Protonation changes upon ligand binding to trypsin and thrombin: Structural interpretation based on pKa calculations and ITC experiments

Autoren

Paul Czodrowski
Christoph A Sotriffer
Gerhard Klebe

DOI

10.1016/j.jmb.2007.01.022

ISSN

0022-2836

Ausgabe der Veröffentlichung

5

Zeitschrift

Journal of Molecular Biology

Sprache

en

Paginierung

1347 - 1356

Datum der Veröffentlichung

2007

Status

Published

Herausgeber

Elsevier BV

Herausgeber URL

http://dx.doi.org/10.1016/j.jmb.2007.01.022

Datum der Datenerfassung

2019

Titel

Protonation Changes upon Ligand Binding to Trypsin and Thrombin: Structural Interpretation Based on pKa Calculations and ITC Experiments

Ausgabe der Zeitschrift

367

Datenquelle: Crossref

Abstract

The protonation states of a protein and a ligand can be altered upon complex formation. Such changes can be detected experimentally by isothermal titration calorimetry (ITC). For a series of ligands binding to the serine proteases trypsin and thrombin, we previously performed an extensive ITC and crystallographic study and were able to identify protonation changes for four complexes. However, since ITC measures only the overall proton exchange, it does not provide structural insights into the functional groups involved in the proton transfer. Using Poisson-Boltzmann calculations based on our recently developed PEOE_PB charges, we compute pK(a) values for all complexes of our former study in order to reveal the residues with altered protonation states. The results indicate that His57, a member of the catalytic triad, is responsible for the most relevant pK(a) shifts leading to the experimentally detected protonation changes. This finding is in contrast to our previous assumption that the observed protonation changes occur at the carboxylic group of the ligands. The newly detected proton acceptor is used for a revised factorization of the ITC data, which is necessary whenever the protonation inventory changes upon complexation. The pK(a) values of complexes showing no protonation change in the ITC experiment are reliably predicted in most cases, whereas predictions of strongly coupled systems remain problematic.

Addresses

Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany.

Autoren

Paul Czodrowski
Christoph A Sotriffer
Gerhard Klebe

DOI

10.1016/j.jmb.2007.01.022

eISSN

1089-8638

Externe Identifier

PubMed Identifier: 17316681

Open access

false

ISSN

0022-2836

Ausgabe der Veröffentlichung

5

Zeitschrift

Journal of molecular biology

Schlüsselwörter

Protons
Multiprotein Complexes
Thrombin
Trypsin
Ligands
Calorimetry
Titrimetry
Protein Binding
Models, Biological
Models, Molecular

Sprache

eng

Medium

Print-Electronic

Online publication date

2007

Paginierung

1347 - 1356

Datum der Veröffentlichung

2007

Status

Published

Datum der Datenerfassung

2007

Titel

Protonation changes upon ligand binding to trypsin and thrombin: structural interpretation based on pK(a) calculations and ITC experiments.

Sub types

Research Support, Non-U.S. Gov't
Journal Article

Ausgabe der Zeitschrift

367

Datenquelle: Europe PubMed Central

Abstract

The protonation states of a protein and a ligand can be altered upon complex formation. Such changes can be detected experimentally by isothermal titration calorimetry (ITC). For a series of ligands binding to the serine proteases trypsin and thrombin, we previously performed an extensive ITC and crystallographic study and were able to identify protonation changes for four complexes. However, since ITC measures only the overall proton exchange, it does not provide structural insights into the functional groups involved in the proton transfer. Using Poisson-Boltzmann calculations based on our recently developed PEOE_PB charges, we compute pK(a) values for all complexes of our former study in order to reveal the residues with altered protonation states. The results indicate that His57, a member of the catalytic triad, is responsible for the most relevant pK(a) shifts leading to the experimentally detected protonation changes. This finding is in contrast to our previous assumption that the observed protonation changes occur at the carboxylic group of the ligands. The newly detected proton acceptor is used for a revised factorization of the ITC data, which is necessary whenever the protonation inventory changes upon complexation. The pK(a) values of complexes showing no protonation change in the ITC experiment are reliably predicted in most cases, whereas predictions of strongly coupled systems remain problematic.

Date of acceptance

2007

Autoren

Paul Czodrowski
Christoph A Sotriffer
Gerhard Klebe

Autoren-URL

https://www.ncbi.nlm.nih.gov/pubmed/17316681

DOI

10.1016/j.jmb.2007.01.022

ISSN

0022-2836

Ausgabe der Veröffentlichung

5

Zeitschrift

J Mol Biol

Schlüsselwörter

Calorimetry
Ligands
Models, Biological
Models, Molecular
Multiprotein Complexes
Protein Binding
Protons
Thrombin
Titrimetry
Trypsin

Sprache

eng

Country

Netherlands

Paginierung

1347 - 1356

PII

S0022-2836(07)00049-6

Datum der Veröffentlichung

2007

Status

Published

Datum, an dem der Datensatz öffentlich gemacht wurde

2007

Titel

Protonation changes upon ligand binding to trypsin and thrombin: structural interpretation based on pK(a) calculations and ITC experiments.

Sub types

Journal Article
Research Support, Non-U.S. Gov't

Ausgabe der Zeitschrift

367

Datenquelle: PubMed

Protonation changes upon ligand binding to trypsin and thrombin: Structural interpretation based on pKa calculations and ITC experiments

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