A synergy between the catalytic and structural Zn(II) ions and the enzyme and substrate dynamics underlies the structure–function relationships of matrix metalloproteinase collagenolysis

Allosteric Communications between Domains Modulate the Activity of Matrix Metalloprotease-1

(2020) Lokender Kumar et al.   BIOPHYSICAL JOURNAL

Thermodynamic and Mechanistic Insights into Coupled Binding and Unwinding of Collagen by Matrix Metalloproteinase 1

(2020) Szymon W. Manka et al.   JOURNAL OF MOLECULAR BIOLOGY

Protein storytelling through physics

(2020) Emiliano Brini et al.   SCIENCE

Beyond the Second Coordination Sphere: Engineering Dirhodium Artificial Metalloenzymes To Enable Protein Control of Transition Metal Catalysis

(2019) Jared C. Lewis   ACCOUNTS OF CHEMICAL RESEARCH

Conformational Dynamics of Matrix Metalloproteinase-1·Triple-Helical Peptide Complexes

(2017) Tatyana G. Karabencheva-Christova et al.   JOURNAL OF PHYSICAL CHEMISTRY B

MCPB.py: A Python Based Metal Center Parameter Builder

(2016) Pengfei Li et al.   Journal of Chemical Information and Modeling

Metal Ion Dependence of the Matrix Metalloproteinase-1 Mechanism

(2015) Hao Yang et al.   BIOCHEMISTRY

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

Examination of Matrix Metalloproteinase-1 in Solution

(2013) Linda Cerofolini et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Interstitial Collagen Catabolism

(2013) Gregg B. Fields   JOURNAL OF BIOLOGICAL CHEMISTRY

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Structural insights into triple-helical collagen cleavage by matrix metalloproteinase 1

(2012) S. W. Manka et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Catalytic Contributions from Remote Regions of Enzyme Structure

(2011) Jeeyeon Lee et al.   CHEMICAL REVIEWS

The Interface between Catalytic and Hemopexin Domains in Matrix Metalloproteinase-1 Conceals a Collagen Binding Exosite

(2011) Laurence H. Arnold et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structural Basis for Matrix Metalloproteinase 1-Catalyzed Collagenolysis

(2011) Ivano Bertini et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Type I collagen from the skin of ornate threadfin bream (Nemipterus hexodon): Characteristics and effect of pepsin hydrolysis

(2010) Sitthipong Nalinanon et al.   FOOD CHEMISTRY

Structural Survey of Zinc-Containing Proteins and Development of the Zinc AMBER Force Field (ZAFF)

(2010) Martin B. Peters et al.   Journal of Chemical Theory and Computation

The metzincins - Topological and sequential relations between the astacins, adamalysins, serralysins, and matrixins (collagenases) define a super family of zinc-peptidases

(2010) Walter Stöcker et al.   PROTEIN SCIENCE

Matrix metalloproteinases: Fold and function of their catalytic domains

(2009) Cynthia Tallant et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Identification of Specific Hemopexin-like Domain Residues That Facilitate Matrix Metalloproteinase Collagenolytic Activity

(2009) Janelle L. Lauer-Fields et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Langevin thermostat for rigid body dynamics

(2009) Ruslan L. Davidchack et al.   JOURNAL OF CHEMICAL PHYSICS

Matrix metalloproteinases and their multiple roles in neurodegenerative diseases

(2009) Gary A Rosenberg   LANCET NEUROLOGY

Structural Bases for Substrate and Inhibitor Recognition by Matrix Metalloproteinases

(2008) Loretta Aureli et al.   CURRENT MEDICINAL CHEMISTRY

Very fast prediction and rationalization of pKa values for protein-ligand complexes

(2008) Delphine C. Bas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS