Mapping the Pathway and Dynamics of Bestatin Inhibition of the Plasmodium falciparum M1 Aminopeptidase Pf A-M1

M1 aminopeptidases as drug targets: broad applications or therapeutic niche?

(2017) Nyssa Drinkwater et al.   FEBS Journal

Generation of AMBER force field parameters for zinc centres of M1 and M17 family aminopeptidases

(2017) Wei Yang et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Two cap residues in the S1 subsite of a Plasmodium falciparum M1-family aminopeptidase promote broad specificity and enhance catalysis

(2017) Matthew Rosati et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

Potent dual inhibitors of Plasmodium falciparum M1 and M17 aminopeptidases through optimization of S1 pocket interactions

(2016) Nyssa Drinkwater et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Commute Maps: Separating Slowly Mixing Molecular Configurations for Kinetic Modeling

(2016) Frank Noé et al.   Journal of Chemical Theory and Computation

Exploring ligand dissociation pathways from aminopeptidase N using random acceleration molecular dynamics simulation

(2016) Ya Liu et al.   JOURNAL OF MOLECULAR MODELING

Estimation and uncertainty of reversible Markov models

(2015) Benjamin Trendelkamp-Schroer et al.   JOURNAL OF CHEMICAL PHYSICS

Kinetic Distance and Kinetic Maps from Molecular Dynamics Simulation

(2015) Frank Noé et al.   Journal of Chemical Theory and Computation

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

PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models

(2015) Martin K. Scherer et al.   Journal of Chemical Theory and Computation

Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models

(2015) Nuria Plattner et al.   Nature Communications

Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement

(2015) Hanlun Jiang et al.   PLoS Computational Biology

Two-Pronged Attack: Dual Inhibition of Plasmodium falciparum M1 and M17 Metalloaminopeptidases by a Novel Series of Hydroxamic Acid-Based Inhibitors

(2014) Shailesh N. Mistry et al.   JOURNAL OF MEDICINAL CHEMISTRY

Reaction Mechanism of Zinc-Dependent Cytosine Deaminase from Escherichia coli: A Quantum-Chemical Study

(2014) Bianca Manta et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Force Field Independent Metal Parameters Using a Nonbonded Dummy Model

(2014) Fernanda Duarte et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Product formation controlled by substrate dynamics in leukotriene A4 hydrolase

(2013) Alena Stsiapanava et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

A Naturally Variable Residue in the S1 Subsite of M1 Family Aminopeptidases Modulates Catalytic Properties and Promotes Functional Specialization

(2013) Seema Dalal et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structural Insights into Central Hypertension Regulation by Human Aminopeptidase A

(2013) Yang Yang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Identification of slow molecular order parameters for Markov model construction

(2013) Guillermo Pérez-Hernández et al.   JOURNAL OF CHEMICAL PHYSICS

Projected and hidden Markov models for calculating kinetics and metastable states of complex molecules

(2013) Frank Noé et al.   JOURNAL OF CHEMICAL PHYSICS

Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9

(2013) Christian R. Schwantes et al.   Journal of Chemical Theory and Computation

Synthesis and Structure–Activity Relationships of Phosphonic Arginine Mimetics as Inhibitors of the M1 and M17 Aminopeptidases from Plasmodium falciparum

(2013) Komagal Kannan Sivaraman et al.   JOURNAL OF MEDICINAL CHEMISTRY

Fuzzy spectral clustering by PCCA+: application to Markov state models and data classification

(2013) Susanna Röblitz et al.   Advances in Data Analysis and Classification

The X-ray Crystal Structure of Human Aminopeptidase N Reveals a Novel Dimer and the Basis for Peptide Processing

(2012) Alan H. M. Wong et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structural basis for multifunctional roles of mammalian aminopeptidase N

(2012) L. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures

(2012) Eva Chovancova et al.   PLoS Computational Biology

Slow dynamics in protein fluctuations revealed by time-structure based independent component analysis: The case of domain motions

(2011) Yusuke Naritomi et al.   JOURNAL OF CHEMICAL PHYSICS

Comparison of Methods to Obtain Force-Field Parameters for Metal Sites

(2011) LiHong Hu et al.   Journal of Chemical Theory and Computation

Synthesis of New (−)-Bestatin-Based Inhibitor Libraries Reveals a Novel Binding Mode in the S1 Pocket of the Essential Malaria M1 Metalloaminopeptidase

(2011) Geetha Velmourougane et al.   JOURNAL OF MEDICINAL CHEMISTRY

Structural basis for antigenic peptide precursor processing by the endoplasmic reticulum aminopeptidase ERAP1

(2011) Tina T Nguyen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Plasmodium falciparum Malaria M1 Alanyl Aminopeptidase (PfA-M1): Insights of Catalytic Mechanism and Function from MD Simulations

(2011) Peter M. Jones et al.   PLoS One

Bestatin-based chemical biology strategy reveals distinct roles for malaria M1- and M17-family aminopeptidases

(2011) M. B. Harbut et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Crystal structures of the endoplasmic reticulum aminopeptidase-1 (ERAP1) reveal the molecular basis for N-terminal peptide trimming

(2011) G. Kochan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Role for Both Conformational Selection and Induced Fit in Ligand Binding by the LAO Protein

(2011) Daniel-Adriano Silva et al.   PLoS Computational Biology

Aminopeptidase N (CD13) as a target for cancer chemotherapy

(2010) Malin Wickström et al.   CANCER SCIENCE

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

Systematic Derivation of AMBER Force Field Parameters Applicable to Zinc-Containing Systems

(2010) Fu Lin et al.   Journal of Chemical Theory and Computation

A Leukotriene A4 Hydrolase-Related Aminopeptidase from Yeast Undergoes Induced Fit upon Inhibitor Binding

(2010) Charlotte Helgstrand et al.   JOURNAL OF MOLECULAR BIOLOGY

Structure of the Plasmodium falciparum M17 aminopeptidase and significance for the design of drugs targeting the neutral exopeptidases

(2010) S. McGowan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural basis for the inhibition of the essentialPlasmodium falciparumM1 neutral aminopeptidase

(2009) Sheena McGowan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The implementation of a fast and accurate QM/MM potential method in Amber

(2007) Ross C. Walker et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY