The emergence of protein complexes: quaternary structure, dynamics and allostery

X-ray crystallographic and computational studies of the O2-tolerant [NiFe]-hydrogenase 1 from Escherichia coli

(2012) A. Volbeda et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantitative, High-Resolution Proteomics for Data-Driven Systems Biology

(2011) Jürgen Cox et al.   Annual Review of Biochemistry

RING: networking interacting residues, evolutionary information and energetics in protein structures

(2011) A. J. M. Martin et al.   BIOINFORMATICS

CMView: Interactive contact map visualization and analysis

(2011) C. Vehlow et al.   BIOINFORMATICS

Three-dimensional modeling of protein interactions and complexes is going ‘omics

(2011) Amelie Stein et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Simulations of allosteric transitions

(2011) Ron Elber   CURRENT OPINION IN STRUCTURAL BIOLOGY

Intrinsically disordered proteins: regulation and disease

(2011) M Madan Babu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Identification of key residues for protein conformational transition using elastic network model

(2011)   JOURNAL OF CHEMICAL PHYSICS

Interaction of the p53 DNA-Binding Domain with Its N-Terminal Extension Modulates the Stability of the p53 Tetramer

(2011) Eviatar Natan et al.   JOURNAL OF MOLECULAR BIOLOGY

A De Novo Protein Binding Pair By Computational Design and Directed Evolution

(2011) John Karanicolas et al.   MOLECULAR CELL

Gain of function of mutant p53 by coaggregation with multiple tumor suppressors

(2011) Jie Xu et al.   Nature Chemical Biology

Protein 3D Structure Computed from Evolutionary Sequence Variation

(2011) Debora S. Marks et al.   PLoS One

Coordinate linkage of HIV evolution reveals regions of immunological vulnerability

(2011) V. Dahirel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transient protein-protein interactions

(2011) S. E. Acuner Ozbabacan et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin

(2011) S. J. Fleishman et al.   SCIENCE

Protein-Protein Complex Structure Predictions by Multimeric Threading and Template Recombination

(2011) Srayanta Mukherjee et al.   STRUCTURE

Dynamic Allostery: Linkers Are Not Merely Flexible

(2011) Buyong Ma et al.   STRUCTURE

Relative Solvent Accessible Surface Area Predicts Protein Conformational Changes upon Binding

(2011) Joseph A. Marsh et al.   STRUCTURE

Changes in Dynamics upon Oligomerization Regulate Substrate Binding and Allostery in Amino Acid Kinase Family Members

(2011) Enrique Marcos et al.   PLoS Computational Biology

Correlated Evolution of Nearby Residues in Drosophilid Proteins

(2011) Benjamin Callahan et al.   PLoS Genetics

Positions 94−98 of the Lactose Repressor N-Subdomain Monomer−Monomer Interface Are Critical for Allosteric Communication

(2010) Hongli Zhan et al.   BIOCHEMISTRY

A Phase Function to Quantify Serial Dependence between Discrete Samples

(2010) Ramana Dodla et al.   BIOPHYSICAL JOURNAL

A Simple Definition of Structural Regions in Proteins and Its Use in Analyzing Interface Evolution

(2010) Emmanuel D. Levy   JOURNAL OF MOLECULAR BIOLOGY

Crystal Structure of the First Plant Urease from Jack Bean: 83 Years of Journey from Its First Crystal to Molecular Structure

(2010) Anuradha Balasubramanian et al.   JOURNAL OF MOLECULAR BIOLOGY

Characteristics of Enzyme-Based Hydrogen Fuel Cells Using an Oxygen-Tolerant Hydrogenase as the Anodic Catalyst

(2010) Annemarie F. Wait et al.   Journal of Physical Chemistry C

Mutational robustness can facilitate adaptation

(2010) Jeremy A. Draghi et al.   NATURE

Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs

(2010) Malka Kitayner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Single-Molecule characterization of oligomerization kinetics and equilibria of the tumor suppressor p53

(2010) S. Rajagopalan et al.   NUCLEIC ACIDS RESEARCH

ASD: a comprehensive database of allosteric proteins and modulators

(2010) Z. Huang et al.   NUCLEIC ACIDS RESEARCH

Self-assembly, modularity, and physical complexity

(2010) S. E. Ahnert et al.   PHYSICAL REVIEW E

Atomic Interaction Networks in the Core of Protein Domains and Their Native Folds

