Seung Joong Kim

An extended dynamical hydration shell around proteins

The focus in protein folding has been very much on the protein backbone and sidechains. However, hydration waters make comparable contributions to the structure and energy of proteins. The coupling between fast hydration dynamics and protein dynamics is considered to play an important role in protein folding. Fundamental questions of protein hydration include, how far out into the solvent does the influence of the biomolecule reach, how is the water affected, and how are the properties of the hydration water influenced by the separation between protein molecules in solution? We show here that Terahertz spectroscopy directly probes such solvation dynamics around proteins, and determines the width of the dynamical hydration layer. We also investigate the dependence of solvation dynamics on protein concentration. We observe an unexpected nonmonotonic trend in the measured terahertz absorbance of the five helix bundle protein λ6–85* as a function of the protein: water molar ratio. The trend can be explained by overlapping solvation layers around the proteins. Molecular dynamics simulations indicate water dynamics in the solvation layer around one protein to be distinct from bulk water out to ≈10 Å. At higher protein concentrations such that solvation layers overlap, the calculated absorption spectrum varies nonmonotonically, qualitatively consistent with the experimental observations. The experimental data suggest an influence on the correlated water network motion beyond 20 Å, greater than the pure structural correlation length usually observed.

The terahertz dance of water with the proteins: the effect of protein flexibility on the dynamical hydration shell of ubiquitin.

The role of water in the functioning of proteins has been a hot topic over the years. We use terahertz (THz) spectroscopy as an experimental tool to probe the protein-induced fast solvation dynamics of ubiquitin. In order to investigate the effect of protein flexibility on the changes in the solvation dynamics, we have measured the concentration-dependent THz absorption of several site-specific ubiquitin mutants. The observed non-linear dependence of absorption on concentration is a signature of a long-range hydration shell with properties distinct from bulk water. We determined a dynamical hydration shell of a thickness of at least 18 A on the protein surface. This exceeds the static hydration layer as it is typically observed by scattering methods (3 A) by far. We also conclude that any increase in flexibility obtained by side-chain truncations that decrease the structural rigidity of the protein results in more bulk-like behaviour of the dynamical hydration shell. Furthermore, our THz measurements show that a single phenylalanine-to-tryptophan substitution to introduce a fluorescent marker leads to measurable changes in the solvation dynamics.

Real‐Time Detection of Protein–Water Dynamics upon Protein Folding by Terahertz Absorption Spectroscopy

Recently,therehasbeenagrowinginterestinprobingnotjustthe dynamics of self-assembling macromolecules but thedynamicsoftheirsolvationshellsaswell.Dielectric,Raman,fluorescence, and NMR spectroscopies, neutron scattering,and crystallography all provide insights, but only terahertzabsorption spectroscopy (wavelength range 0.1–1mm;1THz=1ps

Protein Sequence- and pH-Dependent Hydration Probed by Terahertz Spectroscopy

Solvation free energy changes induced by protein folding and function are comparable to the corresponding overall free energy changes. Yet the structure, dynamics, and energetics of the protein itself have received more attention because they are easier to probe. Here we use terahertz (far-infrared) spectroscopy to directly probe the effect of mutations and solvent pH on the solvent shell−protein interaction. We study absorption spectra of the 80 residue viral protein, a five helix bundle, in the 2.1−2.8 THz region. We find that the wild type at pH 7 has a much more pronounced effect on long-distance solvation water than mutants replacing a single polar glutamine side chain with aromatic residues (tyrosine, histidine). This is true both in the context of enhanced and decreased helix stability (via alanine and glycine substitutions). Bringing the wild type and mutants closer to the unfolding transition by lowering the pH likewise reduces the long distance solvation effect. Thus terahertz spectroscopy can b...

Solvent‐tuning the collapse and helix formation time scales of λ6‐85*

The λ6‐85* pseudo‐wild type of lambda repressor fragment is a fast two‐state folder (kf ≈ 35 μsec−1 at 58°C). Previously, highly stable λ6‐85* mutants with kf > 30 μsec−1 have been engineered to fold nearly or fully downhill. Stabilization of the native state by solvent tuning might also tune λ6‐85* away from two‐state folding. We test this prediction by examining the folding thermodynamics and kinetics of λ6‐85* in a stabilizing solvent, 45% by weight aqueous ethylene glycol at −28°C. Detection of kinetics by circular dichroism at 222 nm (sensitive to helix content) and small angle X‐ray scattering (measuring the radius of gyration) shows that refolding from guanidine hydrochloride denatured conditions exhibits very different time scales for collapse and secondary structure formation: the two processes become decoupled. Collapse remains a low‐barrier activated process, while the fastest of several secondary structure formation time scales approaches the downhill folding limit. Two‐state folding of λ6‐85* is not a robust process.

Simulation-Based Fitting of Protein-Protein Interaction Potentials to SAXS Experiments

We present a new method for computing interaction potentials of solvated proteins directly from small-angle x-ray scattering data. An ensemble of proteins is modeled by Monte Carlo or molecular dynamics simulation. The global x-ray scattering of the whole model ensemble is then computed at each snapshot of the simulation, and averaged to obtain the x-ray scattering intensity. Finally, the interaction potential parameters are adjusted by an optimization algorithm, and the procedure is iterated until the best agreement between simulation and experiment is obtained. This new approach obviates the need for approximations that must be made in simplified analytical models. We apply the method to lambda repressor fragment 6-85 and fyn-SH3. With the increased availability of fast computer clusters, Monte Carlo and molecular dynamics analysis using residue-level or even atomistic potentials may soon become feasible.

Slowing Down Downhill Folding: A Three-Probe Study

The mutant Tyr22Trp/Glu33Tyr/Gly46Ala/Gly48Ala of lambda repressor fragment lambda(6-85) was previously assigned as an incipient downhill folder. We slow down its folding in a cryogenic water-ethylene-glycol solvent (-18 to -28 degrees C). The refolding kinetics are probed by small-angle x-ray scattering, circular dichroism, and fluorescence to measure the radius of gyration, the average secondary structure content, and the native packing around the single tryptophan residue. The main resolved kinetic phase of the mutant is probe independent and faster than the main phase observed for the pseudo-wild-type. Excess helical structure formed early on by the mutant may reduce the formation of turns and prevent the formation of compact misfolded states, speeding up the overall folding process. Extrapolation of our main cryogenic folding phase and previous T-jump measurements to 37 degrees C yields nearly the same refolding rate as extrapolated by Oas and co-workers from NMR line-shape data. Taken together, all the data consistently indicate a folding speed limit of approximately 4.5 micros for this fast folder.

Transient Helical Structure during PI3K and Fyn SH3 Domain Folding

A growing list of proteins, including the β-sheet-rich SH3 domain, is known to transiently populate a compact α-helical intermediate before settling into the native structure. Examples have been discovered in cryogenic solvent as well as by pressure jumps. Earlier studies of λ repressor mutants showed that transient states with excess helix are robust in an all-α protein. Here we extend a previous study of src SH3 domain to two new SH3 sequences, phosphatidylinositol 3-kinase (PI3K) and a Fyn mutant, to see how robust such helix-rich transients are to sequence variations in this β-sheet fold. We quantify helical structure by circular dichroism (CD), protein compactness by small-angle X-ray scattering (SAXS), and transient helical populations by cryo-stopped-flow CD. Our results show that transient compact helix-rich intermediates are easily accessible on the folding landscape of different SH3 domains. In molecular dynamics simulations, force field errors are often blamed for transient non-native structure. We suggest that experimental examples of very fast α-rich transient misfolding could become a more subtle test for further force field improvements than observation of the native state alone.