Naslov
Initial analysis of binding sites in protein-DNA interaction based on affinity of hydrogen bonds and van der Waals contact formation

Autori
Kriško, Anita ; Zoranić, Larisa ; Gromiha, Michael

Vrsta, podvrsta i kategorija rada
Sažeci sa skupova, sažetak, znanstveni

Izvornik
MATH/CHEM/COMP 2002 Book of Abstracts / Graovac, Ante ; Pokrić, Biserka ; Smrečki, Vilko - Zagreb : Institut Ruđer Bošković, 2002

Skup
MATH/CHEM/COMP 2002

Mjesto i datum
Dubrovnik, Hrvatska, 24.06.2002. - 29.06.2002

Vrsta sudjelovanja
Poster

Vrsta recenzije
Međunarodna recenzija

Ključne riječi
protein-DNA complexes; interaction

Sažetak
Vital cellular processes like DNA replication, genetic expression, DNA repair and packing engage binding of proteins to DNA. Recently, many 3D structures of protein-DNA complexes have been elucidated and nature of interaction has been examined. The simplest way to study these interactions is by using binding preferences of amino acids and nucleotides. With respect to the DNA recognition motifs, 62 nonredundant sequences (out of 129 solved tertiary structures of protein-DNA complexes) were classified into eight DNA-binding protein structural families1: (i) helix-turn-helix proteins (21), (ii) zinc-coordinating proteins (11), (iii) zipper-type proteins (4), (iv) other &#945 ; -helical proteins (4), (v) &#946 ; -sheet proteins (3), (vi) the &#946 ; -hairpin/ribbon proteins (6), (vii) enzymes (4), (viii) and others (9). Each group of sequences was aligned using CLUSTAL-X. Experimentally solved binding regions for zinc-coordinating, zipper-type, other &#945 ; -helical and the &#946 ; -hairpin/ribbon proteins were highlighted in multiple sequence alignments. Based on observed frequency of hydrogen bonding, van der Waals contacts and water mediated hydrogen bonding reported by Luscombe et al.2 binding preferences of amino acid-nucleotide interactions were calculated. Preference profiles were made for all 62 sequences. Binding regions in zipper-type proteins are correlated with regions of highest preference values in preference profiles. Binding domains of other &#945 ; -helical proteins have similar profiles: central amino acid(s) with high preference(s) and surrounding amino acids with low or average preferences. The &#946 ; -hairpin/ribbon protein binding regions (except 1CMA_A) have asymmetric profiles: section with lower preferences followed by section with higher amino acid preferences. For all other classes an overall rule for binging regions was not found. 1 N. M. Luscombe, S. E. Austin, H. M. Berman, J. M. Thornton, An overview of the structures of protein-DNA complexes, Genome Biology 1 (2000) 1-10. 2 N. M. Luscombe, R. A. Laskowski, J. M. Thornton, Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level, Nucleic Acids Research 29 (2001) 2860-2874.

Izvorni jezik
Engleski

Znanstvena područja
Fizika

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