File Download

There are no files associated with this item.

  Links for fulltext
     (May Require Subscription)
Supplementary

Article: Exploring the sequence patterns in the α-helices of proteins

TitleExploring the sequence patterns in the α-helices of proteins
Authors
Issue Date2003
PublisherOxford University Press. The Journal's web site is located at http://peds.oxfordjournals.org/
Citation
Protein Engineering, 2003, v. 16 n. 11, p. 799-807 How to Cite?
AbstractThis paper reports an extensive sequence analysis of the α-helices of proteins, α-Helices were extracted from the Protein Data Bank (PDB) and were divided into groups according to their sizes. It was found that some amino acids had differential propensity values for adopting helical conformation in short, medium and long α-helices. Pro and Trp had a significantly higher propensity for helical conformation in short helices than in medium and long helices. Trp was the strongest helix conformer in short helices. Sequence patterns favoring helical conformation were derived from a neighbor-dependent sequence analysis of proteins, which calculated the effect of neighboring amino acid type on the propensity of residues for adopting a particular secondary structure in proteins. This method produced an enhanced statistical significance scale that allowed us to explore the positional preference of amino acids for α-helical conformations. It was shown that the amino acid pair preference for α-helix had a unique pattern and this pattern was not always predictable by assuming proportional contributions from the individual propensity values of the amino acids. Our analysis also yielded a series of amino acid dyads that showed preference for α-helix conformation. The data presented in this study, along with our previous study on loop sequences of proteins, should prove useful for developing potential 'codes' for recognizing sequence patterns that are favorable for specific secondary structural elements in proteins.
Persistent Identifierhttp://hdl.handle.net/10722/147489
ISSN
2003 Impact Factor: 2.065
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorWang, Jen_US
dc.contributor.authorFeng, JAen_US
dc.date.accessioned2012-05-29T06:04:04Z-
dc.date.available2012-05-29T06:04:04Z-
dc.date.issued2003en_US
dc.identifier.citationProtein Engineering, 2003, v. 16 n. 11, p. 799-807en_US
dc.identifier.issn0269-2139en_US
dc.identifier.urihttp://hdl.handle.net/10722/147489-
dc.description.abstractThis paper reports an extensive sequence analysis of the α-helices of proteins, α-Helices were extracted from the Protein Data Bank (PDB) and were divided into groups according to their sizes. It was found that some amino acids had differential propensity values for adopting helical conformation in short, medium and long α-helices. Pro and Trp had a significantly higher propensity for helical conformation in short helices than in medium and long helices. Trp was the strongest helix conformer in short helices. Sequence patterns favoring helical conformation were derived from a neighbor-dependent sequence analysis of proteins, which calculated the effect of neighboring amino acid type on the propensity of residues for adopting a particular secondary structure in proteins. This method produced an enhanced statistical significance scale that allowed us to explore the positional preference of amino acids for α-helical conformations. It was shown that the amino acid pair preference for α-helix had a unique pattern and this pattern was not always predictable by assuming proportional contributions from the individual propensity values of the amino acids. Our analysis also yielded a series of amino acid dyads that showed preference for α-helix conformation. The data presented in this study, along with our previous study on loop sequences of proteins, should prove useful for developing potential 'codes' for recognizing sequence patterns that are favorable for specific secondary structural elements in proteins.en_US
dc.languageengen_US
dc.publisherOxford University Press. The Journal's web site is located at http://peds.oxfordjournals.org/en_US
dc.relation.ispartofProtein Engineeringen_US
dc.subject.meshComputational Biologyen_US
dc.subject.meshModels, Molecularen_US
dc.subject.meshPattern Recognition, Automateden_US
dc.subject.meshProtein Structure, Secondaryen_US
dc.subject.meshProteins - Chemistry - Metabolismen_US
dc.titleExploring the sequence patterns in the α-helices of proteinsen_US
dc.typeArticleen_US
dc.identifier.emailWang, J:junwen@hkucc.hku.hken_US
dc.identifier.authorityWang, J=rp00280en_US
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.pmid14631069-
dc.identifier.scopuseid_2-s2.0-0344305738en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-0344305738&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume16en_US
dc.identifier.issue11en_US
dc.identifier.spage799en_US
dc.identifier.epage807en_US
dc.identifier.isiWOS:000187232200004-
dc.publisher.placeUnited Statesen_US
dc.identifier.scopusauthoridWang, J=8950599500en_US
dc.identifier.scopusauthoridFeng, JA=7403884662en_US

Export via OAI-PMH Interface in XML Formats


OR


Export to Other Non-XML Formats