(2010) Venkataramanan Soundararajan et al.   PLoS One

The structural and energetic basis for high selectivity in a high-affinity protein-protein interaction

(2010) N. A. G. Meenan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural Diversity in Free and Bound States of Intrinsically Disordered Protein Phosphatase 1 Regulators

(2010) Joseph A. Marsh et al.   STRUCTURE

Structure/Function Implications in a Dynamic Complex of the Intrinsically Disordered Sic1 with the Cdc4 Subunit of an SCF Ubiquitin Ligase

(2010) Tanja Mittag et al.   STRUCTURE

Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments

(2010) Lukas Burger et al.   PLoS Computational Biology

Protein Sectors: Evolutionary Units of Three-Dimensional Structure

(2009) Najeeb Halabi et al.   CELL

Allostery in the LacI/GalR family: variations on a theme

(2009) Liskin Swint-Kruse et al.   CURRENT OPINION IN MICROBIOLOGY

Linking folding and binding

(2009) Peter E Wright et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Comparing the Functional Roles of Nonconserved Sequence Positions in Homologous Transcription Repressors: Implications for Sequence/Function Analyses

(2009) Sudheer Tungtur et al.   JOURNAL OF MOLECULAR BIOLOGY

Linking the p53 tumour suppressor pathway to somatic cell reprogramming

(2009) Teruhisa Kawamura et al.   NATURE

A p53-mediated DNA damage response limits reprogramming to ensure iPS cell genomic integrity

(2009) Rosa M. Marión et al.   NATURE

The role of quaternary structure in (β/α)8-barrel proteins: evolutionary happenstance or a higher level of structure-function relationships?

(2009) Sean R A Devenish et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Ultraslow oligomerization equilibria of p53 and its implications

(2009) E. Natan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conformational selection or induced fit: A flux description of reaction mechanism

(2009) G. G. Hammes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Proteome Organization in a Genome-Reduced Bacterium

(2009) S. Kuhner et al.   SCIENCE

Structure-Based Predictive Models for Allosteric Hot Spots

(2009) Omar N. A. Demerdash et al.   PLoS Computational Biology

Dynamic Allostery in the Methionine Repressor Revealed by Force Distribution Analysis

(2009) Wolfram Stacklies et al.   PLoS Computational Biology

Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins

(2009) Michael D. Daily et al.   PLoS Computational Biology

Dimerization Affects Collective Dynamics of Triosephosphate Isomerase†

(2008) Sertan Cansu et al.   BIOCHEMISTRY

Rewiring the Specificity of Two-Component Signal Transduction Systems

(2008) Jeffrey M. Skerker et al.   CELL

Accurate prediction of protein–protein interactions from sequence alignments using a Bayesian method

(2008) Lukas Burger et al.   Molecular Systems Biology

Assembly reflects evolution of protein complexes

(2008) Emmanuel D. Levy et al.   NATURE

Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking

(2008) S. E. Dobbins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure of tumor suppressor p53 and its intrinsically disordered N-terminal transactivation domain

(2008) M. Wells et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of direct residue contacts in protein-protein interaction by message passing

(2008) M. Weigt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Emergence of symmetry in homooligomeric biological assemblies

(2008) I. Andre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms

(2008) K.-i. Okazaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The novel p53 isoform “delta p53” is a misfolded protein and does not bind the p21 promoter site

(2008) Maria M. García-Alai et al.   PROTEIN SCIENCE

Protein–protein interaction and quaternary structure

(2008) Joël Janin et al.   QUARTERLY REVIEWS OF BIOPHYSICS

High-Quality Binary Protein Interaction Map of the Yeast Interactome Network

(2008) H. Yu et al.   SCIENCE

Designed Protein-Protein Association

(2008) D. Grueninger et al.   SCIENCE

An in Vivo Map of the Yeast Protein Interactome

(2008) K. Tarassov et al.   SCIENCE

Fuzzy complexes: polymorphism and structural disorder in protein–protein interactions

(2007) Peter Tompa et al.   TRENDS IN BIOCHEMICAL SCIENCES

Allosteric transition pathways in the lactose repressor protein core domains: Asymmetric motions in a homodimer

(2003) Terence C. Flynn et al.   PROTEIN SCIENCE