Aromatic–Aromatic Interactions Database, A2ID: An analysis of aromatic π-networks in proteins

Chourasia, Mukesh; Sastry, G. Madhavi; Sastry, G. Narahari

doi:10.1016/j.ijbiomac.2011.01.008

Cited by 88 publications

(70 citation statements)

References 46 publications

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“…Further, frequency calculations at B3LYP/6-31G(d) level of theory characterized all monomers as minima on the PES. From the literature, it is well known that the M05-2X functional is suitable for treating non-covalent interactions [15][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30]. In our previous studies of phenylalanine, tyrosine and tryptophan monomers, we have also found the M05-2X functional to give satisfactory results [17][18][19].…”

Section: Methodsmentioning

confidence: 71%

“…Chakrabarti et al [20] reported that the His ring interacts with other aromatic and basic residues and forms hydrogen bonds (HBs) with polar and charged (both negative and positive) residues in proteins. Recent studies on the cooperativity of non-covalent interactions reveal that the manifestation of cooperativity is essential to understand various phenomena such as formation of supramolecular assemblies, catalysis and biological functions [1,[21][22][23][24]. His is an important model for the understanding of cation-π interactions due to its imidazole side chain [25][26][27][28][29][30][31][32][33][34][35][36].…”

Section: Introductionmentioning

confidence: 99%

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A first-principles investigation of histidine and its ionic counterparts

2016

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Section: Methodsmentioning

confidence: 71%

Section: Introductionmentioning

confidence: 99%

A first-principles investigation of histidine and its ionic counterparts

2016

Self Cite

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“…DNA–protein complexes were identified in the PDB using similar criteria to those previously used in the literature to detect nucleobase–amino acid π–π contacts (Supplementary Figure S3) (8,30). Specifically, X–ray crystal structures published before 24 May 2011 with a resolution better than 2.0 Å and less than 90% sequence identity were chosen for analysis (428 crystal structures total).…”

Section: Methodsmentioning

confidence: 99%

DNA–protein π-interactions in nature: abundance, structure, composition and strength of contacts between aromatic amino acids and DNA nucleobases or deoxyribose sugar

Wilson

Kellie

Wetmore

2014

Nucleic Acids Research

129

172

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Four hundred twenty-eight high-resolution DNA–protein complexes were chosen for a bioinformatics study. Although 164 crystal structures (38% of those searched) contained no interactions, 574 discrete π–contacts between the aromatic amino acids and the DNA nucleobases or deoxyribose were identified using strict criteria, including visual inspection. The abundance and structure of the interactions were determined by unequivocally classifying the contacts as either π–π stacking, π–π T-shaped or sugar–π contacts. Three hundred forty-four nucleobase–amino acid π–π contacts (60% of all interactions identified) were identified in 175 of the crystal structures searched. Unprecedented in the literature, 230 DNA–protein sugar–π contacts (40% of all interactions identified) were identified in 137 crystal structures, which involve C–H···π and/or lone–pair···π interactions, contain any amino acid and can be classified according to sugar atoms involved. Both π–π and sugar–π interactions display a range of relative monomer orientations and therefore interaction energies (up to –50 (–70) kJ mol−1 for neutral (charged) interactions as determined using quantum chemical calculations). In general, DNA–protein π-interactions are more prevalent than perhaps currently accepted and the role of such interactions in many biological processes may yet to be uncovered.

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“…Following the protocols previously employed in the literature to identify π-interactions in biological systems (Baker & Grant, 2007;Chourasia, Sastry, & Sastry, 2011;Wilson et al, 2014), search functions available in the PDB were used to select experimental X-ray structures containing protein and DNA, but not RNA or hybrid DNA/RNA, with resolution better than 2.0 Å, less than 90% sequence identity and published prior to 2 January 2014. This selection criterion thereby identifies complexes containing any type of DNA, including, but not limited to, single-stranded DNA, double-stranded DNA, DNA cofactors, and DNA quadruplexes.…”

Section: Datasetsmentioning

confidence: 99%

Landscape ofπ–πand sugar–πcontacts in DNA–protein interactions

Wilson

Wells

Abendong

et al. 2015

Journal of Biomolecular Structure and Dynamics

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There were 1765 contacts identified between DNA nucleobases or deoxyribose and cyclic (W, H, F, Y) or acyclic (R, E, D) amino acids in 672 X-ray structures of DNA-protein complexes. In this first study to compare π-interactions between the cyclic and acyclic amino acids, visual inspection was used to categorize amino acid interactions as nucleobase π-π (according to biological edge) or deoxyribose sugar-π (according to sugar edge). Overall, 54% of contacts are nucleobase π-π interactions, which involve all amino acids, but are more common for Y, F, and R, and involve all DNA nucleobases with similar frequencies. Among binding arrangements, cyclic amino acids prefer more planar (stacked) π-systems than the acyclic counterparts. Although sugar-π interactions were only previously identified with the cyclic amino acids and were found to be less common (38%) than nucleobase-cyclic amino acid contacts, sugar-π interactions are more common than nucleobase π-π contacts for the acyclic series (61% of contacts). Similar to DNA-protein π-π interactions, sugar-π contacts most frequently involve Y and R, although all amino acids adopt many binding orientations relative to deoxyribose. These DNA-protein π-interactions stabilize biological systems, by up to approximately -40 kJ mol(-1) for neutral nucleobase or sugar-amino acid interactions, but up to approximately -95 kJ mol(-1) for positively or negatively charged contacts. The high frequency and strength, despite variation in structure and composition, of these π-interactions point to an important function in biological systems.

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Aromatic–Aromatic Interactions Database, A2ID: An analysis of aromatic π-networks in proteins

Cited by 88 publications

References 46 publications

A first-principles investigation of histidine and its ionic counterparts

A first-principles investigation of histidine and its ionic counterparts

DNA–protein π-interactions in nature: abundance, structure, composition and strength of contacts between aromatic amino acids and DNA nucleobases or deoxyribose sugar

Landscape ofπ–πand sugar–πcontacts in DNA–protein interactions

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