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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
2010-2013
Postdoctoral fellow, University of California, Irvine (Douglas J. Tobias)
2010
Visiting scholar, Weizmann Institute (Irit Sagi)
2006-2010
Doctoral studies, Ruhr-University Bochum (Martina Havenith)
2006
Visiting scholar, University of Nevada, Reno (David M. Leitner)
2001–2006
Biochemistry studies, Ruhr-University Bochum
1981
born in Düsseldorf
2011
Postdoctoral fellowship of the German Academy of Sciences Leopoldina
2011
Peter A. Salamon Award of the Telluride Science Research Center
2010
Victoria Buch Memorial poster prize of the Gordon Research Conference Water & Aqueous Solutions
2009
Participant of the 59th meeting of the Nobel laureates in Lindau, Germany
2008
Doctoral scholarship of the German National Academic Foundation
2007
PCCP poster prize of the International Bunsen Discussion Meeting: “Exploring THz spectroscopy”
2007
Fellowship of the Ruhr-University Research School
2006
Short term foreign exchange scholarship by the German Academic Exchange Service (DAAD)
2014
Chair of the Gordon Research Seminar Water & Aqueous Solutions
2014
Speaker of the RESOLV Early Career Researcher Board
 

14.    invited by Prof. Christian Ochsenfeld (scheduled)
Triennial Congress of the World Association of Theoretical and Computational (WATOC)
Title: to be announced
27th of August – 1st of September 2017, Munich, Germany

13.    invited by Prof. Andrea Markelz (scheduled)
253rd American Chemical Society (ACS) National Meeting
Symposium: Long-range Correlated Motions in Proteins
Title: to be announced
2nd – 6th of April 2017, San Francisco, CA, USA

12.    invited by Prof. Roland Netz (scheduled)
SFB/CRC 1114 conference: „Scaling Cascades in Complex Systems“, Freie Universität Berlin
Title: to be announced
27th – 29th of March 2017, Berlin, Germany

11.    invited by Prof. Dor Ben-Amotz
Telluride Science Research Center (TSRC) workshop:
Interfacial molecular and electronic structure and dynamics

3D-2PT: Analyzing the thermodynamics of solvation via intermolecular vibrations
18th – 22nd of July 2016, Telluride, CO, USA

10.    invited by Dr. Martin Weik, Prof. John Straub and Prof. Douglas J. Tobias
Telluride Science Research Center (TSRC) workshop: Protein dynamics
Thermodynamic properties of water solvating biomolecular surfaces
3rd – 8th of April 2016, Les Houches, France

9.    invited by Prof. Douglas J. Tobias
American Physical Society (APS) March Meeting
Session: Water at Biological Interfaces
Thermodynamic properties of water solvating biomolecular surfaces
14th – 18th of March 2016, Baltimore, MD, USA

8.    invited by Prof. Alenka Luzar
Pacifichem 2015
Symposium: Recent Advances in Dynamics of Confined Liquids
Water in the pocket: Exploring local entropies and dynamics of water confined on biomolecular surfaces in atomistic simulations
15th – 20th of December 2015, Honolulu, Hawaii, USA

7.    invited by Dr. Ali Hassanali
Workshop on Water at the Interface between Biology, Chemistry, Physics and Materials Science
The dynamic footprint of biomolecules in their local solvation environment
5th – 9th of October 2015, Abdus Salam International Center for Theoretical Physics (ICTP), Trieste, Italy

6.    invited by Prof. Sihyun Ham
15th KIAS Conference on Protein Structure and Function
Interactions of proteins with their solvating environment
17th – 19th of September 2015, Korea Institute for Advanced Study (KIAS), Seoul, Republic of Korea

5.    invited by Prof. Dr. Dominik Marx
CECAM-Jülich School on Computational Trends in Solvation and Transport in Liquids
Biomolecular solvation
23rd – 27th of March 2015, Jülich Sompercomputing Centre, Jülich, Germany

4.    invited by Prof. Douglas J. Tobias
Gordon Research Conference (GRC) on Water & Aqueous Solutions 2014
Correlated vibrations of proteins and their hydration water
27th of July – 1st of August 2014, Holderness, NH, USA

3.    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
18th – 23rd of May 2014, Les Houches, France

2.    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
24th – 27th of September 2013, Lausanne, Switzerland

1.    invited by Prof. Dor Ben-Amotz
243rd American Chemical Society (ACS) National Meeting
Symposium: Water-mediated chemical assembly
Correlated intermolecular motion in solvation water of biomolecules

25th – 29th of March 2012, San Diego, CA, USA

25.    invited by Dr. Jan Heyda
Department of Physical Chemistry, University of Chemistry and Technology, Prague
Extracting solvation entropies and free energies from equilibrium intermolecular vibrations
4th of November 2016, Prague, Czech Republic

