F ROM F OLDING T HEORIES TO F OLDING P ROTEINS: A Review and Assessment of Simulation Studies of Protein Folding and Unfolding
Abstract
▪ Abstract Beginning with simplified lattice and continuum “minimalist” models and progressing to detailed atomic models, simulation studies have augmented and directed development of the modern landscape perspective of protein folding. In this review we discuss aspects of detailed atomic simulation methods applied to studies of protein folding free energy surfaces, using biased-sampling free energy methods and temperature-induced protein unfolding. We review studies from each on systems of particular experimental interest and assess the strengths and weaknesses of each approach in the context of “exact” results for both free energies and kinetics of a minimalist model for a beta-barrel protein. We illustrate in detail how each approach is implemented and discuss analysis methods that have been developed as components of these studies. We describe key insights into the relationship between protein topology and the folding mechanism emerging from folding free energy surface calculations. We further describe the determination of detailed “pathways” and models of folding transition states that have resulted from unfolding studies. Our assessment of the two methods suggests that both can provide, often complementary, details of folding mechanism and thermodynamics, but this success relies on (a) adequate sampling of diverse conformational regions for the biased-sampling free energy approach and (b) many trajectories at multiple temperatures for unfolding studies. Furthermore, we find that temperature-induced unfolding provides representatives of folding trajectories only when the topology and sequence (energy) provide a relatively funneled landscape and “off-pathway” intermediates do not exist.
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AlphaFold does not resolve the protein folding problem and does not identify folding pathways.
“AlphaFold does not resolve the decades-long protein folding challenge, nor does it identify the folding pathways.”
From AlphaFold, Artificial Intelligence (AI), and Allostery (2022) · cites this paper as [57]
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Hierarchy of structure loss in MD simulations of src SH3 domain unfolding
Tsai, J. W., Levitt, M., & Baker, D. A. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.2949 · Cited by 95 · see citing works
Molecular dynamics simulations of hydrophobic collapse of ubiquitin
Alonso, D. O. V., & Daggett, V. (1998) · Protein Science · doi:10.1002/pro.5560070404 · Cited by 95 · see citing works
Shea, J., Nochomovitz, Y. D., Guo, Z., & Brooks, C. L. (1998) · The Journal of Chemical Physics · doi:10.1063/1.476842 · Cited by 95 · see citing works
Self-citationAlonso, D. O. V., & Daggett, V. (1995) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.0156 · Cited by 94 · see citing works
Bursulaya, B. D., & Brooks, C. L. (2000) · The Journal of Physical Chemistry B · doi:10.1021/jp0027602 · Cited by 94 · see citing works
Nanosecond timescale folding dynamics of a pentapeptide in water
Tobias, D. J., Mertz, J. E., & Brooks, C. L. (1991) · Biochemistry · doi:10.1021/bi00238a032 · Cited by 93 · see citing works
Molecular dynamics with internal coordinate constraints
Tobias, D. J., & Brooks, C. L. (1988) · The Journal of Chemical Physics · doi:10.1063/1.455654 · Cited by 91 · see citing works
Folding Free Energy Surface of a Three-Stranded β-Sheet Protein
Bursulaya, B. D., & Brooks, C. L. (1999) · Journal of the American Chemical Society · doi:10.1021/ja991764l · Cited by 90 · see citing works
Thermodynamics of amide hydrogen bond formation in polar and apolar solvents
Sneddon, S. F., Tobias, D. J., & Brooks, C. L. (1989) · Journal of Molecular Biology · doi:10.1016/0022-2836(89)90609-8 · Cited by 88 · see citing works
Park, S.-H., O’Neil, K. T., & Röder, H. (1997) · Biochemistry · doi:10.1021/bi971914+ · Cited by 88 · see citing works
Dinner, A. R., & Karplus, M. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.3051 · Cited by 87 · see citing works
Zhang, L., & Hermans, J. (1994) · Journal of the American Chemical Society · doi:10.1021/ja00105a034 · Cited by 87 · see citing works
Jendeberg, L., Tashiro, M., Tejero, R., et al. (1996) · Biochemistry · doi:10.1021/bi9512814 · Cited by 86 · see citing works
Coupling protein stability and protein function in Escherichia coli CspA
Hillier, B. J., Rodrı́guez, H. M., & Gregoret, L. M. (1998) · Folding and Design · doi:10.1016/s1359-0278(98)00014-5 · Cited by 83 · see citing works
Stability and folding properties of a model β‐sheet protein, Escherichia coli CspA
Reid, K. L., Rodrı́guez, H. M., Hillier, B. J., et al. (1998) · Protein Science · doi:10.1002/pro.5560070228 · Cited by 83 · see citing works
310 Helixes in Peptides and Proteins As Studied by Modified Zimm-Bragg Theory
Sheinerman, F. B., & Brooks, C. L. (1995) · Journal of the American Chemical Society · doi:10.1021/ja00145a022 · Cited by 83 · see citing works
Energetic frustration and the nature of the transition state in protein folding
Shea, J., Onuchic, J. N., & Brooks, C. L. (2000) · The Journal of Chemical Physics · doi:10.1063/1.1313792 · Cited by 81 · see citing works
Self-citationReverse turns in blocked dipeptides are intrinsically unstable in water
Tobias, D. J., Sneddon, S. F., & Brooks, C. L. (1990) · Journal of Molecular Biology · doi:10.1016/0022-2836(90)90399-7 · Cited by 81 · see citing works
Computer simulations of protein folding by targeted molecular dynamics
Ferrara, P., Apostolakis, J., & Caflisch, A. (2000) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(20000515)39:3 · Cited by 78 · see citing works
Gouda, H., Shiraishi, M., Takahashi, H. K., et al. (1998) · Biochemistry · doi:10.1021/bi970923f · Cited by 77 · see citing works
Molecular Dynamics Simulations of Isolated Helixes of Myoglobin
Hirst, J. D., & Brooks, C. L. (1995) · Biochemistry · doi:10.1021/bi00023a007 · Cited by 76 · see citing works
Rey, A., & Skolnick, J. (1991) · Chemical Physics · doi:10.1016/0301-0104(91)87067-6 · Cited by 75 · see citing works
Calculation of free energy surfaces using the methods of thermodynamic perturbation theory
Tobias, D. J., & Brooks, C. L. (1987) · Chemical Physics Letters · doi:10.1016/0009-2614(87)80646-2 · Cited by 74 · see citing works
Barchi, J. J., Grasberger, B. L., Gronenborn, A. M., et al. (1994) · Protein Science · doi:10.1002/pro.5560030103 · Cited by 74 · see citing works
The Family of Cold Shock Proteins of Bacillus subtilis
Schindler, T. H., Graumann, P. L., Perl, D., et al. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.6.3407 · Cited by 67 · see citing works
Mechanical Unfolding of a β-Hairpin Using Molecular Dynamics
Bryant, Z. D., Pande, V. S., & Rokhsar, D. S. (2000) · Biophysical Journal · doi:10.1016/s0006-3495(00)76618-5 · Cited by 66 · see citing works
Characterization 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 65 · see citing works
Helix−Coil Kinetics: Folding Time Scales for Helical Peptides from a Sequential Kinetic Model
Brooks, C. L. (1996) · The Journal of Physical Chemistry · doi:10.1021/jp952674f · Cited by 63 · see citing works
Backbone dynamics, fast folding, and secondary structure formation in helical proteins and peptides
Hardin, C., Luthey-Schulten, Z. A., & Wolynes, P. G. (1999) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(19990215)34:3 · Cited by 59 · see citing works
Dynamics of a type VI reverse turn in a linear peptide in aqueous solution
Demchuk, E., Bashford, D., & Case, D. A. (1997) · Folding and Design · doi:10.1016/s1359-0278(97)00004-7 · Cited by 57 · see citing works
Protein folding↔unfolding dynamics
Daggett, V., & Levitt, M. (1994) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(94)90322-0 · Cited by 54 · see citing works
Promotion of helix formation in peptides dissolved in alcohol and water-alcohol mixtures
Brooks, C. L., & Nilsson, L. (1993) · Journal of the American Chemical Society · doi:10.1021/ja00076a089 · Cited by 54 · see citing works
Long-range electrostatic effects in biomolecular simulations
Darden, T., Toukmaji, A. Y., & Pedersen, L. (1997) · Journal de Chimie Physique · doi:10.1051/jcp/1997941346 · Cited by 54 · see citing works
Clore, G. M., & Gronenborn, A. M. (1992) · Journal of Molecular Biology · doi:10.1016/0022-2836(92)90247-h · Cited by 48 · see citing works
Gutin, A. M., Abkevich, V. I., & Shakhnovich, E. I. (1998) · Folding and Design · doi:10.1016/s1359-0278(98)00026-1 · Cited by 48 · see citing works
DiCapua, F. M., Swaminathan, S., & Beveridge, D. L. (1990) · Journal of the American Chemical Society · doi:10.1021/ja00175a004 · Cited by 44 · see citing works
Bartels, C., Schaefer, M. R., & Karplus, M. (1999) · The Journal of Chemical Physics · doi:10.1063/1.480139 · Cited by 43 · see citing works
DiCapua, F. M., Swaminathan, S., & Beveridge, D. L. (1991) · Journal of the American Chemical Society · doi:10.1021/ja00016a034 · Cited by 42 · see citing works
Stability of a model β-sheet in water
Tobias, D. J., Sneddon, S. F., & Brooks, C. L. (1992) · Journal of Molecular Biology · doi:10.1016/0022-2836(92)90534-q · Cited by 42 · see citing works
Thermodynamics of a reverse turn motif. Solvent effects and side-chain packing
Demchuk, E., Bashford, D., Gippert, G. P., et al. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1103 · Cited by 39 · see citing works
Parallel computations of molecular dynamics trajectories using the stochastic path approach
Zaloj, V., & Elber, R. (2000) · Computer Physics Communications · doi:10.1016/s0010-4655(00)00038-2 · Cited by 38 · see citing works
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 · see citing works
Yan, Y., Tropsha, A., Hérmans, J. J., et al. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.16.7898 · Cited by 31 · see citing works
