Exosite Binding in Thrombin: A Global Structural/Dynamic Overview of Complexes with Aptamers and Other Ligands

Light Chain Mutation Effects on the Dynamics of Thrombin

(2021) Dizhou Wu et al.   Journal of Chemical Information and Modeling

EXPANDING THE RECOGNITION INTERFACE OF THE THROMBIN BINDING APTAMER HD1 THROUGH MODIFICATION OF RESIDUES T3 AND T12

(2021) Igor Smirnov et al.   Molecular Therapy-Nucleic Acids

Thrombin Activatable Fibrinolysis Inhibitor (TAFI): An Updated Narrative Review

(2021) Machteld Sillen et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Structural and functional analysis of the simultaneous binding of two duplex/quadruplex aptamers to human α-thrombin

(2021) Romualdo Troisi et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

Sodium-induced population shift drives activation of thrombin

(2020) Ursula Kahler et al.   Scientific Reports

Molecular dynamics simulations of human α-thrombin in different structural contexts: evidence for an aptamer-guided cooperation between the two exosites

(2020) Romualdo Troisi et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Genetic Variants in the FGB and FGG Genes Mapping in the Beta and Gamma Nodules of the Fibrinogen Molecule in Congenital Quantitative Fibrinogen Disorders Associated with a Thrombotic Phenotype

(2020) Tomas Simurda et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Transient association between proteins elicits alteration of dynamics at sites far away from interfaces

(2020) Himani Tandon et al.   STRUCTURE

A Novel Nonsense Mutation in FGB (c.1421G>A; p.Trp474Ter) in the Beta Chain of Fibrinogen Causing Hypofibrinogenemia with Bleeding Phenotype

(2020) Tomas Simurda et al.   Biomedicines

Direct measurement of through-bond effects in molecular multivalent interactions

(2019) Xueyan Feng et al.   CHEMISTRY-A EUROPEAN JOURNAL

Thrombin Exosite Maturation and Ligand Binding at ABE II Help Stabilize PAR-Binding Competent Conformation at ABE I

(2019) Ramya Billur et al.   BIOCHEMISTRY

Impact of the Position of the Chemically Modified 5-Furyl-2′-Deoxyuridine Nucleoside on the Thrombin DNA Aptamer–Protein Complex: Structural Insights into Aptamer Response from MD Simulations

(2019) Preethi Seelam Prabhakar et al.   MOLECULES

Aptamer-peptide conjugates as a new strategy to modulate human α-thrombin binding affinity

(2019) Anna Aviñó et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Probing light chain mutation effects on thrombin via molecular dynamics simulations and machine learning

(2018) Jiajie Xiao et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Crystal structures of thrombin in complex with chemically modified thrombin DNA aptamers reveal the origins of enhanced affinity

(2018) Rafal Dolot et al.   NUCLEIC ACIDS RESEARCH

Several structural motifs cooperate in determining the highly effective anti-thrombin activity of NU172 aptamer

(2018) Romualdo Troisi et al.   NUCLEIC ACIDS RESEARCH

Avathrin: a novel thrombin inhibitor derived from a multicopy precursor in the salivary glands of the ixodid tick, Amblyomma variegatum

(2017) Janaki Krishnamoorthy Iyer et al.   FASEB JOURNAL

Functional analyses yield detailed insight into the mechanism of thrombin inhibition by the antihemostatic salivary protein cE5 fromAnopheles gambiae

(2017) Luciano Pirone et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Tyrosine sulfation modulates activity of tick-derived thrombin inhibitors

(2017) Robert E. Thompson et al.   Nature Chemistry

Mechanistic insights into thrombin's switch between “slow” and “fast” forms

(2017) Jiajie Xiao et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

How the Linker Connecting the Two Kringles Influences Activation and Conformational Plasticity of Prothrombin

(2016) Nicola Pozzi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Molecular dynamics simulations of aptamer-binding reveal generalized allostery in thrombin

(2016) Jiajie Xiao et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Na+ Binding Is Ineffective in Forming a Primary Substrate Pocket of Thrombin

(2016) Ikuo Kurisaki et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Evoking picomolar binding in RNA by a single phosphorodithioate linkage

(2016) N. Dinuka Abeydeera et al.   NUCLEIC ACIDS RESEARCH

Through-bond effects in the ternary complexes of thrombin sandwiched by two DNA aptamers

(2016) Andrea Pica et al.   NUCLEIC ACIDS RESEARCH

Fibrinolysis and the control of blood coagulation

(2015) John C. Chapin et al.   BLOOD REVIEWS

Toward Understanding Allosteric Activation of Thrombin: A Conjecture for Important Roles of Unbound Na+ Molecules around Thrombin

(2015) Ikuo Kurisaki et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Discovery and characterization of an antibody directed against exosite I of thrombin

(2015) T. P. Baglin et al.   JOURNAL OF THROMBOSIS AND HAEMOSTASIS

Different duplex/quadruplex junctions determine the properties of anti-thrombin aptamers with mixed folding

(2015) Irene Russo Krauss et al.   NUCLEIC ACIDS RESEARCH

Dynamics Govern Specificity of a Protein-Protein Interface: Substrate Recognition by Thrombin

(2015) Julian E. Fuchs et al.   PLoS One

Study of the Differential Activity of Thrombin Inhibitors Using Docking, QSAR, Molecular Dynamics, and MM-GBSA

(2015) Karel Mena-Ulecia et al.   PLoS One

The linker connecting the two kringles plays a key role in prothrombin activation

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

Duplex–quadruplex motifs in a peculiar structural organization cooperatively contribute to thrombin binding of a DNA aptamer

