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Cited by 91Protein Structure and DynamicsRNA and protein synthesis mechanismsEnzyme Structure and Function

De novo and inverse folding predictions of protein structure and dynamics

Godzik, Adam, Kolinski, Andrzej, Skolnick, Jeffrey·1993·Journal of Computer-Aided Molecular Design
DOI 10.1007/bf02337559
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Abstract

In the last two years, the use of simplified models has facilitated major progress in the globular protein folding problem, viz., the prediction of the three-dimensional (3D) structure of a globular protein from its amino acid sequence. A number of groups have addressed the inverse folding problem where one examines the compatibility of a given sequence with a given (and already determined) structure. A comparison of extant inverse protein-folding algorithms is presented, and methodologies for identifying sequences likely to adopt identical folding topologies, even when they lack sequence homology, are described. Extension to produce structural templates or fingerprints from idealized structures is discussed, and for eight-membered beta-barrel proteins, it is shown that idealized fingerprints constructed from simple topology diagrams can correctly identify sequences having the appropriate topology. Furthermore, this inverse folding algorithm is generalized to predict elements of supersecondary structure including beta-hairpins, helical hairpins and alpha/beta/alpha fragments. Then, we describe a very high coordination number lattice model that can predict the 3D structure of a number of globular proteins de novo; i.e. using just the amino acid sequence. Applications to sequences designed by DeGrado and co-workers [Biophys. J., 61 (1992) A265] predict folding intermediates, native states and relative stabilities in accord with experiment. The methodology has also been applied to the four-helix bundle designed by Richardson and co-workers [Science, 249 (1990) 884] and a redesigned monomeric version of a naturally occurring four-helix dimer, rop. Based on comparison to the rop dimer, the simulations predict conformations with rms values of 3-4 A from native. Furthermore, the de novo algorithms can assess the stability of the folds predicted from the inverse algorithm, while the inverse folding algorithms can assess the quality of the de novo models. Thus, the synergism of the de novo and inverse folding algorithm approaches provides a set of complementary tools that will facilitate further progress on the protein-folding problem.

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Authors
Godzik, A., Kolinski, A., & Skolnick, J.
Affiliations
Scripps Research Institute (US)
ORCID
Venue
Journal of Computer-Aided Molecular Design
Publisher
Springer Science and Business Media LLC
Published
1993-08
Volume
7
Issue
4
Pages
397-438
ISSN
  • 0920-654X (ISSN-L)
  • 1573-4951
DOI
10.1007/bf02337559
OpenAlex
W2016610222
Cited by
91
References
124
Citations by year
2025: 2 · 2022: 2 · 2021: 1 · 2020: 1 · 2018: 2 · 2017: 3 · 2016: 1 · 2014: 1 · 2013: 1 · 2012: 1
FWCI
2.82
Type
journal article
Language
en
Open access
closed
Licence
www.springer.com/tdm (tdm)
Locations
  • Journal of Computer-Aided Molecular Design (publishedVersion)
  • PubMed (publishedVersion)
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 › Materials Science › Materials Chemistry › Enzyme Structure and Function
Keywords
protein folding, de novo protein structure prediction, inverse folding, protein structure prediction, protein dynamics, structural fingerprints, beta-barrel proteins, supersecondary structure, lattice model, folding intermediates, protein stability, four-helix bundle, Rop protein, protein design
MeSH terms
Algorithms, Amino Acid Sequence, Computer Simulation, Models, Molecular, Molecular Sequence Data, Sequence Alignment, Protein Structure, Tertiary, Protein Folding

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