ArticleActa crystallographica. Section D, Biological crystallography2014
Local dynamics of proteins and DNA evaluated from crystallographic B factors.
Article in Acta crystallographica. Section D, Biological crystallography, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed.
- Differential Responses in the Core, Active Site and Peripheral Regions of Cytochrome c Peroxidase to Extreme Pressure and Temperature.Journal of molecular biology · 2024Article
- Discovery of Nonretinoid Inhibitors of CRBP1: Structural and Dynamic Insights for Ligand-Binding Mechanisms.ACS chemical biology · 2023Article
- Knowledge-based prediction of DNA hydration using hydrated dinucleotides as building blocks.Acta crystallographica. Section D, Structural biology · 2022Article
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- Decline of protein structure rigidity with interatomic distance.BMC bioinformatics · 2021Article
- Structural Insights into the Interaction of Clinically Relevant Phosphorothioate mRNA Cap Analogs with Translation Initiation Factor 4E Reveal Stabilization via Electrostatic Thio-Effect.ACS chemical biology · 2021Article
- BANΔIT: B'-Factor Analysis for Drug Design and Structural Biology.Molecular informatics · 2021Article
- Local and global analysis of macromolecular atomic displacement parameters.Acta crystallographica. Section D, Structural biology · 2020Article
- Essential site scanning analysis: A new approach for detecting sites that modulate the dispersion of protein global motions.Computational and structural biotechnology journal · 2020Article
- Ligand-Induced Conformational Dynamics of A Tyramine Receptor from Sitophilus oryzae.Scientific reports · 2019Article
- DNA-protein interaction: identification, prediction and data analysis.Molecular biology reports · 2019Review
- Structural changes in DNA-binding proteins on complexation.Nucleic acids research · 2018Article
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- DNA conformational transitions inferred from re-evaluation of m|FActa crystallographica. Section D, Structural biology · 2017Article
- Crystal structure of a DNA aptamer bound to PvLDH elucidates novel single-stranded DNA structural elements for folding and recognition.Scientific reports · 2016Article
- Ligand Binding Induces Conformational Changes in Human Cellular Retinol-binding Protein 1 (CRBP1) Revealed by Atomic Resolution Crystal Structures.The Journal of biological chemistry · 2016Article
- Crystal structure of group II intron domain 1 reveals a template for RNA assembly.Nature chemical biology · 2015Article
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4 authors.
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Abstract
The dynamics of protein and nucleic acid structures is as important as their average static picture. The local molecular dynamics concealed in diffraction images is expressed as so-called B factors. To find out how the crystal-derived B factors represent the dynamic behaviour of atoms and residues of proteins and DNA in their complexes, the distributions of scaled B factors from a carefully curated data set of over 700 protein-DNA crystal structures were analyzed [Schneider et al. (2014), Nucleic Acids Res. 42, 3381-3394]. Amino acids and nucleotides were categorized based on their molecular neighbourhood as solvent-accessible, solvent-inaccessible (i.e. forming the protein core) or lying at protein-protein or protein-DNA interfaces; the backbone and side-chain atoms were analyzed separately. The B factors of two types of crystal-ordered water molecules were also analyzed. The analysis confirmed several expected features of protein and DNA dynamics, but also revealed surprising facts. Solvent-accessible amino acids have B factors that are larger than those of residues at the biomolecular interfaces, and core-forming amino acids are the most restricted in their movement. A unique feature of the latter group is that their side-chain and backbone atoms are restricted in their movement to the same extent; in all other amino-acid groups the side chains are more floppy than the backbone. The low values of the B factors of water molecules bridging proteins with DNA and the very large fluctuations of DNA phosphates are surprising. The features discriminating different types of residues are less pronounced in structures with lower crystallographic resolution. Some of the observed trends are likely to be the consequence of improper refinement protocols that may need to be rectified.
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