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Influence of the solvating environment on protein dynamics and stability

Proteins, the building blocks of life, and in particular enzymes, which catalyze the essential chemical and biochemical processes of life, have been optimized to their specific tasks by evolution. One of the specific adaptations is to work optimally in a specific environment, for example in aqueous solutions with high concentrations of other biopolymers and metabolites or as an integral part of a lipid bilayer.
As a part of the cluster of excellence RESOLV (EXC 1069), which focuses specifically on the effects of solvents on chemical and biochemical processes, we employ in our group molecular dynamics and Monte Carlo simulations to study the influence of the environment on solvated proteins by manipulating the solvent properties in a controlled way. In the current focus of our research are correlations of collective motion in proteins and their solvent, as well as the influence of high protein concentrations on protein folding.

Matthias Heyden

Dr. Matthias Heyden

since 2013
RESOLV Early Career Research Group Leader, Max-Planck-Institute for Coal Research
Postdoctoral fellow, University of California, Irvine (Douglas J. Tobias)
Visiting scholar, Weizmann Institute (Irit Sagi)
Doctoral studies, Ruhr-University Bochum (Martina Havenith)
Visiting scholar, University of Nevada, Reno (David M. Leitner)
Biochemistry studies, Ruhr-University Bochum
born in Düsseldorf
Postdoctoral fellowship of the German Academy of Sciences Leopoldina
Peter A. Salamon Award of the Telluride Science Research Center
Victoria Buch Memorial poster prize of the Gordon Research Conference Water & Aqueous Solutions
Participant of the 59th meeting of the Nobel laureates in Lindau, Germany
Doctoral scholarship of the German National Academic Foundation
PCCP poster prize of the International Bunsen Discussion Meeting: “Exploring THz spectroscopy”
Fellowship of the Ruhr-University Research School
Short term foreign exchange scholarship by the German Academic Exchange Service (DAAD)
Chair of the Gordon Research Seminar Water & Aqueous Solutions
Speaker of the RESOLV Early Career Researcher Board

16.    Invited by Prof. Dr. Gerhard Stock
Physikalisches Institut , Albert-Ludwigs-Universität Freiburg
Analyzing the effects of the solvating environments on proteins in simulations
July 17, 2014, Freiburg, Deutschland

15.    Invited by Prof. Dr. Rebecca Wade
Heidelberg Institute for Theoretical Studies
Monte Carlo sampling of flexible proteins and polymers in many-molecule systems
July 15, 2014, Heidelberg, Deutschland

14.    Invited by Prof. Dr. Joachim Dzubiella
Institut Weiche Materie und Funktionale Materialien, Helmholtz-Zentrum Berlin
Analyzing the interactions between bimolecular solutes and their solvating environment
June 20, 2014, Berlin, Deutschland

13.    Invited by Prof. Dr. Christel Marian
Theoretische Chemie, Heinrich-Heine-Universität Düsseldorf
Coupled solute-solvent dynamics in biomolecular solutions
May 28, 2014, Düsseldorf, Deutschland

12.    Invited by Dr. Martin Weik, Prof. John Straub and Prof. Douglas J. Tobias
Telluride Science Research Center (TSRC) workshop: Protein dynamics
Correlations in protein and solvent dynamics studied with atomistic molecular dynamics simulations
May 19, 2014, Les Houches, Frankreich

11.    Invited by Dr. Martin Weik
Insitute de Biologie Structurale
Understanding the influence of the solvating environment on biomolecular properties
Mai 16, 2014, Grenoble, Frankreich

10.   Invited by Prof. Dr. Ana-Nicoleta Bondar
CECAM workshop: Coupling between protein, water, and lipid dynamics in complex biological systems
Dynamics of a fast activating G-protein coupled receptor in extended simulations
September 26, 2013, Lausanne, Schweiz

9.    Invited by Dr. Jens Kortmann
School of Medicine, Stanford University
Molecular dynamics simulations and the role of solvation in biological processes
May 6, 2013, Palo Alto, CA, USA

8.    Invited by RESOLV Cluster of Excellence
Max-Planck-Institute for Coal Research
Role of collective vibrations for solute-solvent interactions of proteins and enzymes
February 27, 2013, Mülheim / Ruhr, Germany

7.    Invited by Professor Dor Ben-Amotz
243rd ACS National Meeting, San Diego Convention Center
Correlated intermolecular motion in solvation water of biomolecules
March 28, 2012, San Diego, CA, USA

