Cart
Article
Polypeptide Folding Using Monte Carlo Sampling, Concerted Rotation, and Continuum Solvation
Full Text HTML
Hi-Res PDFPurchase the full-text
- PDF/HTML,
figures/images,
references and tables,
(where available)
Section:Abstract
An efficient concerted rotation algorithm for use in Monte Carlo statistical mechanics simulations is applied to fold three polypeptides, U(1−17)T9D, α1, and trpzip2, which exhibit native β-hairpin and α-helix folds. The method includes flexible bond and dihedral angles, and a Gaussian bias is applied with driver bond and dihedral angles to optimize the sampling efficiency. Solvation in water is implemented with the generalized Born (GBSA) model. The computed lowest-energy manifolds for the folded structures of the two β-hairpins agree closely with the corresponding NMR structures. In the case of the α1 peptide, the folded α-helical state, which is observed as oligomers in concentrated solution and crystals, is not stable in isolation. The computed preference for random coil structures is in agreement with NMR experiments at low concentration. The fact that native states can be located on high dimensional energy surfaces starting from extended conformations shows that the present methodology samples all relevant parts of the conformational space. The OPLS-AA force field with the GBSA solvent model was also found to perform well in leading to clear energetic separation of the correctly folded structures from misfolded structures for the two peptides that form β-turns.
Citing Articles
Citation data is made available by participants in CrossRef's Cited-by Linking service. For a more comprehensive list of citations to this article, users are encouraged to perform a search in SciFinder.
This article has been cited by 22 ACS Journal articles (5 most recent appear below).
Folding of Small Proteins Using Constrained Molecular Dynamics
Gouthaman S. Balaraman, In-Hee Park, Abhinandan Jain, and Nagarajan VaidehiThe Journal of Physical Chemistry B2011 Article ASAPFolding of Small Proteins Using Constrained Molecular Dynamics
Gouthaman S. Balaraman, In-Hee Park, Abhinandan Jain, and Nagarajan VaidehiThe Journal of Physical Chemistry B2011 Article ASAPThe focus of this paper is to examine whether conformational search using constrained molecular dynamics (MD) method is more enhanced and enriched toward “native-like” structures compared to all-atom MD for the protein folding as a model problem. ...
RNA Conformational Sampling: II. Arbitrary Length Multinucleotide Loop Closure
C. H. Mak, Wen-Yeuan Chung, and Nikolay D. MarkovskiyJournal of Chemical Theory and Computation2011 7 (4), 1198-1207RNA Conformational Sampling: II. Arbitrary Length Multinucleotide Loop Closure
C. H. Mak, Wen-Yeuan Chung, and Nikolay D. MarkovskiyJournal of Chemical Theory and Computation2011 7 (4), 1198-1207In this paper, we describe how the inverse kinematic solution to the loop closure problem may be generalized to reclose a RNA segment of arbitrary length containing any number of nucleotides without disturbing the atomic positions of the rest of the ...
Conformational Analysis of a Nitroxide Side Chain in an α-Helix with Density Functional Theory
Dora Toledo Warshaviak, Laura Serbulea, K. N. Houk, and Wayne L. HubbellThe Journal of Physical Chemistry B2011 115 (2), 397-405Conformational Analysis of a Nitroxide Side Chain in an α-Helix with Density Functional Theory
Dora Toledo Warshaviak, Laura Serbulea, K. N. Houk, and Wayne L. HubbellThe Journal of Physical Chemistry B2011 115 (2), 397-405In site directed spin labeling, a nitroxide side chain is introduced at a selected site in a protein; the most commonly used is a disulfide-linked side chain designated R1. The electron paramagnetic resonance (EPR) spectra of R1, and the interspin ...
PACE Force Field for Protein Simulations. 2. Folding Simulations of Peptides
Wei Han, Cheuk-Kin Wan, and Yun-Dong WuJournal of Chemical Theory and Computation2010 6 (11), 3390-3402PACE Force Field for Protein Simulations. 2. Folding Simulations of Peptides
Wei Han, Cheuk-Kin Wan, and Yun-Dong WuJournal of Chemical Theory and Computation2010 6 (11), 3390-3402We present the application of our recently developed PACE force field to the folding of peptides. These peptides include α-helical (AK17 and Fs), β-sheet (GB1m2 and Trpzip2), and mixed helical/coil (Trp-cage) peptides. With replica exchange molecular ...
Conformational Preferences of a 14-Residue Fibrillogenic Peptide from Acetylcholinesterase
Ranjit Vijayan and Philip C. BigginBiochemistry2010 49 (17), 3678-3684Conformational Preferences of a 14-Residue Fibrillogenic Peptide from Acetylcholinesterase
Ranjit Vijayan and Philip C. BigginBiochemistry2010 49 (17), 3678-3684A 14-residue fragment from near the C-terminus of the enzyme acetylcholinesterase (AChE) is believed to have a neurotoxic/neurotrophic effect acting via an unknown pathway. While the peptide is α-helical in the full-length enzyme, the structure and ...
Tools
-
Add to Favorites
-
Download Citation
-
Email a Colleague -
Permalink
Order Reprints
Rights & Permissions
Citation Alerts
Accession Codes
History
- Published In Issue February 18, 2004
- Received August 12, 2003
ACS
Network
Facebook
Tweet This
CiteULike
Newsvine
Digg This
Delicious
