Linked Life Data

17132017

Source:http://linkedlifedata.com/resource/pubmed/id/17132017

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
48
pubmed:dateCreated
2006-11-29
pubmed:abstractText
The coiled coil is one of the simplest and best-studied protein structural motifs, consisting of two to five helices wound around each other. Empirical rules have been established on the tendency of different core sequences to form a certain oligomeric state but the physical forces behind this specificity are unclear. In this work, we model four sequences onto the structures of dimeric, trimeric, tetrameric, and pentameric coiled coils. We first examine the ability of an effective energy function (EEF1.1) to discriminate the correct oligomeric state for a given sequence. We find that inclusion of the translational, rotational, and side-chain conformational entropy is necessary for discriminating the native structures from their misassembled counterparts. The decomposition of the effective energy into residue contributions yields theoretical values for the oligomeric propensity of different residue types at different heptad positions. We find that certain calculated residue propensities are general and consistent with existing rules. For example, leucine at d favors dimers, leucine at a favors tetramers or pentamers, and isoleucine at a favors trimers. Other residue propensities are sequence context dependent. For example, glutamine at d favors trimers in one context and pentamers in another. Charged residues at e and g positions usually destabilize higher oligomers due to higher desolvation. Nonpolar residues at these positions confer pentamer specificity when combined with certain residues at positions a and d. Specifically, the pair Leua-Alag' or the inverse was found to stabilize the pentamer. The small energy gap between the native and misfolded counterparts explains why a few mutations at the core sites are sufficient to induce a change in the oligomeric state of these peptides. A large number of possible experiments are suggested by these results.
pubmed:grant
pubmed:commentsCorrections
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Dec
pubmed:issn
0002-7863
pubmed:author
pubmed:issnType
Print
pubmed:day
6
pubmed:volume
128
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
15499-510
pubmed:dateRevised
2007-11-14
pubmed:meshHeading
pubmed:year
2006
pubmed:articleTitle
Energetic determinants of oligomeric state specificity in coiled coils.
pubmed:affiliation
Department of Chemistry, The City College of CUNY Convent Avenue & 138 Street, New York, New York 10031, USA.
pubmed:publicationType
Journal Article, Research Support, U.S. Gov't, Non-P.H.S., Research Support, N.I.H., Extramural