Zobrazeno 1 - 10
of 14
pro vyhledávání: '"Chaya S. Rapp"'
Publikováno v:
Proteins: Structure, Function, and Bioinformatics. 82:1494-1502
Cation–π interactions of methylated ammonium ions play a key role in a broad range of biochemical systems. These include methyl-lysine binding proteins which bind to methylated sites on histone proteins, lysine demethylase enzymes which demethylat
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::0b1b612a98b7f49d6223a47290d18465
https://doi.org/10.1002/prot.24519
https://doi.org/10.1002/prot.24519
Publikováno v:
Protein Science. 22:1025-1036
Oligomerization of G protein-coupled receptors is a recognized mode of regulation of receptor activities, with alternate oligomeric states resulting in different signaling functions. The CXCR4 chemokine receptor is a G protein-coupled receptor that i
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::7ec9955c816596e85be843965d60661e
https://doi.org/10.1002/pro.2288
https://doi.org/10.1002/pro.2288
Publikováno v:
Proteins, 69(1), 69-74. Wiley-Liss Inc.
The ability to determine the structure of a protein in solution is a critical tool for structural biology, as proteins in their native state are found in aqueous environments. Using a physical chemistry based prediction protocol, we demonstrate the a
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::dd80a55f6daeea4f33d2cf03cd472840
https://doi.org/10.1002/prot.21503
https://doi.org/10.1002/prot.21503
Autor:
Matthew P. Jacobson, Chaya S. Rapp, Ilya Chorny, Eli S. Groban, Sergio Wong, Daniel J. Mandell, Elisheva Levine
Publikováno v:
Journal of the American Chemical Society. 129:820-827
Post-translational phosphorylation plays a key role in regulating protein function. Here, we provide a quantitative assessment of the relative strengths of hydrogen bonds involving phosphorylated amino acid side chains (pSer, pAsp) with several commo
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a845397f7e7921425427e4f5019b8045
https://doi.org/10.1021/ja063019w
https://doi.org/10.1021/ja063019w
Publikováno v:
The Journal of Physical Chemistry B. 108:6643-6654
Salt bridges play an important role in protein stability, protein-protein interactions, and protein folding. The electrostatic solvation free energies of the analogues of charged amino acid side chains were calculated using both explicit solvent free
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::2e641e27c77937ced77a3c9f1b031bbd
https://doi.org/10.1021/jp037821l
https://doi.org/10.1021/jp037821l
Autor:
Chaya S. Rapp, Richard A. Friesner
Publikováno v:
Proteins: Structure, Function, and Genetics. 35:173-183
We have carried out an extensive exploration of the possibility of predicting the structure of long loops in proteins, using an 8- and a 12-residue loop in ribonuclease A as models. The native X-ray structure is used as a template while allowing for
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::b9f6ed6fe6554097b0ac35d1cc9d6fad
https://doi.org/10.1002/(sici)1097-0134(19990501)35:2<173::aid-prot4>3.0.co
https://doi.org/10.1002/(sici)1097-0134(19990501)35:2<173::aid-prot4>3.0.co
Publikováno v:
The Journal of Physical Chemistry B. 102:10983-10990
We have derived a surface-area-based version of the generalized Born model (S-GB) as a well-defined approximation to the boundary element formulation of the Poisson−Boltzmann (PB) equation. The relationship of the surface area methodology to the vo
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::867d2969b5ecc7e43f09b49b5fe86d4c
https://doi.org/10.1021/jp982533o
https://doi.org/10.1021/jp982533o
Autor:
Aviva Schiffmiller, Chaya S. Rapp, Matthew P. Jacobson, Esther Leah Schoenbrun, Chakrapani Kalyanaraman
Publikováno v:
Journal of chemical information and modeling. 51(9)
We introduce the "Prime-ligand" method for ranking ligands in congeneric series. The method employs a single scoring function, the OPLS-AA/GBSA molecular mechanics/implicit solvent model, for all stages of sampling and scoring. We evaluate the method
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3295e876a9ba13181f29237786deeb7e
https://pubmed.ncbi.nlm.nih.gov/21780805
https://pubmed.ncbi.nlm.nih.gov/21780805
Hydrogen atoms are not typically observable in X-ray crystal structures, but inferring their locations is often important in structure-based drug design. In addition, protonation states of the protein can change in response to ligand binding, as can
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3245ad73e47320674fe8508de2d68f0e
https://europepmc.org/articles/PMC2744578/
https://europepmc.org/articles/PMC2744578/
Autor:
Rena M. Pollack, Chaya S. Rapp
Publikováno v:
Proteins. 60(1)
The effects of crystal packing on protein loop structures are examined by (1) a comparison of loops in proteins that have been crystallized in alternate packing arrangements, and (2) theoretical prediction of loops both with and without the inclusion
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4044cde1639bc0a19ba352310935096f
https://pubmed.ncbi.nlm.nih.gov/15852307
https://pubmed.ncbi.nlm.nih.gov/15852307