Cited by 129
Discretized model of proteins. I. Monte Carlo study of cooperativity in homopolypeptides
Koliński, A., & Skolnick, J. (1992) · The Journal of Chemical Physics · doi:10.1063/1.463317 · Cited by 122
Self-citationDoes reptation describe the dynamics of entangled, finite length polymer systems? A model simulation
Koliński, A., Skolnick, J., & Yaris, R. (1987) · The Journal of Chemical Physics · doi:10.1063/1.452196 · Cited by 113
Self-citationBowie, J. U., Clarke, N. D., Pabo, C. O., & Sauer, R. T. (1990) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340070307 · Cited by 98
Computer Simulations of Globular Protein Folding and Tertiary Structure
Skolnick, J., & Koliński, A. (1989) · Annual Review of Physical Chemistry · doi:10.1146/annurev.pc.40.100189.001231 · Cited by 98
Self-citationLattice representations of globular proteins: How good are they?
Godzik, A., Koliński, A., & Skolnick, J. (1993) · Journal of Computational Chemistry · doi:10.1002/jcc.540141009 · Cited by 92
Self-citationDe novo and inverse folding predictions of protein structure and dynamics
Godzik, A., Kolinski, A., & Skolnick, J. (1993) · Journal of Computer-Aided Molecular Design · doi:10.1007/bf02337559 · Cited by 91
Self-citationHow Consistent are Molecular Dynamics Simulations?
Elofsson, A., & Nilsson, L. (1993) · Journal of Molecular Biology · doi:10.1006/jmbi.1993.1551 · Cited by 87
Folding proteins: finding a needle in a haystack
Dill, K. A. (1993) · Current Opinion in Structural Biology · doi:10.1016/0959-440x(93)90208-3 · Cited by 81
A method for predicting protein structure from sequence
Skolnick, J., Koliński, A., Brooks, C. L., Godzik, A., & Rey, A. (1993) · Current Biology · doi:10.1016/0960-9822(93)90348-r · Cited by 80
Self-citationRaleigh, D. P., & DeGrado, W. F. (1992) · Journal of the American Chemical Society · doi:10.1021/ja00051a061 · Cited by 79
Koliński, A., Skolnick, J., & Yaris, R. (1987) · The Journal of Chemical Physics · doi:10.1063/1.452366 · Cited by 78
Self-citationRegularities in interaction patterns of globular proteins
Godzik, A., Skolnick, J., & Koliński, A. (1993) · Protein Engineering Design and Selection · doi:10.1093/protein/6.8.801 · Cited by 73
Self-citationCharacterization of “native” apomyoglobin by molecular dynamics simulation
Brooks, C. L. (1992) · Journal of Molecular Biology · doi:10.1016/0022-2836(92)90893-o · Cited by 66
Static and dynamic properties of a new lattice model of polypeptide chains
Koliński, A., Milik, M., & Skolnick, J. (1991) · The Journal of Chemical Physics · doi:10.1063/1.460675 · Cited by 60
Self-citationEfficient algorithm for the reconstruction of a protein backbone from the α‐carbon coordinates
Rey, A., & Skolnick, J. (1992) · Journal of Computational Chemistry · doi:10.1002/jcc.540130407 · Cited by 50
Self-citationKoliński, A., Skolnick, J., & Yaris, R. (1987) · The Journal of Chemical Physics · doi:10.1063/1.452367 · Cited by 47
Self-citationSimulations of the folding pathway of triose phosphate isomerase-type alpha/beta barrel proteins.
Godzik, A., Skolnick, J., & Koliński, A. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.7.2629 · Cited by 46
Self-citationLevitt, M. (1991) · Current Opinion in Structural Biology · doi:10.1016/0959-440x(91)90065-2 · Cited by 35
Molecular simulations of peptide and protein unfolding: in quest of a molten globule
Brooks, C. L. (1993) · Current Opinion in Structural Biology · doi:10.1016/0959-440x(93)90207-2 · Cited by 33
Jernigan, R. L. (1992) · Current Opinion in Structural Biology · doi:10.1016/0959-440x(92)90154-y · Cited by 27
Cited by
Funnels, pathways, and the energy landscape of protein folding: A synthesis
Bryngelson, J. D., Onuchic, J. N., Socci, N. D., & Wolynes, P. G. (1995) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.340210302 · Cited by 2,648
THEORY OF PROTEIN FOLDING: The Energy Landscape Perspective
Onuchic, J. N., Luthey-Schulten, Z., & Wolynes, P. G. (1997) · Annual Review of Physical Chemistry · doi:10.1146/annurev.physchem.48.1.545 · Cited by 2,210
Principles of protein folding — A perspective from simple exact models
Dill, K. A., Bromberg, S., Yue, K., Chan, H. S., Fiebig, K. M., Yee, D. P., & Thomas, P. D. (1995) · Protein Science · doi:10.1002/pro.5560040401 · Cited by 1,525
Global Optimization of Clusters, Crystals, and Biomolecules
Wales, D. J., & Scheraga, H. A. (1999) · Science · doi:10.1126/science.285.5432.1368 · Cited by 1,114
Dosztányi, Z., Csizmók, V., Tompa, P., & Simon, I. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.01.071 · Cited by 1,019
Metadata
- Authors
- Kolinski, A., & Skolnick, J.
- Venue
- Proteins: Structure, Function, and Bioinformatics
- Publisher
- Wiley
- Published
- 1994-04
- Volume
- 18
- Issue
- 4
- Pages
- 338-352
- ISSN
- 0887-3585 (ISSN-L)
- 1097-0134
- OpenAlex
- W2076488922
- Cited by
- 295
- References
- 55
- FWCI
- 8.82
- Type
- journal article
- Language
- en
- Open access
- closed
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