Investigation of protein unfolding and stability by computer simulation
van Gunsteren, W. F., Hünenberger, P. H., Kovacs, H., et al. (1995) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.1995.0045 · Cited by 25 · see citing works
Wang, L., O'Connell, T., Tropsha, A., et al. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.24.10924 · Cited by 20 · see citing works
Local fluctuations and global unfolding of partially folded BPTI detected by NMR
Barbar, E. J., LiCata, V. J., Bárány, G., et al. (1997) · Biophysical Chemistry · doi:10.1016/s0301-4622(96)02210-7 · Cited by 19 · see citing works
Hansmann, U. H. E., & Okamoto, Y. (1999) · The Journal of Chemical Physics · doi:10.1063/1.479320 · Cited by 18 · see citing works
Selection of partitions from a hierarchy
Xu, S. C., Kamath, M. V., & Capson, D. W. (1993) · Pattern Recognition Letters · doi:10.1016/0167-8655(93)90127-y · Cited by 18 · see citing works
The slow-exchange core and protein folding
Woodward, C. K., & Li, R. (1998) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(98)01282-1 · Cited by 18 · see citing works
Entropy Sampling Monte Carlo for Polypeptides and Proteins
Scheraga, H. A., & Hao, M. (1999) · Advances in chemical physics · doi:10.1002/9780470141649.ch8 · Cited by 17 · see citing works
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The Stability of Protein Secondary Structures in Aqueous Solution
Tobias, D. J., Sneddon, S. F., & Brooks, C. L. (1991) · AIP conference proceedings · doi:10.1063/1.41337 · Cited by 14 · see citing works
Witte, K. L., Skolnick, J., & Wong, C. (1998) · Journal of the American Chemical Society · doi:10.1021/ja982203h · Cited by 12 · see citing works
THE H-HELIX OF MYOGLOBIN AS A POTENTIAL INDEPENDENT PROTEIN FOLDING DOMAIN
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An Analysis on Protein Folding Problem by Replica-Exchange Method
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Protein Folding Simulations by Simulated Annealing and Generalized-Ensemble Algorithms
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Stability and folding properties of a model β‐sheet protein, escherichia coli cspa
Reid, K. L., Rodrı́guez, H. M., Hillier, B. J., et al. (1998) · Protein Science · doi:10.1002/pro.5560070923 · Cited by 2 · see citing works
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Protein folding and misfolding
Dobson, C. M. (2003) · Nature · doi:10.1038/nature02261 · Cited by 4,791 · see citing works
The Protein-Folding Problem, 50 Years On
Dill, K. A., & MacCallum, J. L. (2012) · Science · doi:10.1126/science.1219021 · Cited by 1,699 · see citing works
Dill, K. A., Ozkan, S. B., Shell, M. S., & Weikl, T. R. (2008) · Annual Review of Biophysics · doi:10.1146/annurev.biophys.37.092707.153558 · Cited by 1,163 · see citing works
Das, P., Moll, M., Stamati, H., Kavraki, L. E., & Clementi, C. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0603553103 · Cited by 331 · see citing works
AlphaFold, Artificial Intelligence (AI), and Allostery
Nussinov, R., Zhang, M., Liu, Y., & Jang, H. (2022) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.2c04346 · Cited by 190 · see citing works
A quantitative measure for protein conformational heterogeneity
Lyle, N., Das, R. K., & Pappu, R. V. (2013) · The Journal of Chemical Physics · doi:10.1063/1.4812791 · Cited by 85 · see citing works
Deng, N.-J., Dai, W., & Levy, R. M. (2013) · The Journal of Physical Chemistry B · doi:10.1021/jp401962k · Cited by 64 · see citing works
- Authors
- Shea, J.-E., & Brooks III, C. L.
- Affiliations
- Scripps Research Institute (US)
- Department of Molecular Biology, TPC6 The Scripps Research Institute La Jolla, California 92037;
- ORCID
- Shea, Joan-Emma
- Venue
- Annual Review of Physical Chemistry
- Publisher
- Annual Reviews
- Published
- 2001-10
- Volume
- 52
- Issue
- 1
- Pages
- 499-535
- ISSN
- 0066-426X (ISSN-L)
- 1545-1593
- OpenAlex
- W2147396853
- Cited by
- 481
- References
- 177
- Citations by year
- 2026: 7 · 2025: 5 · 2024: 9 · 2023: 5 · 2022: 6 · 2021: 11 · 2020: 8 · 2019: 7 · 2018: 13 · 2017: 13 · 2016: 16 · 2015: 21 · 2014: 15 · 2013: 21 · 2012: 21
- FWCI
- 2.63
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Annual Review of Physical Chemistry (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institute of General Medical Sciences (GM-57513, GM 48807, R01GM057513, R01GM048807)
- National Center for Research Resources (RR 06009, RR12255, P41RR012255)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
- Keywords
- protein folding, protein unfolding, biased sampling, thermal denaturation, folding kinetics, folding pathways, folding transition state, folding energy landscape, beta-barrel proteins, lattice model, continuum model, atomistic simulation
- MeSH terms
- Models, Molecular, Protein Folding
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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