6.    Invited by Professor Mounir Tarek
Équipe de Chimie et Biochimie Théoriques, Université Henri Poincaré Nancy
Vibrations in water at THz frequencies and membrane protein dynamics at timescales from ps to µs
─ insights from various molecular dynamics approaches

June 30, 2011, Nancy, France

5.    Invited by Professor Dr. Ana-Nicoleta Bondar
Department of Theoretical Molecular Biophysics, Free University Berlin
Membrane protein dynamics in different lipid environments:
Native membranes vs. reconstitution in artificial lipid bilayers studied with molecular dynamics simulations

June 6, 2011, Berlin, Germany

4.    Invited by Professor Mark Sherwin
Institute for Terahertz Science And Technology, University of California, Santa Barbara,
Tuning in on the frequencies of the hydrogen bond network of water
April 28, 2011, Santa Barbara, CA, USA

3.    Invited by Professor Dr. Walter Thiel
Department of Theoretical Chemistry at the Max-Planck-Institute for Coal Research
Water seen through Terahertz glasses
July 14, 2010, Mülheim / Ruhr, Germany

2.    Invited by Professor Douglas J. Tobias
Department of Theoretical Chemistry at the University of California, Irvine
Water seen through Terahertz glasses
- Picosecond dynamics and THz vibrational modes in water and aqueous solutions

March 29, 2010, Irvine, CA, USA

1.    Invited by Professor Dr. Paul Tavan and Dr. Gerald Mathias
Department of Biomolecular Optics at the Ludwig-Maximilian University Munich
Vibrational modes of water in ab initio molecular dynamics simulations
July 10, 2009, Munich, Germany


Correlated collective dynamics in proteins and their solvating environment
Correlated collective dynamics in proteins and their solvating environment

Correlated collective dynamics in proteins and their solvating environment

We analyze the mutual influence between dynamical processes in solvated biomolecules and their surrounding solvent in molecular dynamics simulations. Particularly for water-soluble proteins, vibrational motions in the far-infrared frequency range between 30 and 300 cm-1, i.e. 1 to 10 terahertz, play a special role. In this spectral range we find the intermolecular vibrations of the water hydrogen bond network, as well a multitude of vibrations of the proteins solvated therein. Using cross correlation functions resolved in time and space, we were able to show that the vibrations of the protein and water in the surrounding hydration shell are influencing each other in this frequency range over distance of up to 10 Å. With this, we were able to provide, for the first time, a theoretical explanation for the experimental observation of a modified absorption of the water vibrations in this part of the spectrum.
The goal of this project is to study in detail the consequences of these correlated vibrational motions for the dynamics of solvated proteins, for example by perturbing the underlying the mechanical coupling between the protein and its surrounding solvent, in simulations as well as in accompanying experiments of our collaborators.
Of particular interest is the question, if the observed long ranged correlations resemble an adaption of protein, in particular enzymes, to their natural environment, which is relevant for their function. Existing experimental approaches, which modify the catalytical properties of enzymes through the applied solvent, make the existence of such a mechanism seem very plausible.
A detailed understanding of such an active role of the solvent will be of great importance for knowledge-based modifications of biochemical processes, for example the development of highly specific drugs or the use of enzymes in the synthesis of complex chemical compounds.

Modeling of folding equilibria in the interior of the cell
Modeling of folding equilibria in the interior of the cell

Modeling of folding equilibria in the interior of the cell

Based on existing interaction models, which are being used for Brownian dynamics simulations of complex protein solutions with up to 1000 proteins, we are developing in our group simulation methods which allow us to take into account the internal degrees of freedom of the proteins. Due to the use of Monte Carlo sampling, we have to pass on the ability to study dynamical processes in detail. However, our simulations allow us to study equilibria, for example between folded and unfolded states, as well as to analyze the influence of the environment on those. Here, we focus on the influence of specific and unspecific interactions between the molecules in the solution, which we can modify by tampering with the different terms of the interactions potential.
Our simulations accompany the experimental work in the group of Jun.-Prof. Dr. Simon Ebbinghaus at the Ruhr-University Bochum, which studies protein and polymer folding in vitro as well as in vivo.
The goal of this project is to understand the influence of the special environment of a protein in the interior of a cell, which is characterized by high concentrations of proteins and other biopolymers. A current scientific question is, whether the differences between experimental observations at high dilution in vitro and more recent studies in complex biological environments such as the interior of a cell, which have become feasible only recently, can be explained purely by volume exclusion effects, so-called “molecular crowding”, or if attractive interactions between the proteins need to be taken into account as well.



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