N V Dokholyan
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Explore the profile of N V Dokholyan including associated specialties, affiliations and a list of published articles.
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13
Citations
559
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Recent Articles
1.
Reynolds J, Vishweshwaraiah Y, Chirasani V, Pritchard J, Dokholyan N
J Biol Chem
. 2023 Feb;
299(4):103069.
PMID: 36841477
Transferases are ubiquitous across all known life. While much work has been done to understand and describe these essential enzymes, there have been minimal efforts to exert tight and reversible...
2.
Cloer E, Siesser P, Cousins E, Goldfarb D, Mowrey D, Harrison J, et al.
Mol Cell Biol
. 2018 Aug;
38(22).
PMID: 30126895
Cancer-derived loss-of-function mutations in the KEAP1 tumor suppressor gene stabilize the NRF2 transcription factor, resulting in a prosurvival gene expression program that alters cellular metabolism and neutralizes oxidative stress. In...
3.
Lam A, Borreguero J, Ding F, Dokholyan N, Buldyrev S, Stanley H, et al.
J Mol Biol
. 2007 Sep;
373(5):1348-60.
PMID: 17900612
The transition-state ensemble (TSE) is the set of protein conformations with an equal probability to fold or unfold. Its characterization is crucial for an understanding of the folding process. We...
4.
Urbanc B, Cruz L, Ding F, Sammond D, Khare S, Buldyrev S, et al.
Biophys J
. 2004 Sep;
87(4):2310-21.
PMID: 15454432
Recent experiments with amyloid beta (Abeta) peptide indicate that formation of toxic oligomers may be an important contribution to the onset of Alzheimer's disease. The toxicity of Abeta oligomers depends...
5.
Peng S, Ding F, Urbanc B, Buldyrev S, Cruz L, Stanley H, et al.
Phys Rev E Stat Nonlin Soft Matter Phys
. 2004 Jun;
69(4 Pt 1):041908.
PMID: 15169044
We study the aggregation of peptides using the discrete molecular dynamics simulations. Specifically, at temperatures above the alpha-helix melting temperature of a single peptide, the model peptides aggregate into a...
6.
Vendruscolo M, Dokholyan N, Paci E, Karplus M
Phys Rev E Stat Nonlin Soft Matter Phys
. 2002 Aug;
65(6 Pt 1):061910.
PMID: 12188762
We use geometrical considerations to provide a different perspective on the fact that a few selected amino acids, the so-called "key residues," act as nucleation centers for protein folding. By...
7.
Lee Y, Andrade Jr J, Buldyrev S, Dokholyan N, Havlin S, King P, et al.
Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics
. 2002 Apr;
60(3):3425-8.
PMID: 11970164
We study traveling time and traveling length for tracer dispersion in two-dimensional bond percolation, modeling flow by tracer particles driven by a pressure difference between two points separated by Euclidean...
8.
Dokholyan N, Shakhnovich E
J Mol Biol
. 2001 Sep;
312(1):289-307.
PMID: 11545603
We propose a model that explains the hierarchical organization of proteins in fold families. The model, which is based on the evolutionary selection of proteins by their native state stability,...
9.
Scala A, Dokholyan N, Buldyrev S, Stanley H
Phys Rev E Stat Nonlin Soft Matter Phys
. 2001 Apr;
63(3 Pt 1):032901.
PMID: 11308693
We introduce a quantity, the entropic susceptibility, that measures the thermodynamic importance-for the folding transition-of the contacts between amino acids in model proteins. Using this quantity, we find that only...
10.
Dokholyan N, Buldyrev S, Stanley H, Shakhnovich E
J Mol Biol
. 2000 Mar;
296(5):1183-8.
PMID: 10698625
Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble...