ArticleProceedings of the National Academy of Sciences of the United States of America2003
Atomically detailed folding simulation of the B domain of staphylococcal protein A from random structures.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Einstein Model of a Graph to Characterize Protein Folded/Unfolded States.Molecules (Basel, Switzerland) · 2023Article
- Rethinking the protein folding problem from a new perspective.European biophysics journal : EBJ · 2023Article
- Personalized cancer vaccines from bacteria-derived outer membrane vesicles with antibody-mediated persistent uptake by dendritic cells.Fundamental research · 2022Article
- Sampling of the conformational landscape of small proteins with Monte Carlo methods.Scientific reports · 2020Article
- Outline of an experimental design aimed to detect a protein A mirror image in solution.PeerJ physical chemistry · 2019Article
- Protein Folding and Structure Prediction from the Ground Up II: AAWSEM for α/β Proteins.The journal of physical chemistry. B · 2017Article
- Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction.The Journal of chemical physics · 2016Article
- All-Atom Internal Coordinate Mechanics (ICM) Force Field for Hexopyranoses and Glycoproteins.Journal of chemical theory and computation · 2015Article
- My 65 years in protein chemistry.Quarterly reviews of biophysics · 2015Review
- Accounting for a mirror-image conformation as a subtle effect in protein folding.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Kinks, loops, and protein folding, with protein A as an example.The Journal of chemical physics · 2014Article
- Hidden protein folding pathways in free-energy landscapes uncovered by network analysis.Journal of chemical theory and computation · 2012Article
- Coarse-grained force field: general folding theory.Physical chemistry chemical physics : PCCP · 2011Review
- Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling.Proteins · 2011Article
- Trends in template/fragment-free protein structure prediction.Theoretical chemistry accounts · 2011Article
- Evidence, from simulations, of a single state with residual native structure at the thermal denaturation midpoint of a small globular protein.Journal of the American Chemical Society · 2010Article
- Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. I. The method.Journal of computational chemistry · 2010Article
- Relation between free energy landscapes of proteins and dynamics.Journal of chemical theory and computation · 2010Article
- Folding simulations of a de novo designed protein with a betaalphabeta fold.Biophysical journal · 2010Article
- Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field.Journal of computational chemistry · 2009Article
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3 authors.
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Abstract
The conformational space of the 10-55 fragment of the B-domain of staphylococcal protein A has been investigated by using the electrostatically driven Monte Carlo (EDMC) method. The ECEPP/3 (empirical conformational energy program for peptides) force-field plus two different continuum solvation models, namely SRFOPT (Solvent Radii Fixed with atomic solvation parameters OPTimized) and OONS (Ooi, Oobatake, Némethy, and Scheraga solvation model), were used to describe the conformational energy of the chain. After an exhaustive search, starting from two different random conformations, three of four runs led to native-like conformations. Boltzmann-averaged root-mean-square deviations (RMSD) for all of the backbone heavy atoms with respect to the native structure of 3.35 A and 4.54 A were obtained with SRFOPT and OONS, respectively. These results show that the protein-folding problem can be solved at the atomic detail level by an ab initio procedure, starting from random conformations, with no knowledge except the amino acid sequence. To our knowledge, the results reported here correspond to the largest protein ever folded from a random conformation by an initial-value formulation with a full atomic potential, without resort to knowledge-based information.
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