ArticleProceedings of the National Academy of Sciences of the United States of America2007
Protein folding by zipping and assembly.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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Who cites it
71 citing papers in PubMed.
- TruMPET: A New Method for Protein Secondary Structure Prediction Using Neural Networks Trained on Multiple Pre-Selected Physicochemical and Structural Features.International journal of molecular sciences · 2025Article
- Transcription reshapes RNA hairpin folding pathways revealed by all-atom molecular dynamics simulations.PLoS computational biology · 2025Article
- A Perspective on Interdicting in Protein Misfolding for Therapeutic Drug Design: Modulating the Formation of Nonlocal Contacts in α-Synuclein as a Strategy against Parkinson's Disease.The journal of physical chemistry. B · 2024Review
- Hairpin trimer transition state of amyloid fibril.Nature communications · 2024Article
- Interdiction in the Early Folding of the p53 DNA-Binding Domain Leads to Its Amyloid-Like Misfolding.Molecules (Basel, Switzerland) · 2022Article
- Protein Folding Interdiction Strategy for Therapeutic Drug Development in Viral Diseases: Ebola VP40 and Influenza A M1.International journal of molecular sciences · 2022Article
- Prediction of protein secondary structure based on an improved channel attention and multiscale convolution module.Frontiers in bioengineering and biotechnology · 2022Article
- Identification of Two Early Folding Stage Prion Non-Local Contacts Suggested to Serve as Key Steps in Directing the Final Fold to Be Either Native or Pathogenic.International journal of molecular sciences · 2021Article
- Protein folding - seeing is deceiving.Protein science : a publication of the Protein Society · 2021Article
- The Last Secret of Protein Folding: The Real Relationship Between Long-Range Interactions and Local Structures.The protein journal · 2020Review
- A hybrid, bottom-up, structurally accurate, Go¯-like coarse-grained protein model.The Journal of chemical physics · 2019Article
- Experimental accuracy in protein structure refinement via molecular dynamics simulations.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Sixty-five years of the long march in protein secondary structure prediction: the final stretch?Briefings in bioinformatics · 2018Article
- Helical Propensity Affects the Conformational Properties of the Denatured State of Cytochrome c'.Biophysical journal · 2018Article
- Equilibrium folding dynamics of meACP in water, heavy water, and low concentration of urea.Scientific reports · 2017Article
- Partial unfolding and refolding for structure refinement: A unified approach of geometric simulations and molecular dynamics.Proteins · 2015Article
- Selective refinement and selection of near-native models in protein structure prediction.Proteins · 2015Article
- Structure and dynamics of the N-terminal domain of the Cu(I) binding protein CusB.Biochemistry · 2013Article
- PRIMO: A Transferable Coarse-grained Force Field for Proteins.Journal of chemical theory and computation · 2013Article
- The loop hypothesis: contribution of early formed specific non-local interactions to the determination of protein folding pathways.Biophysical reviews · 2013Review
11 more citing papers are in PubMed but not listed here.
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4 authors.
Funding
Abstract
How do proteins fold so quickly? Some denatured proteins fold to their native structures in only microseconds, on average, implying that there is a folding "mechanism," i.e., a particular set of events by which the protein short-circuits a broader conformational search. Predicting protein structures using atomically detailed physical models is currently challenging. The most definitive proof of a putative folding mechanism would be whether it speeds up protein structure prediction in physical models. In the zipping and assembly (ZA) mechanism, local structuring happens first at independent sites along the chain, then those structures either grow (zip) or coalescence (assemble) with other structures. Here, we apply the ZA search mechanism to protein native structure prediction by using the AMBER96 force field with a generalized Born/surface area implicit solvent model and sampling by replica exchange molecular dynamics. Starting from open denatured conformations, our algorithm, called the ZA method, converges to an average of 2.2 A from the Protein Data Bank native structures of eight of nine proteins that we tested, which ranged from 25 to 73 aa in length. In addition, experimental Phi values, where available on these proteins, are consistent with the predicted routes. We conclude that ZA is a viable model for how proteins physically fold. The present work also shows that physics-based force fields are quite good and that physics-based protein structure prediction may be practical, at least for some small proteins.
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