Document Detail


Environment influences on the aromatic character of nucleobases and amino acids.
MedLine Citation:
PMID:  20668897     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Geometric (HOMA) and magnetic (NICS) indices of aromaticity were estimated for aromatic rings of amino acids and nucleobases. Cartesian coordinates were taken directly either from PDB files deposited in public databases at the finest resolution available (≤ 1.5 Å), or from structures resulting from full gradient geometry optimization in a hybrid QM/MM approach. Significant environmental effects imposing alterations of HOMA values were noted for all aromatic rings analysed. Furthermore, even extra fine resolution (≤ 1.0 Å) is not sufficient for direct estimation of HOMA values based on Cartesian coordinates provided by PDB files. The values of mean bond errors seem to be much higher than the 0.05 Å often reported for PDB files. The use of quantum chemistry geometry optimization is strongly advised; even a simple QM/MM model comprising only the aromatic substructure within the QM region and the rest of biomolecule treated classically within the MM framework proved to be a promising means of describing aromaticity inside native environments. According to the results presented, three consequences of the interaction with the environment can be observed that induce changes in structural and magnetic indices of aromaticity. First, broad ranges of HOMA or NICS values are usually obtained for different conformations of nearest neighborhood. Next, these values and their means can differ significantly from those characterising isolated monomers. The most significant increase in aromaticities is expected for the six-membered rings of guanine, thymine and cytosine. The same trend was also noticed for all amino acids inside proteins but this effect was much smaller, reaching the highest value for the five-membered ring of tryptophan. Explicit water solutions impose similar changes on HOMA and NICS distributions. Thus, environment effects of protein, DNA and even explicit water molecules are non-negligible sources of aromaticity changes appearing in the rings of nucleobases and aromatic amino acids residues.
Authors:
Piotr Cysewski; Beata Szefler
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't     Date:  2010-07-29
Journal Detail:
Title:  Journal of molecular modeling     Volume:  16     ISSN:  0948-5023     ISO Abbreviation:  J Mol Model     Publication Date:  2010 Nov 
Date Detail:
Created Date:  2010-10-05     Completed Date:  2011-01-24     Revised Date:  2013-05-29    
Medline Journal Info:
Nlm Unique ID:  9806569     Medline TA:  J Mol Model     Country:  Germany    
Other Details:
Languages:  eng     Pagination:  1709-20     Citation Subset:  IM    
Affiliation:
Department of Physical Chemistry, Collegium Medicum, Nicolaus Copernicus University, Kurpińskiego 5, 85-950, Bydgoszcz, Poland. piotr.cysewski@cm.umk.pl
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MeSH Terms
Descriptor/Qualifier:
Amino Acids / chemistry*
Databases, Protein
Environment*
Hydrocarbons, Aromatic / chemistry*
Magnetics
Models, Molecular
Molecular Conformation
Purines / chemistry*
Pyrimidines / chemistry*
Chemical
Reg. No./Substance:
0/Amino Acids; 0/Hydrocarbons, Aromatic; 0/Purines; 0/Pyrimidines
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