MHC class II complexes sample intermediate states along the peptide exchange pathway

Computational approaches to detect allosteric pathways in transmembrane molecular machines

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F pocket flexibility influences the tapasin dependence of two differentially disease-associated MHC Class I proteins

(2015) Esam T. Abualrous et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Mechanism of the Association between Na+Binding and Conformations at the Intracellular Gate in Neurotransmitter:Sodium Symporters

(2015) Sebastian Stolzenberg et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Estimation and uncertainty of reversible Markov models

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

The Thermodynamic Mechanism of Peptide–MHC Class II Complex Formation Is a Determinant of Susceptibility to HLA-DM

(2015) Andrea Ferrante et al.   JOURNAL OF IMMUNOLOGY

Plasticity of empty major histocompatibility complex class I molecules determines peptide-selector function

(2015) Andy van Hateren et al.   MOLECULAR IMMUNOLOGY

Probing Gαi1 protein activation at single–amino acid resolution

(2015) Dawei Sun et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Probing Gαi1 protein activation at single–amino acid resolution

(2015) Dawei Sun et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Selector function of MHC I molecules is determined by protein plasticity

(2015) Alistair Bailey et al.   Scientific Reports

The role of protein dynamics in GPCR function: insights from the β2AR and rhodopsin

(2014) Aashish Manglik et al.   CURRENT OPINION IN CELL BIOLOGY

Susceptibility to HLA-DM Protein Is Determined by a Dynamic Conformation of Major Histocompatibility Complex Class II Molecule Bound with Peptide

(2014) Liusong Yin et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Complexes of Two Cohorts of CLIP Peptides and HLA-DQ2 of the Autoimmune DR3-DQ2 Haplotype Are Poor Substrates for HLA-DM

(2014) L.-E. Fallang et al.   JOURNAL OF IMMUNOLOGY

HLA-DMA Polymorphisms Differentially Affect MHC Class II Peptide Loading

(2014) Miguel Álvaro-Benito et al.   JOURNAL OF IMMUNOLOGY

Kinetic modulation of a disordered protein domain by phosphorylation

(2014) Nathaniel Stanley et al.   Nature Communications

Pathways of Antigen Processing

(2013) Janice S. Blum et al.   Annual Review of Immunology

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

HLA-DM and HLA-DO, key regulators of MHC-II processing and presentation

(2013) Elizabeth D Mellins et al.   CURRENT OPINION IN IMMUNOLOGY

Identification of slow molecular order parameters for Markov model construction

(2013) Guillermo Pérez-Hernández 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

Molecular signatures of G-protein-coupled receptors

(2013) A. J. Venkatakrishnan et al.   NATURE

Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

(2013) Kai J. Kohlhoff et al.   Nature Chemistry

Molecular Dynamics Simulations to Provide Insights into Epitopes Coupled to the Soluble and Membrane-Bound MHC-II Complexes

(2013) Martiniano Bello et al.   PLoS One

The MHC I loading complex: a multitasking machinery in adaptive immunity

(2013) Sabine Hulpke et al.   TRENDS IN BIOCHEMICAL SCIENCES

Mechanisms of peptide repertoire selection by HLA-DM

(2013) Wouter Pos et al.   TRENDS IN IMMUNOLOGY

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

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

Structural Characteristics of HLA-DQ that May Impact DM Editing and Susceptibility to Type-1 Diabetes

(2013) Zemin Zhou et al.   Frontiers in Immunology

Ion-Controlled Conformational Dynamics in the Outward-Open Transition from an Occluded State of LeuT

(2012) Chunfeng Zhao et al.   BIOPHYSICAL JOURNAL

Crystal Structure of the HLA-DM–HLA-DR1 Complex Defines Mechanisms for Rapid Peptide Selection

(2012) Wouter Pos et al.   CELL

On the perils of poor editing: regulation of peptide loading by HLA-DQ and H2-A molecules associated with celiac disease and type 1 diabetes

(2012) Robert Busch et al.   EXPERT REVIEWS IN MOLECULAR MEDICINE

For many but not for all: how the conformational flexibility of the peptide/MHCII complex shapes epitope selection

(2012) Andrea Ferrante   IMMUNOLOGIC RESEARCH

Conformational variation in structures of classical and non-classical MHCII proteins and functional implications

(2012) Corrie A. Painter et al.   IMMUNOLOGICAL REVIEWS

HLA-DM: arbiter conformationis

(2012) Andrea Ferrante   IMMUNOLOGY

EMMA: A Software Package for Markov Model Building and Analysis

(2012) Martin Senne et al.   Journal of Chemical Theory and Computation

Peptide Linkage to the α-Subunit of MHCII Creates a Stably Inverted Antigen Presentation Complex

(2012) Andreas Schlundt et al.   JOURNAL OF MOLECULAR BIOLOGY

HLA-DO acts as a substrate mimic to inhibit HLA-DM by a competitive mechanism

(2012) Abigail I Guce et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Drug hypersensitivity caused by alteration of the MHC-presented self-peptide repertoire

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

Markov models of molecular kinetics: Generation and validation

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

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKaPredictions

(2011) Mats H. M. Olsson et al.   Journal of Chemical Theory and Computation

An Insertion Mutant in DQA1*0501 Restores Susceptibility to HLA-DM: Implications for Disease Associations

(2011) T. Hou et al.   JOURNAL OF IMMUNOLOGY

Characterization of Structural Features Controlling the Receptiveness of Empty Class II MHC Molecules

(2011) Bernd Rupp et al.   PLoS One

Conformational lability in the class II MHC 310 helix and adjacent extended strand dictate HLA-DM susceptibility and peptide exchange

(2011) C. A. Painter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

XDS

(2010) Wolfgang Kabsch   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Features and development ofCoot

(2010) P. Emsley et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

PHENIX: a comprehensive Python-based system for macromolecular structure solution

(2010) Paul D. Adams et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

HLA-DP, HLA-DQ, and HLA-DR Have Different Requirements for Invariant Chain and HLA-DM

(2010) Marcel van Lith et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

HLA-DM captures partially empty HLA-DR molecules for catalyzed removal of peptide

(2010) Anne-Kathrin Anders et al.   NATURE IMMUNOLOGY

Bidirectional binding of invariant chain peptides to an MHC class II molecule

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

A Xenon-129 Biosensor for Monitoring MHC-Peptide Interactions

(2009) Andreas Schlundt et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

(2009) M. J. Harvey et al.   Journal of Chemical Theory and Computation

In Vivo Enhancement of Peptide Display by MHC Class II Molecules with Small Molecule Catalysts of Peptide Exchange

(2009) Melissa J. Call et al.   JOURNAL OF IMMUNOLOGY

Cutting Edge: HLA-DM Functions through a Mechanism That Does Not Require Specific Conserved Hydrogen Bonds in Class II MHC-Peptide Complexes

(2009) Z. Zhou et al.   JOURNAL OF IMMUNOLOGY

Flexibility of the MHC class II peptide binding cleft in the bound, partially filled, and empty states: A molecular dynamics simulation study

(2008) Rakina Yaneva et al.   BIOPOLYMERS

Coarse Master Equations for Peptide Folding Dynamics†

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

Anchor Side Chains of Short Peptide Fragments Trigger Ligand-Exchange of Class II MHC Molecules

(2008) Shashank Gupta et al.   PLoS One

Model for the Peptide-Free Conformation of Class II MHC Proteins

(2008) Corrie A. Painter et al.   PLoS One