24.    invited by Prof. Jeremy Harvey
Department of  Chemistry, Katholieke Universiteit Leuven
Mini-symposium solutions and solvation: a computational viewpoint
Vibrations in the water hydrogen bond network
18th of August 2016, Leuven, Belgium

23.    invited by Prof. Dr. Nico van der Vegt
Computational Physical Chemistry, Technische Universität Darmstadt
Simulating solvation: Understanding native biomolecular environments in atomistic detail
15th of June 2016, Darmstadt, Germany

22.    invited by Prof. Dr. Eckhard Spohr
Department of Chemistry, Universität Duisburg-Essen
What local water dynamics can tell us about solvation thermodynamics?
13th of April 2016, Essen, Germany

21.    invited by Prof. Damien Laage
Ecole Normale Supérieure Paris
Thermodynamic properties of water solvating biomolecular surfaces
31st of March 2016, Paris, France

20.    invited by Prof. Dor Ben-Amotz
Department of Chemistry, Purdue University
Thermodynamic properties of water solvating biomolecular surfaces
12th of January 2016, West Lafayette, IN, USA

19.    invited by Prof. Heather Allen
Department of Chemistry, Ohio State University
Thermodynamic properties of water solvating biomolecular surfaces
11th of January 2016, Columbus, OH, USA

18.    invited by Prof. Francesco Paesani
Department of Chemistry, University of California, San Diego
Thermodynamic properties of water solvating biomolecular surfaces
8th of January 2016, San Diego, CA, USA

17.    invited by Prof. Douglas J. Tobias
Department of Chemistry, University of California, Irvine
Thermodynamic properties of water solvating biomolecular surfaces
7th of January 2016, Irvine, CA, USA

16.    invited by Prof. Dr. Daniel Sebastiani
Department of Chemistry, Martin-Luther-Universität Halle-Wittenberg
The dynamic footprint of biomolecules in their local solvation environment
19th of November 2015, Halle, Germany

15.    invited by Prof. Sihyun Ham
Sookmyung Women’s University Seoul
Biomoleular Solvation
14th of September 2015, Seoul, Republic of Korea

14.    invited by Prof. Dr. Roland Netz
Department of Theoretical Physics, Freie Universität Berlin
Biomolecular stability and dynamics in the context of the solvating environment
16th of July 2015, Berlin, Germany

13.    invited by Prof. Dr. Gerhard Stock
Department of Physics, Albert-Ludwigs-Universität Freiburg
Analyzing the effects of the solvating environments on proteins in simulations
17th of July 2014, Freiburg, Germany

12.    invited by Prof. Dr. Rebecca Wade
Heidelberg Institute for Theoretical Studies (HITS)
Monte Carlo sampling of flexible proteins and polymers in many-molecule systems
15th of July 2014, Heidelberg, Germany

11.    invited by Prof. Dr. Joachim Dzubiella
Soft Matter and Functional Materials Institute, Helmholtz-Zentrum Berlin
Analyzing the interactions between bimolecular solutes and their solvating environment
20th of June 2014, Berlin, Germany

10.    invited by Prof. Dr. Christel Marian
Department of Theoretical Chemistry, Heinrich-Heine-Universität Düsseldorf
Coupled solute-solvent dynamics in biomolecular solutions
28th of May 2014, Düsseldorf, Germany

9.    invited by Dr. Martin Weik
Institute de Biologie Structurale (IBS)
Understanding the influence of the solvating environment on biomolecular properties
16th of May 2014, Grenoble, France

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

7.    invited by RESOLV Cluster of Excellence
Max-Planck-Institut für Kohlenforschung
Role of collective vibrations for solute-solvent interactions of proteins and enzymes
27th of February 2013, Mülheim an der Ruhr, Germany

6.    invited by Prof. 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
30th of June 2011, Nancy, France

5.    invited by Prof. Dr. Ana-Nicoleta Bondar
Theoretical Molecular Biophysics, Freie Universität Berlin
Membrane protein dynamics in different lipid environments: Native membranes vs. reconstitution in artificial lipid bilayers studied with molecular dynamics simulations
6th of June 2011, Berlin, Germany

4.    invited by Prof. 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
28th of April 2011, Santa Barbara, CA, USA

3.    invited by Prof. Dr. Walter Thiel
Department of Theoretical Chemistry, Max-Planck-Institut für Kohlenforschung
Water seen through terahertz glasses
14th of July 2010, Mülheim an der Ruhr, Germany

