The role of solvent in the protein dynamical transition [Elektronische Ressource] / presented by Alexander Louis Tournier

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Dissertationsubmitted to theCombined Faculties for the Natural Sciences and for Mathematicsof the Ruperto-Carola University of Heidelberg, Germanyfor the degree ofDoctor of Natural Sciencespresented byAlexander Louis Tournierborn in Bebington (UK)oral examination:The Role of the Solvent inthe Protein Dynamical TransitionReferees:Prof. Dr. Jeremy C. SmithProf. Dr. Jor¨ g LangowskiThe Role of the Solvent inthe Protein Dynamical TransitionAlexander Louis TournierABSTRACTExperimental and computer simulation studies have revealed the presence of a transition in thedynamics of hydrated proteins around 220 K. This transition has been compared with that of a glassphase transition. It manifests itself by a nonlinear behavior in the temperature dependence of theaverage atomic mean-square displacements and involves an increase of the amplitude of proteindynamics. This increase in flexibility has been correlated with the onset of protein activity. Inthis thesis, the mechanisms behind the protein dynamical transition are explored using moleculardynamics simulations and neutron scattering experiments.The driving force behind the protein transition is investigated by performing simulations ofmyoglobin surrounded by a shell of water. A dual heatbath simulation method is used in whichthe protein and solvent are held at different temperatures, and sets of simulations are performedvarying the temperature of the two components.

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Published 01 January 2004
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Dissertation
submitted to the
Combined Faculties for the Natural Sciences and for Mathematics
of the Ruperto-Carola University of Heidelberg, Germany
for the degree of
Doctor of Natural Sciences
presented by
Alexander Louis Tournier
born in Bebington (UK)
oral examination:The Role of the Solvent in
the Protein Dynamical Transition
Referees:
Prof. Dr. Jeremy C. Smith
Prof. Dr. Jor¨ g LangowskiThe Role of the Solvent in
the Protein Dynamical Transition
Alexander Louis TournierABSTRACT
Experimental and computer simulation studies have revealed the presence of a transition in the
dynamics of hydrated proteins around 220 K. This transition has been compared with that of a glass
phase transition. It manifests itself by a nonlinear behavior in the temperature dependence of the
average atomic mean-square displacements and involves an increase of the amplitude of protein
dynamics. This increase in flexibility has been correlated with the onset of protein activity. In
this thesis, the mechanisms behind the protein dynamical transition are explored using molecular
dynamics simulations and neutron scattering experiments.
The driving force behind the protein transition is investigated by performing simulations of
myoglobin surrounded by a shell of water. A dual heatbath simulation method is used in which
the protein and solvent are held at different temperatures, and sets of simulations are performed
varying the temperature of the two components. The results show that the protein transition is
driven by a dynamical transition in the hydration water that induces increased fluctuations primar-
ily in side-chains in the external regions of the protein. The water dynamical transition involves
activation of translational, but not rotational, diffusion and occurs even in simulations where the
protein atoms are held fixed.
In order to determine the protein motions involved in the transition, longer molecular dy-
namics trajectories are decomposed using principal component analysis. The results indicate that
the nonlinearity in mean-square displacement arises from only a very small number of principal
components. These components, activated by the solvent:surface interaction, describe collective
dynamics propagated through to the interior of the protein. The onset of the transition at∼180 K
is characterized by the appearance of a single double-well mode involving a global relative motion
of two rigid-body groups of helices. As the temperature is raised a few more multiminimum and
quasiharmonic principal components successively appear.
Finally, experimental results from neutron scattering on xylanase in solution at varying
methanol concentrations reveal that the protein dynamics is strongly influenced by the dynam-
ics of its surrounding solvent on short timescales. On longer timescales the results indicate the
presence of a collaborative effect between the protein surface and the solvent which lowers the
freezing temperature of the protein hydration layer. All together, the results indicate that the pro-
tein hydration shell plays a central role in the appearance of the transition in the temperature
dependence of protein dynamics.