(2013) Irene Russo Krauss et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Neutron and X-ray crystallographic analysis of the human α-thrombin–bivalirudin complex at pD 5.0: Protonation states and hydration structure of the enzyme–product complex

(2013) Taro Yamada et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Mechanisms of fibrin polymerization and clinical implications

(2013) J. W. Weisel et al.   BLOOD

Dissecting the contribution of thrombin exosite I in the recognition of thrombin binding aptamer

(2013) Andrea Pica et al.   FEBS Journal

Ligand Binding to Anion-binding Exosites Regulates Conformational Properties of Thrombin

(2013) Marina V. Malovichko et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Crystal Structure of Prothrombin Reveals Conformational Flexibility and Mechanism of Activation

(2013) Nicola Pozzi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Correlated Motions and Residual Frustration in Thrombin

(2013) Brian Fuglestad et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Thrombin inhibition by the serpins

(2013) J. A. Huntington   JOURNAL OF THROMBOSIS AND HAEMOSTASIS

The transition of prothrombin to thrombin

(2013) S. Krishnaswamy   JOURNAL OF THROMBOSIS AND HAEMOSTASIS

An ensemble view of thrombin allostery

(2012) Bernhard C. Lechtenberg et al.   BIOLOGICAL CHEMISTRY

High-resolution structures of two complexes between thrombin and thrombin-binding aptamer shed light on the role of cations in the aptamer inhibitory activity

(2012) Irene Russo Krauss et al.   NUCLEIC ACIDS RESEARCH

Unique thrombin inhibition mechanism by anophelin, an anticoagulant from the malaria vector

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

Measurement of Aptamer–Protein Interactions with Back-Scattering Interferometry

(2011) Ian R. Olmsted et al.   ANALYTICAL CHEMISTRY

Thrombin plasticity

(2011) James A. Huntington   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Structural basis of thrombin-mediated factor V activation: the Glu666-Glu672 sequence is critical for processing at the heavy chain-B domain junction

(2011) M. A. Corral-Rodriguez et al.   BLOOD

Thrombin–aptamer recognition: a revealed ambiguity

(2011) Irene Russo Krauss et al.   NUCLEIC ACIDS RESEARCH

Structure and Behavior of Human α-Thrombin upon Ligand Recognition: Thermodynamic and Molecular Dynamics Studies

(2011) Vivian de Almeira Silva et al.   PLoS One

Crystal Structure of Thrombin in Complex with S-Variegin: Insights of a Novel Mechanism of Inhibition and Design of Tunable Thrombin Inhibitors

(2011) Cho Yeow Koh et al.   PLoS One

Regulation of the Protein C Anticoagulant and Antiinflammatory Pathways

(2010) A.R. Rezaie   CURRENT MEDICINAL CHEMISTRY

Thrombin Inhibition by Serpins Disrupts Exosite II

(2010) Wei Li et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Crystal Structure of Thrombin Bound to the Uncleaved Extracellular Fragment of PAR1

(2010) Prafull S. Gandhi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Thrombin Inhibitors from Different Animals

(2010) A. M. Tanaka-Azevedo et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Crystal structure of prethrombin-1

(2010) Z. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hirunorms are true hirudin mimetics. The crystal structure of human α-thrombin-hirunorm V complex

(2010) Giuseppina De Simone et al.   PROTEIN SCIENCE

Synthesis, structure, and structure-activity relationships of divalent thrombin inhibitors containing an α-keto-amide transition-state mimetic

(2010) Raman Krishnan et al.   PROTEIN SCIENCE

The crystal structure of α-thrombin-hirunorm IV complex reveals a novel specificity site recognition mode

(2010) Angela Lombardi et al.   PROTEIN SCIENCE

The refined 1.9-Å X-ray crystal structure of d-Phe-Pro-Arg chloromethylketone-inhibited human α-thrombin: Structure analysis, overall structure, electrostatic properties, detailed active-site geometry, and structure-function relationships

(2010) Wolfram Bode et al.   PROTEIN SCIENCE

Biophysical Investigation of GpIbα Binding to Thrombin Anion Binding Exosite II

(2009) T. Michael Sabo et al.   BIOCHEMISTRY

Structural and thermodynamic analysis of thrombin:suramin interaction in solution and crystal phases

(2009) Luis Maurício T.R. Lima et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Long Range Communication between Exosites 1 and 2 Modulates Thrombin Function

(2009) Nicolas S. Petrera et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Thrombin allosteric modulation revisited: a molecular dynamics study

(2009) Hermes Luís Neubauer de Amorim et al.   JOURNAL OF MOLECULAR MODELING

Synergistic effect of aptamers that inhibit exosites 1 and 2 on thrombin

(2009) S. M. Nimjee et al.   RNA

Anticoagulant characteristics of HD1-22, a bivalent aptamer that specifically inhibits thrombin and prothrombinase

(2008) J. MÜLLER et al.   JOURNAL OF THROMBOSIS AND HAEMOSTASIS

Thrombin

(2008) Enrico Di Cera   MOLECULAR ASPECTS OF MEDICINE

Isolation, Cloning and Structural Characterisation of Boophilin, a Multifunctional Kunitz-Type Proteinase Inhibitor from the Cattle Tick

(2008) Sandra Macedo-Ribeiro et al.   PLoS One

Crystal structure of an RNA aptamer bound to thrombin

(2008) S. B. Long et al.   RNA

Anticoagulants from hematophagous animals

(2008) Cho Yeow Koh et al.   Expert Review of Hematology