Statistical analysis of structural determinants for protein–DNA‐binding specificity

Corona, Rosario I.; Guo, Jun‐tao

doi:10.1002/prot.25061

Cited by 28 publications

(69 citation statements)

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“…As a result, the binding affinities of VapBC LT2 mutants that interacted with the DNA backbone were weaker than those of VapBC LT2 mutants that interacted with DNA bases. Previous studies on protein‐DNA interactions have shown that each residue has a different way of interacting with DNA . In particular, arginine and lysine are most frequently involved in protein‐DNA interactions.…”

Section: Discussionmentioning

confidence: 99%

“…In addition, the interaction between protein and DNA may be different depending on the DNA sequence or DNA shape. [61][62][63] DNA sequences are related to specificity by interactions between protein and DNA bases in DNA-protein interactions. Differences in DNA conformation such as the width of the major groove or minor groove and the overall shape of the DNA are also known to play a major role in protein-DNA interactions.…”

Section: Discussionmentioning

confidence: 99%

“…Previous studies on protein-DNA interactions have shown that each residue has a different way of interacting with DNA. [61][62][63] In particular, arginine and lysine are most frequently involved in protein-DNA interactions. Two positively charged residues bind to a negatively charged DNA backbone via electrostatic interaction.…”

Section: Discussionmentioning

confidence: 99%

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Crystal structure of proteolyzed VapBC and DNA‐bound VapBC from Salmonella enterica Typhimurium LT2 and VapC as a putative Ca ²⁺ ‐dependent ribonuclease

et al. 2019

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Bacterial toxin‐antitoxin (TA) system has gained attention for its essential roles in cellular maintenance and survival under harsh environmental conditions such as nutrient deficiency and antibiotic treatment. There are at least 14 TA systems in Salmonella enterica serovar Typhimurium LT2, a pathogenic bacterium, and none of the structures of these TA systems have been determined. We determined the crystal structure of the VapBC TA complex from S. Typhimurium LT2 in proteolyzed and DNA‐bound forms at 2.0 Å and 2.8 Å resolution, respectively. The VapC toxin possesses a pilT N‐terminal domain (PIN‐domain) that shows ribonuclease activity, and the VapB antitoxin has an AbrB‐type DNA binding domain. In addition, the structure revealed details of interaction mode between VapBC and the cognate promoter DNA, including the inhibition of VapC by VapB and linear conformation of bound DNA in the VapBC complex. The complexation of VapBC with the linear DNA is not consistent with known structures of VapBC homologs in complex with bent DNA. We also identified VapC from S. Typhimurium LT2 as a putative Ca2+‐dependent ribonuclease, which differs from previous data showing that VapC homologs have Mg2+ or Mn2+‐dependent ribonuclease activities. The present studies could provide structural understanding of the physiology of VapBC systems and foundation for the development of new antibiotic drugs against Salmonella infection.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Crystal structure of proteolyzed VapBC and DNA‐bound VapBC from Salmonella enterica Typhimurium LT2 and VapC as a putative Ca ²⁺ ‐dependent ribonuclease

et al. 2019

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“…Некоторые авторы полагают, что следует раздельно рассматривать комплексы белок-ДНК с разной специфичностью. Так, выделяют высоко-, мульти-и не-специфические комплексы (Corona, Guo, 2016). При этом под высокоспецифическими понимают белки, которые распознают единственный сайт на ДНК.…”

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“…Неспецифические белки связывают ДНК независимо от последовательности. Соответственно, комплексы разде-лены на группы по типу распознающего белка (Corona, Guo, 2016). Мы полагаем, что такое деление является достаточно условным.…”

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Protein-DNA interactions: statistical analysis of interatomic contacts in major and minor grooves

