Linked Life Data

18300253

Source:http://linkedlifedata.com/resource/pubmed/id/18300253

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
3
pubmed:dateCreated
2008-7-15
pubmed:abstractText
It has recently been shown that in proteins the atomic mean-square displacement (or B-factor) can be related to the number of the neighboring atoms (or protein contact number), and that this relationship allows one to compute the B-factor profiles directly from protein contact number. This method, referred to as the protein contact model, is appealing, since it requires neither trajectory integration nor matrix diagonalization. As a result, the protein contact model can be applied to very large proteins and can be implemented as a high-throughput computational tool to compute atomic fluctuations in proteins. Here, we show that this relationship can be further refined to that between the atomic mean-square displacement and the weighted protein contact-number, the weight being the square of the reciprocal distance between the contacting pair. In addition, we show that this relationship can be utilized to compute the cross-correlation of atomic motion (the B-factor is essentially the auto-correlation of atomic motion). For a nonhomologous dataset comprising 972 high-resolution X-ray protein structures (resolution <2.0 A and sequence identity <25%), the mean correlation coefficient between the X-ray and computed B-factors based on the weighted protein contact-number model is 0.61, which is better than those of the original contact-number model (0.51) and other methods. We also show that the computed correlation maps based on the weighted contact-number model are globally similar to those computed through normal model analysis for some selected cases. Our results underscore the relationship between protein dynamics and protein packing. We believe that our method will be useful in the study of the protein structure-dynamics relationship.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Aug
pubmed:issn
1097-0134
pubmed:author
pubmed:issnType
Electronic
pubmed:day
15
pubmed:volume
72
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
929-35
pubmed:meshHeading
pubmed:year
2008
pubmed:articleTitle
Deriving protein dynamical properties from weighted protein contact number.
pubmed:affiliation
Institute of Bioinformatics, National Chiao Tung University, HsinChu 30050, Taiwan, Republic of China.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't