Biological Water, Protein Structure and the Dynamical Transition Yunfen He and Andrea Markelz Department of Physics, University at Buffalo, SUNY PRF 39554-AC6 NSF CAREER PHY-0349256

The “Protein Dynamical Transition” Applying THz to an Outstanding Biomolecular Question The “Protein Dynamical Transition” D. Ringe and G. A. Petsko, Biophysical Chemistry 105 (2003) 667.680 Ribonuclease A Roh, J.H. et al., Biophys J, (2006) 91, 2573-88. The requirement of minimum hydration level suggests the rapid increase in flexibility arises from a change in the dynamics of the solvent in direct contact with the biological molecule, the biological water.

interfacial water & bulk water Samir Kumar Pal and Ahmed H. Zewail, Chemical Reviews, 2004, Vol. 104, No. 4 2099-2123

What is the Dynamical Transition? Solvent mediated diffusive motions: solvent slaved motions Activated side chain motions Activated solvent motions Transition in solvent dynamics

Strong Glass Fragile Glass Observation of fragile-to-strong dynamic crossover in protein hydration water S.-H. Chen, L. Liu, E. Fratini, P. Baglioni, A. Faraone, and E. Mamontov Proceedings of National Academy of Sciences of America, 9012–9016 June 13, 2006 103 Strong Glass Fragile Glass EQUATIONS FOR FRAGILE ---VFT, AND STRONG ---ARRHENIUS …ROLE OF CONFINEMENT…PICTURE OF PROTEIN SURFACE WITH WATER…

1BWH.PDB Neutron Scattering Investigations Of Proton Dynamics Of Water And Hydroxyl Species In Confined Geometries S.-H. Chen and C.-K. Loong Nuclear Engineering And Technology, VOL.38 NO.3 APRIL 2006 201-224 EQUATIONS FOR FRAGILE ---VFT, AND STRONG ---ARRHENIUS …ROLE OF CONFINEMENT…PICTURE OF PROTEIN SURFACE WITH WATER…

Does Structure Play a Role in the Dynamical Transition? EQUATIONS FOR FRAGILE ---VFT, AND STRONG ---ARRHENIUS …ROLE OF CONFINEMENT…PICTURE OF PROTEIN SURFACE WITH WATER… Does Structure Play a Role in the Dynamical Transition?

Terahertz dielectric response is sensitive to the transition MOST MEASUREMENTS USE NEUTRON…LARGE SAMPLE REQUIREMENTS (~100MG) AND CAREFUL DEUTERATION THZ DIELECTRIC RESPONSE TABLE TOP MEASUREMENT WITH SMALLER SAMPLE REQUIREMENT (~1 MG) A. Markelz et al. Chemical Physics Letters 442 (2007) 413–417

Terahertz Time Domain Spectroscopy (THz TDS) Solution cell EMPHASIZE ALL MEASUREMENTS IN SOLUTION, EQUATION FOR DIELECTRIC RESPONSE… g(w): density of states; f(w): oscillator strength; g(w): damping coefficient; h(t): distribution of relaxation times

Net increase in low frequency response with denaturing EXPLANATION OF WHY MIGHT EXPECT INCREASE -KARPLUS CALCULATION -HUNT KERR MEASUREMENTS POSSIBLE CONTRIBUTIONS -RED SHIFTING OF MODES WITH LOSS OF STRUCTURE—KARPLUS -INCREASE IN SIDE CHAIN EXPOSURE RESULTS IN INCREASE IN RELAXATIONAL CONTRIBUTION -NOT THE SAME RESULT AS SUGGESTED BY MET/H20 DENATURING IN HUNT ET AL, BUT INAGREEMENT WITH THERMAL DENATURING OF HUNT.

Terahertz Dielectric response Herman W. T. van Vlijmen and Martin Karplus, J. Phys. Chem. B 1999, 103, 3009-3021

Protein structure is not necessary for dynamical transition (HEWL) NOTE THAT ALL THZ MEASUREMENTS OF DYNAMICAL TRANSITION FOR NATIVE SOLUTIONS DO NOT SHOW CLEAR TRANSITION IN INDEX, HOWEVER HYDRATED POWDER MEASUREMENTS DO SHOW TRANSITION… “BULK” SOLVENT INDEX TEMPERATURE DEPENDENCE DOMINATES AS WILL BE DISCUSSED IN LATER TALK.

Protein structure is not necessary for dynamical transition (random coil poly-L-lysine) NOTE THAT ALL THZ MEASUREMENTS OF DYNAMICAL TRANSITION FOR NATIVE SOLUTIONS DO NOT SHOW CLEAR TRANSITION IN INDEX, HOWEVER HYDRATED POWDER MEASUREMENTS DO SHOW TRANSITION… “BULK” SOLVENT INDEX TEMPERATURE DEPENDENCE DOMINATES AS WILL BE DISCUSSED IN LATER TALK.

Molecular dynamics simulation COULD THE LACK OF DYNAMICAL TRANSITION IN DIMER AND TRIMER BE DUE TO LESS NET BIOWATER, TRANSITION CONTRIBUTION TO TOTAL SIGNAL BELOW SIGNAL TO NOISE. -MOLAR CONCENTRATION HIGHER FOR DIMER AND TRIMER TABLE OF MOLAR CONCENTRATIONS….NET BIO WATER ACTUALLY GREATER FOR THESE -MD SIMULATIONS DIRECTLY EXAMINING DYNAMICS OF INDIVIDUAL PROTEIN, BACKGROUND FREE SHOW THAT INDEED FOR HYDRATED SMALL ALPHA HELIX TRANSITION OCCURS, BUT FOR STRUCTURE FREE HYDRATED TRIMER TRANSITION ABSENT

Solvent or side chain diffusive motions?? Data do not support Fragile to Strong transition Arrhenius Temperature dependence only No structural dependence The dynamical transition is caused by activated diffusive motions!! Solvent or side chain diffusive motions??

Chain length dependence of dynamical transition

What causes the dynamical transition? Activated diffusive motions of adjacent solvent responsible for dynamical transition. Apparent minimum chain length required for dynamical transition. The temperature dependence of the diffusive motions is the result of the polypeptide on the dynamics of biological water. SHOW ARRENHIUS PLOT --- NO SIGN OF VTF TEMPERATURE DEPENDENCE…POSSIBLE THAT THZ SIGNAL DOMINATED BY PROTEIN AND NOT SHOWING TRUE TEMPERATURE DEPENDENCE OF SOLVENT…BUT IN AGREEMENT WITH SOKOLOV’S GROUP LOW FREQUENCY (KHZ????) DIELECTRIC MEASUREMENTS. When this dynamic crossover occurs, the biological water changes from the “more fluid” high-density liquid form (which induces the protein to adopt more flexible conformational substates) to the “less fluid” low-density liquid structure (which induces the protein to adopt more rigid conformational substates). The dynamical transition does not require a protein!!

Thanks & Questions?