Anashkina¹,

Kuznetsov²,

Batianovskii³

et al. 2017

Vestn. VOGiS

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The interactions between protein and DNA in essence underlie all processes in a living cell. Understanding the principles of specific recognition of DNA sites will open the way to understand how these processes are controlled and to interfere in their operation. In the paper we studied contacts between the protein and DNA at the atomic level in the structures of all the 3 518 proteinDNA complexes available in PDB by the Voronoi-Delaunay tessellation method. The method unambiguously defines contacts between atoms with out any parameters, and characterizes each contact by the distance between atoms and the contact area, which is determined by the corresponding face of the Voronoi polyhedron. It was shown that most contacts are formed between the protein atoms and the sugar phosphate backbone of the DNA (72.9 %). The contact with the atoms of the nucleic bases emerging into the grooves of DNA is 17.0 % for a major groove and 10.1 % for all atomic contacts for a minor groove. Totally, the interaction between protein atoms and nucleic base atoms accounts for 27.1 % of all contacts. Analysis of the accessible surface area of atoms in the major and the minor grooves showed a correlation with the num ber of contacts (coefficient of linear correlation 0.94 and 0.93, respectively), however, nucleic acid atoms forming hydrogen bonds make contacts more often than may be expected from statistical considerations. It was shown that conformationally stable peptides oc cur sometimes in the binding regions with DNA. Ana lysis of the residues in a predefined conformation in 3 518 proteinDNA complexes revealed 159 amino acid residues in a predefined βbend type I conformation, 15 residues in the conformation of βbend type I' , and 6 residues in the conformation of βbend type II. No residues in the conformation of βbend type II' were Взаимодействия между белком и ДНК по существу лежат в основе всех процессов, происходящих в живой клетке. Познание принци пов специфического распознавания сайтов ДНК позволит понять, как управляются эти процессы, и даст возможность сознательно вмешиваться в управление ими. В работе изучены методом Воро ного -Делоне контакты белокДНК на атомном уровне в структу рах 3 518 комплексов из PDB (все имеющиеся на май 2017 г.), содержа щих как белковые цепи, так и ДНК. Метод не содержит параметров и позволяет однозначно выявлять непосредственные контакты между атомами и характеризовать каждый контакт, помимо рас стояния между атомами, площадью контакта, определяемой соот ветствующей гранью полиэдра Вороного. Показано, что большая часть контактов образуется между атомами белка и атомами са ха рофосфатного остова ДНК (72.9 %). На контакты с атомами нуклеи новых оснований, выходящих в бороздки ДНК, приходится для большой бороздки 17.0 % и для малой бороздки 10.1 % от всех атомных контактов. Суммарно на взаимодействия между атомами белка и атомами нуклеиновых оснований приходится 27.1 % всех атомных контактов. Анализ площади доступной поверхности ато мов большой и малой бороздок показал, что она коррелирует с числом ...

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Insights into protein–DNA interactions from hydrogen bond energy‐based comparative protein–ligand analyses

Malik

Guo

2022

Proteins

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Hydrogen bonds play important roles in protein folding and protein-ligand interactions, particularly in specific protein-DNA recognition. However, the distributions of hydrogen bonds, especially hydrogen bond energy (HBE) in different types of protein-ligand complexes, is unknown. Here we performed a comparative analysis of hydrogen bonds among three non-redundant datasets of protein-protein, proteinpeptide, and protein-DNA complexes. Besides comparing the number of hydrogen bonds in terms of types and locations, we investigated the distributions of HBE. Our results indicate that while there is no significant difference of hydrogen bonds within protein chains among the three types of complexes, interfacial hydrogen bonds are significantly more prevalent in protein-DNA complexes. More importantly, the interfacial hydrogen bonds in protein-DNA complexes displayed a unique energy distribution of strong and weak hydrogen bonds whereas majority of the interfacial hydrogen bonds in protein-protein and protein-peptide complexes are of predominantly high strength with low energy. Moreover, there is a significant difference in the energy distributions of minor groove hydrogen bonds between protein-DNA complexes with different binding specificity. Highly specific protein-DNA complexes contain more strong hydrogen bonds in the minor groove than multi-specific complexes, suggesting important role of minor groove in specific protein-DNA recognition. These results can help better understand protein-DNA interactions and have important implications in improving quality assessments of protein-DNA complex models.

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Statistical analysis of structural determinants for protein–DNA‐binding specificity

Cited by 28 publications

References 69 publications

Crystal structure of proteolyzed VapBC and DNA‐bound VapBC from Salmonella enterica Typhimurium LT2 and VapC as a putative Ca ²⁺ ‐dependent ribonuclease

Crystal structure of proteolyzed VapBC and DNA‐bound VapBC from Salmonella enterica Typhimurium LT2 and VapC as a putative Ca ²⁺ ‐dependent ribonuclease

Protein-DNA interactions: statistical analysis of interatomic contacts in major and minor grooves

Insights into protein–DNA interactions from hydrogen bond energy‐based comparative protein–ligand analyses

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Statistical analysis of structural determinants for protein–DNA‐binding specificity

Cited by 28 publications

References 69 publications

Crystal structure of proteolyzed VapBC and DNA‐bound VapBC from Salmonella enterica Typhimurium LT2 and VapC as a putative Ca 2+ ‐dependent ribonuclease

Crystal structure of proteolyzed VapBC and DNA‐bound VapBC from Salmonella enterica Typhimurium LT2 and VapC as a putative Ca 2+ ‐dependent ribonuclease

Protein-DNA interactions: statistical analysis of interatomic contacts in major and minor grooves

Insights into protein–DNA interactions from hydrogen bond energy‐based comparative protein–ligand analyses

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Crystal structure of proteolyzed VapBC and DNA‐bound VapBC from Salmonella enterica Typhimurium LT2 and VapC as a putative Ca ²⁺ ‐dependent ribonuclease

Crystal structure of proteolyzed VapBC and DNA‐bound VapBC from Salmonella enterica Typhimurium LT2 and VapC as a putative Ca ²⁺ ‐dependent ribonuclease