Document Detail


Integrating the intrinsic conformational preferences of noncoded α-amino acids modified at the peptide bond into the noncoded amino acids database.
MedLine Citation:
PMID:  21491493     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Recently, we reported a database (Noncoded Amino acids Database; http://recerca.upc.edu/imem/index.htm) that was built to compile information about the intrinsic conformational preferences of nonproteinogenic residues determined by quantum mechanical calculations, as well as bibliographic information about their synthesis, physical and spectroscopic characterization, the experimentally established conformational propensities, and applications (Revilla-López et al., J Phys Chem B 2010;114:7413-7422). The database initially contained the information available for α-tetrasubstituted α-amino acids. In this work, we extend NCAD to three families of compounds, which can be used to engineer peptides and proteins incorporating modifications at the--NHCO--peptide bond. Such families are: N-substituted α-amino acids, thio-α-amino acids, and diamines and diacids used to build retropeptides. The conformational preferences of these compounds have been analyzed and described based on the information captured in the database. In addition, we provide an example of the utility of the database and of the compounds it compiles in protein and peptide engineering. Specifically, the symmetry of a sequence engineered to stabilize the 3(10)-helix with respect to the α-helix has been broken without perturbing significantly the secondary structure through targeted replacements using the information contained in the database.
Authors:
Guillem Revilla-López; Francisco Rodríguez-Ropero; David Curcó; Juan Torras; M Isabel Calaza; David Zanuy; Ana I Jiménez; Carlos Cativiela; Ruth Nussinov; Carlos Alemán
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't     Date:  2011-04-12
Journal Detail:
Title:  Proteins     Volume:  79     ISSN:  1097-0134     ISO Abbreviation:  Proteins     Publication Date:  2011 Jun 
Date Detail:
Created Date:  2011-05-11     Completed Date:  2011-09-01     Revised Date:  2013-06-30    
Medline Journal Info:
Nlm Unique ID:  8700181     Medline TA:  Proteins     Country:  United States    
Other Details:
Languages:  eng     Pagination:  1841-52     Citation Subset:  IM    
Copyright Information:
© 2011 Wiley-Liss, Inc.
Affiliation:
Departament d'Enginyeria Química, ETS d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain.
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MeSH Terms
Descriptor/Qualifier:
Amino Acid Motifs
Amino Acids / chemistry*
Databases, Factual
Diamines / chemistry
Models, Molecular
Peptides / chemistry*
Protein Engineering
Protein Structure, Secondary
Sulfhydryl Compounds / chemistry
Grant Support
ID/Acronym/Agency:
HHSN261200800001E/CO/NCI NIH HHS
Chemical
Reg. No./Substance:
0/Amino Acids; 0/Diamines; 0/Peptides; 0/Sulfhydryl Compounds
Comments/Corrections

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