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

Markov state models of biomolecular conformational dynamics

(2014) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Computational Screening and Selection of Cyclic Peptide Hairpin Mimetics by Molecular Simulation and Kinetic Network Models

(2014) Asghar M. Razavi et al.   Journal of Chemical Information and Modeling

Automatic State Partitioning for Multibody Systems (APM): An Efficient Algorithm for Constructing Markov State Models To Elucidate Conformational Dynamics of Multibody Systems

(2014) Fu Kit Sheong et al.   Journal of Chemical Theory and Computation

On-the-Fly Learning and Sampling of Ligand Binding by High-Throughput Molecular Simulations

(2014) S. Doerr et al.   Journal of Chemical Theory and Computation

Both protein dynamics and ligand concentration can shift the binding mechanism between conformational selection and induced fit

(2014) N. Greives et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular Mechanisms of RNA Interference

(2013) Ross C. Wilson et al.   Annual Review of Biophysics

A transient reversal of miRNA-mediated repression controls macrophage activation

(2013) Anup Mazumder et al.   EMBO REPORTS

Identification of slow molecular order parameters for Markov model construction

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

Argonaute proteins: functional insights and emerging roles

(2013) Gunter Meister   NATURE REVIEWS GENETICS

Large Domain Motions in Ago Protein Controlled by the Guide DNA-Strand Seed Region Determine the Ago-DNA-mRNA Complex Recognition Process

(2013) Zhen Xia et al.   PLoS One

Minimal mechanistic model of siRNA-dependent target RNA slicing by recombinant human Argonaute 2 protein

(2013) A. Deerberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Eukaryote-Specific Insertion Elements Control Human ARGONAUTE Slicer Activity

(2013) Kotaro Nakanishi et al.   Cell Reports

The Making of a Slicer: Activation of Human Argonaute-1

(2013) Christopher R. Faehnle et al.   Cell Reports

The Structure of Human Argonaute-2 in Complex with miR-20a

(2012) Elad Elkayam et al.   CELL

Identifying Metastable States of Folding Proteins

(2012) Abhinav Jain et al.   Journal of Chemical Theory and Computation

Structure of yeast Argonaute with guide RNA

(2012) Kotaro Nakanishi et al.   NATURE

The true core of RNA silencing revealed

(2012) Hiroshi M Sasaki et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

microRNAs associated with the different human Argonaute proteins

(2012) A. Dueck et al.   NUCLEIC ACIDS RESEARCH

Distinct AGO1 and AGO2 associated miRNA profiles in human cells and blood plasma

(2012) Andrey Turchinovich et al.   RNA Biology

MicroRNA therapeutics

(2011) J A Broderick et al.   GENE THERAPY

Markov models of molecular kinetics: Generation and validation

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology

(2011) Sarel J. Fleishman et al.   JOURNAL OF MOLECULAR BIOLOGY

RNA and protein 3D structure modeling: similarities and differences

(2011) Kristian Rother et al.   JOURNAL OF MOLECULAR MODELING

Simulating the T-Jump-Triggered Unfolding Dynamics of trpzip2 Peptide and Its Time-Resolved IR and Two-Dimensional IR Signals Using the Markov State Model Approach

(2011) Wei Zhuang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Dynamics of Pyrophosphate Ion Release and Its Coupled Trigger Loop Motion from Closed to Open State in RNA Polymerase II

(2011) Lin-Tai Da et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Multi-domain conformational selection underlies pre-mRNA splicing regulation by U2AF

(2011) Cameron D. Mackereth et al.   NATURE

Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations

(2011) I. Buch 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

From Induced Fit to Conformational Selection: A Continuum of Binding Mechanism Controlled by the Timescale of Conformational Transitions

(2010) Huan-Xiang Zhou   BIOPHYSICAL JOURNAL

Thelet-7microRNA reduces tumor growth in mouse models of lung cancer

(2010) Aurora Esquela-Kerscher et al.   CELL CYCLE

Structural insights into RNA interference

(2010) Dipali G. Sashital et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Taming the complexity of protein folding

(2010) Gregory R Bowman et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Molecular Simulation ofab InitioProtein Folding for a Millisecond Folder NTL9(1−39)

(2010) Vincent A. Voelz et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Phosphorylation of human Argonaute proteins affects small RNA binding

(2010) Sabine Rüdel et al.   NUCLEIC ACIDS RESEARCH

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events

(2010) Peter Csermely et al.   TRENDS IN BIOCHEMICAL SCIENCES

Making RISC

(2010) Tomoko Kawamata et al.   TRENDS IN BIOCHEMICAL SCIENCES

Ancestral Roles of Small RNAs: An Ago-Centric Perspective

(2010) L. Joshua-Tor et al.   Cold Spring Harbor Perspectives in Biology

Mechanism of MicroRNA-Target Interaction: Molecular Dynamics Simulations and Thermodynamics Analysis

(2010) Yonghua Wang et al.   PLoS Computational Biology

Modeling Conformational Ensembles of Slow Functional Motions in Pin1-WW

(2010) Faruck Morcos et al.   PLoS Computational Biology

The RNA-induced Silencing Complex: A Versatile Gene-silencing Machine

(2009) Ashley J. Pratt et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Using generalized ensemble simulations and Markov state models to identify conformational states

(2009) Gregory R. Bowman et al.   METHODS

Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes

(2009) Yanli Wang et al.   NATURE

The role of dynamic conformational ensembles in biomolecular recognition

(2009) David D Boehr et al.   Nature Chemical Biology

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

Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin

(2009) T. Wlodarski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid equilibrium sampling initiated from nonequilibrium data

(2009) X. Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations

(2009) Frank Noé et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transition networks for modeling the kinetics of conformational change in macromolecules

(2008) Frank Noé et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Building Markov state models along pathways to determine free energies and rates of transitions

(2008) Albert C. Pan et al.   JOURNAL OF CHEMICAL PHYSICS

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Coarse Master Equations for Peptide Folding Dynamics†

(2008) Nicolae-Viorel Buchete et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex

(2008) Yanli Wang et al.   NATURE

Structure of the guide-strand-containing argonaute silencing complex

(2008) Yanli Wang et al.   NATURE

The evolution of RNAi as a defence against viruses and transposable elements

(2008) D. J Obbard et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Characterization of endogenous human Argonautes and their miRNA partners in RNA silencing

(2008) A. Azuma-Mukai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA