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Internet Electronic Journal of Molecular Design - IEJMD, ISSN 1538-6414, CODEN IEJMAT
| ABSTRACT - Internet Electron. J. Mol. Des. August 2005, Volume 4, Number 8, 579-590 |
Hydrogen Bond Analysis in DNA and RNA Based on Mulliken Overlap Population
Cezar Bendic
Internet Electron. J. Mol. Des. 2005, 4, 579-590
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Abstract:
Hydrogen bonds belong to the most important interactions in the
biopolymer structure. Up to now, due to the dimension of the
biopolymers and to the limited computer resources, only
geometrical criteria were used to identify possible candidates for
an attractive interaction (see the Hbexplore and HBplus programs).
We have proposed the Mulliken overlap population (OP) as a
quantitative quantum chemical criterion, not only for the
identification of possible interactions, but also for the evaluation of
their relative strength. An original program SHB_interactions was
developed to identify and to analyze intermolecular interactions in
biopolymers. Mulliken overlap population values are calculated
with the Extended Hückel (EH) method. This method, due to its
simplicity, offers the possibility to perform such calculations for a
large set of biopolymer structures in a relative short time. The
program uses PDB files containing NMR structures, builds a
possible interaction table with all the residue pairs that have atoms
placed at a distance less than 3.5 Å, cuts off from the structure the
corresponding residue pairs, adds hydrogen atoms to satisfy the
oxygen and phosphorus valences, and performs EH calculation of
the overlap population values. Although SHB_interactions was
initially developed for the nucleic acid structures, it can be applied
to proteins as well. The application of SHB_interactions is
described for the 1g70 structure, an RNA/protein complex of HIV-1
RRE-IIB RNA with the peptide RSG-1.2. A comparison between
the results obtained for 1g70 and those obtained using geometrical
criteria (HBexplore) was made. 56 DNA and 22 RNA NMR
structures from Protein Data Bank have been scanned in order to
identify and to analyze the hydrogen bond intermolecular
interactions using the OP criterion. Our results show that there is a
clear delimitation between H-bond overlap population values when
the acceptor is an oxygen atom and those when the acceptor is a
nitrogen atom. This is evidence for the capability of the overlap
population to make distinction between different H-bond types,
and allows comparative analysis of the results for the same type of
H-bonds. For classical H-bonds interactions (r > 1.7 Å) the overlap
population values are in the range 0.01 - 0.15. The OP criterion
allows makes possible the detection of weaker H-bonds. In spite of
the limitations of the EH method, the results obtained with
SHB_interactions allow a rationalization of the H-bonds in nucleic
acids as well as in protein structures. The results obtained outline
the capability of the OP criterion to substitute all of the five
geometrical parameters used by HBexplore. In addition, the use of
the overlap population as a quantum selection criterion presents the
advantage to detect not only the weaker H-bonds like C-H…A, but
also any other atom-atom intermolecular interactions. The source
code for SHB_interactions, written in C, instructions and some
examples are available at
http://gw-chimie.math.unibuc.ro/staff/cbendic/shb/SHB_interactions.html.
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