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Advances in protein chemistry and structural biology. Volume ninety one, Protein-nucleic acids interactions
- Summary
-
Published continuously since 1944, the Advances in Protein Chemistry and Structural Biology serial has been a continuous, essential resource for protein chemists. Covering reviews of methodology an...
Published continuously since 1944, the Advances in Protein Chemistry and Structural Biology serial has been a continuous, essential resource for protein chemists. Covering reviews of methodology and research in all aspects of protein chemistry, including purification/expression, proteomics, modeling and structural determination and design, each volume brings forth new information about protocols and analysis of proteins while presenting the most recent findings from leading experts in a broad range of protein-related topics. Covers reviews of methodology and research in all as
Details
- Creator
- edited by Rossen Donev, Institute of Life Sciences, College of Medicine, Swansea University, United Kingdom
- Format
- Books
- Language
- English
- Contributors
- Publication
-
- 1st ed
- Oxford : Academic Press, 2013
- Oxford : Academic Press, 2013
- Series
- Physical Details
-
- 1 online resource (viii, 202 pages) : illustrations (some color)
- ISBNs
- 9780124116283, 0124116280, 012411637X, 1299684718
- OCLC
- ocn881385234
- "ISSN: 1876-1623."
- Includes bibliographical references and indexes.
- English
- Front Cover; Protein-Nucleic Acids Interactions; Copyright; Contents; Preface; Chapter One: Proliferating Cell Nuclear Antigen Structure and Interactions: Too Many Partners for One Dancer?; 1. DNA Sliding Clamps; 2. PCNA Structure, Stability, and Dynamics; 3. Interactions of PCNA with Other Proteins; 4. Crystal Structure of FEN1 Bound to PCNA and Observation of the Interaction in Solution by NMR; 5. Interactions of PCNA with PIP-Box Peptides; 6. Binding of MCL-1, Gadd45α, and CDK2 Proteins to PCNA Is Not Direct or Extremely Weak in Solution; 6.1. MCL-1/PCNA interaction
- 6.2. Gadd45α/PCNA interaction6.3. CDK2/PCNA interaction; 7. Revisiting the PIP-Box Pattern Definition; 8. More Caution Should Be Exerted When Characterizing Direct Protein Interactions with PCNA; 9. The Problem of Binding Competition Among PCNA Partners; 10. PCNA and Disease and Its Potential as a Pharmacological Target; Acknowledgments; References; Chapter Two: Anomalous Protein-DNA Interactions Behind Neurological Disorders; 1. Introduction; 2. Proteins Involved in DNA Packaging; 3. Proteins Interacting with Nucleic Acids in Transcription; 4. Protein-DNA Interactions in Cell Division
- 5. Polyglutamine Diseases6. Aggregation; 7. Nuclear Location; 8. DNA Interaction; Acknowledgment; References; Chapter Three: Computational Approaches for Predicting the Binding Sites and Understanding the Recognition Mechanism of P ...; 1. Introduction; 2. Databases for Protein-DNA Complexes/Interactions; 2.1. Protein-nucleic acid complex database; 2.2. Databases for the interactions between amino acid residues and nucleotides; 2.3. Transcription factor-DNA interaction data depository; 2.4. Thermodynamic database for protein-nucleic acid interactions
- 3. Structural Analysis of Protein-DNA Complexes3.1. Hydrogen bonds; 3.2. Energetic contributions; 3.3. Conformational changes of DNA and water-mediated contacts; 3.4. Classification of protein-DNA complexes; 4. Discrimination of DNA-Binding Proteins; 5. Prediction of DNA-Binding Sites and Protein-DNA Binding Specificity; 5.1. Binding site residues in protein-DNA complexes; 5.2. Predicting the binding sites in proteins; 5.3. Prediction of protein-DNA binding specificity; 6. Recognition Mechanism of Protein-DNA Complexes; 6.1. Base-amino acid interactions
- 6.2. DNA stiffness and protein-DNA binding specificity6.3. Inter- and intramolecular interactions in protein-DNA recognition; 6.3.1. Calculation of intermolecular interaction energies; 6.3.2. Calculation of intramolecular interaction energies; 6.3.3. Role of inter- and intramolecular interactions in protein-DNA recognition; 6.3.4. Combination of inter- and intramolecular interactions; 6.4. Energy-based approach; 6.4.1. Occurrence of residues at various ranges of interaction energies; 6.4.2. Binding propensity of amino acid residues
- 6.4.3. Contribution of different types of atoms in protein-DNA interactions