7ZUSAMMENFASSUNG
¨Experimentelle Untersuchungen, wie auch Computersimulationen, zeigen markante Anderungen des dy-
namischen Verhaltens hydratisierter Proteine bei einer Temperatur von ∼ 200 K. Die experimentellen
Beobachtungen zeigen charakteristische Gemeinsamkeiten mit dem Glasuber¨ gang komplexer Systeme und
¨in Analogie spricht man vom Protein-Glasuber¨ gang. Kennzeichnend fur¨ diesen Ubergang ist der nicht-
¨lineare Temperaturverlauf der mittleren quadratischen Auslenkung des Proteins. Bei Temperaturen uber
200 K ist ein deutliches Ansteigen der Amplituden zu beobachten. In der vorliegenden Arbeit werden die
¨Mechanismen dieses Ubergangs mittels Molekulardynamik Simulationen und Neutronenstreuexperimenten
untersucht.
Die Ursachen und Charakteristika des Protein-Glasuber¨ gangs werden anhand des Proteins Myo-
globin untersucht. Mit Hilfe einer Doppeltenwarmebad-Simulation¨ konnen¨ Protein und die umgebende
¨ ¨Wasserhulle auf unterschiedlichen Temperaturen gehalten werden. Dies ermoglicht, den Temperaturverlauf
dynamischer Prozesse in Wasserhulle¨ und Protein unabangig¨ voneinander zu kontrollieren und gegenseitige
Wechselwirkungen zu untersuchen. Die Ergebnisse der Simulationen zeigen, dass der Protein Glasuber¨ gang
¨durch Anderungen im dynamischen Verhalten der Wassermolekule¨ verursacht wird. Dies betrifft vor allem
die Translationsbewegung der Wassermolekule,¨ wahrend¨ Rotationen durchgehend normales Temperaturver-
halten zeigen. Das Einsetzen der Translationsbewegungen fuhrt¨ zu erhohten¨ Fluktuation vor allem der
¨Seitenketten und oberflachennahen Bereiche des Proteins.
Die Simulationen werden mit Hilfe einer Hauptkomponentenanalyse in charakteristische Bewe-
gungsmoden zerlegt. Diese Analyse zeigt, dass die beobachtete Nichtliniaritat¨ der mittleren quadratis-
chen Auslenkung von einer sehr geringen Anzahl an Moden verursacht wird. Diese Moden werden durch
Wechselwirkungen zwischen Proteinoberflache¨ und Wasserhulle¨ aktiviert und beschreiben kollektive Be-
¨wegungen, die sich bis ins innere des Proteins ausbreiten. Der beobachtete Ubergang bei ∼ 180 K ist
¨gekennzeichnet durch die qualitative Anderung einer einzigen Mode von einem quasi-harmonischen zu
einem anharmonischen doppelminimum Verlauf. Mit steigender Temperatur zeigen weitere Moden diesen
¨Ubergang zu anharmonischem Profil.
Anhand von Losungen¨ des Proteins Xylanase in unterschiedlichen Methanolkonzentrationen, wurde die
Abhangigk¨ eit der Proteindynamik vom umgebenden Losungsmittel¨ mittels Neutronenstreuung untersucht.
Auf kurzen Zeitskalen (< 100 ps) kann eine deutliche Abhangigk¨ eit der Proteindynamik vom umgebenden
Losungsmittel¨ beobachtet werden. Langsamere Prozesse (∼ 1 ns) deuten auf Wechselwirkungen zwischen
Proteinoberflache¨ und Losungsmittel¨ hin, die das Gefrieren des Losungsmittels¨ in unmittelbarer Nahe¨ derache¨ verhindern.
Die Ergebnisse dieser Arbeit verdeutlichen die Bedeutung der Wasserhulle¨ fur¨ ein Verstandnis¨ dy-
namischer Prozesse in biologischen Makromolekulen.¨
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