2.    invited by Prof. Douglas J. Tobias
Department of Chemistry, University of California, Irvine
Water seen through terahertz glasses ─ Picosecond dynamics and THz vibrational modes in water and aqueous solutions
29th of March 2010, Irvine, CA, USA

1.    invited by Prof. Dr. Paul Tavan and Dr. Gerald Mathias
Biomolecular Optics, Ludwig-Maximilians-Universität (LMU) München
Vibrational modes of water in ab initio molecular dynamics simulations
10th of July 2009, Munich, Germany

16.    52nd Symposium on Theoretical Chemistry (STC) (scheduled)
Solvation thermodynamics probed by intermolecular vibrations in molecular dynamics simulations
26th – 29th of September 2016, Bochum, Germany

15.    115th General Assembly of the German Bunsen Society for Physical Chemistry (Bunsentagung)
Thermodynamic properties of water solvating biomolecular surfaces
5th – 7th of May 2016, Rostock, Germany

14.    Molecular Graphics and Modeling Society Meeting: Exploring Mechanisms in Biology – Theory and Experiment
Understanding molecules in their natural habitat – How the solvating environment affects protein dynamics and stability
25th – 27th of November 2015, Singapore

13.    572th WE-Heraeus-Seminar: “Exploring Solvation Science”
Resolving anisotropic distributions of correlated vibrational motion in protein hydration water
27th – 30th of October 2014, Bad Honnef, Germany

12.    50th Symposium on Theoretical Chemistry (STC)
Spatial resolution of long-ranged dynamical coupling between proteins and hydration water
14th – 18th of September 2014, Vienna, Austria

11.    Condensed Matter Days 2014 (CMD 25 – JMC 14)
Tracking correlations of vibrational motion from biomolecular solutes into the surrounding solvent
24th – 29th of August 2014, Paris, France

10.    113th General Assembly of the German Bunsen Society for Physical Chemistry (Bunsentagung)
Analyzing coupled solute/solvent dynamics via correlated vibrational motion in protein hydration shells
29th – 31st of May 2014, Hamburg, Germany

9.    Telluride Science Research Center (TSRC) workshop: Vibrational Dynamics
Intermolecular vibrations in water and aqueous solutions
25th – 29th of July 2011, Telluride, CO, USA

8.     International Workshop on Optical Terahertz Science and Technology (OTST) 2011
Solvation water of biomolecules seen through THz glasses
13th – 17th of March 2011, Santa Barbara, CA, USA

7.    AirUCI workshop
Ions in motion: Intermolecular vibrations of solvated ions in the far infrared
19th – 20th of January 2011, Laguna Beach, CA, USA

6.    21st Faltertage
Solvation water of biomolecules seen through terahertz glasses
15th – 17th of October 2010, Regensburg, Germany

5.    Gordon Research Conference (GRC) on Water & Aqueous Solutions
Invited short talk: Water seen through terahertz glasses
8th – 13th of August 2010, Holderness, NH, USA

4.    HLRB2 Workshop for Supercomputer Users
Statistically converged properties of water from ab initio molecular dynamics simulations
8th – 9th of December 2009, Garching, Germany

3.    108th Annual Meeting of the German Bunsen Society for Physical Chemistry (Bunsentagung)
THz vibrational modes in ab initio water simulations
21st – 23rd of May 2009, Köln, Germany

2.    63rd OSU International Symposium on Molecular Spectroscopy 2008
Probing hydrogen bond network vibrations in carbohydrate solvation shells at THz frequencies
16th – 20th of June 2008, Columbus, OH, USA
(presented by S. Ebbinghaus)

1.    106th General Assembly of the German Bunsen Society for Physical Chemistry (Bunsentagung)
Characteristics of solvation water around carbohydrates and proteins
17th – 19th of May 2007, Graz, Austria

Forschungsthemen

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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  • Dr. Matthias Heyden

    Dr. Heyden, Matthias

    Jan 14 – Sep 17 Independent Group Leader (RESOLV)

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  •  Bibhab Bandhu Majumdar

    Majumdar, Bibhab Bandhu

    +49(0)208/306-2148

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  •  Christopher Päslack

    Päslack, Christopher

    Feb 15 – Sep 15 Graduating Student; Oct 15 – Sep 17 PhD Student (Heyden Group)

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  •  Viren Pattni

    Pattni, Viren

    +49(0)208/306-2148

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  • Dr. Rasmus Persson A. X.

    Dr. Persson A. X., Rasmus

    Sep 14 – Aug 15 Post-doc (Heyden Group)

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  •  Dhiman Ray

    Ray, Dhiman

    May 16 – Jul 16 Visiting PhD Student (Heyden-Group)

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  • Dr. Yao Xu

    Dr. Xu, Yao

    Sep 16 – Mar 17 Post-doc (Heyden Group)

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