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

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

G-Quadruplex-Forming Aptamers—Characteristics, Applications, and Perspectives

(2019) Carolina Roxo et al.   MOLECULES

The intrinsic flexibility of the aptamer targeting the ribosomal protein S8 is a key factor for the molecular recognition

(2018) Ida Autiero et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Duplex/quadruplex oligonucleotides: Role of the duplex domain in the stabilization of a new generation of highly effective anti-thrombin aptamers

(2018) Irene Russo Krauss et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

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

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

Accurate Prediction of Amide Exchange in the Fast Limit Reveals Thrombin Allostery

(2018) Phineus R.L. Markwick et al.   BIOPHYSICAL JOURNAL

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

(2018) Romualdo Troisi et al.   NUCLEIC ACIDS RESEARCH

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

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

NMR reveals a dynamic allosteric pathway in thrombin

(2017) Lindsey D. Handley et al.   Scientific Reports

Structural transitions during prothrombin activation: On the importance of fragment 2

(2016) Ty E. Adams et al.   BIOCHIMIE

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

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

Aptamers as targeted therapeutics: current potential and challenges

(2016) Jiehua Zhou et al.   NATURE REVIEWS DRUG DISCOVERY

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

(2016) Andrea Pica et al.   NUCLEIC ACIDS RESEARCH

Why Ser and Not Thr Brokers Catalysis in the Trypsin Fold

(2015) Leslie A. Pelc et al.   BIOCHEMISTRY

A family of DNA aptamers with varied duplex region length that forms complexes with thrombin and prothrombin

(2015) V.A. Spiridonova et al.   FEBS LETTERS

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

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

Targeting the GPIbα Binding Site of Thrombin To Simultaneously Induce Dual Anticoagulant and Antiplatelet Effects

(2014) Akul Y. Mehta et al.   JOURNAL OF MEDICINAL CHEMISTRY

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

Aptamers Act as Activators for the Thrombin Mediated-Hydrolysis of Peptide Substrates

(2013) Xiaohong Tan et al.   CHEMBIOCHEM

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

Directly investigating the interaction between aptamers and thrombin by atomic force microscopy

(2013) Fang Jiao et al.   JOURNAL OF MOLECULAR RECOGNITION

The Dynamic Structure of Thrombin in Solution

(2012) Brian Fuglestad et al.   BIOPHYSICAL JOURNAL

DNA Aptamers for Human Thrombin with High Anticoagulant Activity Demonstrate Target- and Species-Specificity

(2012) E. Zavyalova et al.   CURRENT MEDICINAL 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

Measurement of Aptamer–Protein Interactions with Back-Scattering Interferometry

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

Investigation of the Interaction between a Bivalent Aptamer and Thrombin by AFM

(2011) Lin Ge et al.   LANGMUIR

Thrombin–aptamer recognition: a revealed ambiguity

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

Crystallization and preliminary X-ray analysis of the complex of human α-thrombin with a modified thrombin-binding aptamer

(2010) Irene Russo Krauss et al.   Acta Crystallographica Section F-Structural Biology and Crystallization Communications

Aptamers as therapeutics

(2010) Anthony D. Keefe et al.   NATURE REVIEWS DRUG DISCOVERY

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

The effects of exosite occupancy on the substrate specificity of thrombin

(2009) Natasha May-Yoke Ng et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Biophysical Investigation of GpIbα Binding to Thrombin Anion Binding Exosite II

(2009) T. Michael Sabo et al.   BIOCHEMISTRY

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

Thrombin

(2008) Enrico Di Cera   MOLECULAR ASPECTS OF MEDICINE

Structural identification of the pathway of long-range communication in an allosteric enzyme

(2008) P. S. Gandhi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular assembly for high-performance bivalent nucleic acid inhibitor

(2008) Y. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA