Hydration Dynamics and Time Scales of Coupled Water−Protein Fluctuations

Li, Tanping; Hassanali, Ali; Kao, Ya-Ting; Zhong, Dongping; Singer, Sherwin J.

doi:10.1021/ja0685957

Cited by 235 publications

(372 citation statements)

References 71 publications

Supporting

Mentioning

335

Contrasting

Unclassified

Order By: Relevance

“…Using this single intrinsic tryptophan as a local optical probe and from the measurements of three mutants with a charged, polar, or hydrophobic residue around the probe, we unambiguously determined the time scales of hydration dynamics at the active site to be 0.47-0.67 and 10.8-13.2 ps. The former time is the result of local reorientational/translational motions of water near the active site; the latter is a direct measure of surface hydration coupled with the local protein fluctuation (45). These results are consistent with our recent studies of surface hydration dynamics in enzyme Staphylococcus nuclease (26).…”

Section: Discussionsupporting

confidence: 92%

See 1 more Smart Citation

Dissection of complex protein dynamics in human thioredoxin

Wang

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

View full text Add to dashboard Cite

We report our direct study of complex protein dynamics in human thioredoxin by dissecting into elementary processes and determining their relevant time scales. By combining site-directed mutagenesis with femtosecond spectroscopy, we have distinguished four partly time-overlapped dynamical processes at the active site of thioredoxin. Using intrinsic tryptophan as a molecular probe and from mutation studies, we ascertained the negligible contribution to solvation by protein sidechains and observed that the hydration dynamics at the active site occur in 0.47-0.67 and 10.8 -13.2 ps. With reduced and oxidized states, we determined the electron-transfer quenching dynamics between excited tryptophan and a nearby disulfide bond in 10 -17.5 ps for three mutants. A robust dynamical process in 95-114 ps, present in both redox states and all mutants regardless of neighboring charged, polar, and hydrophobic residues around the probe, is attributed to the charge transfer reaction with its adjacent peptide bond. Site-directed mutations also revealed the electronic quenching dynamics by an aspartate residue at a hydrogen bond distance in 275-615 ps. The local rotational dynamics determined by the measurement of anisotropy changes with time unraveled a relatively rigid local configuration but implies that the protein fluctuates on the time scale of longer than nanoseconds. These results elucidate the temporal evolution of hydrating water motions, electron-transfer reactions, and local protein fluctuations at the active site, and show continuously synergistic dynamics of biological function over wide time scales.active site hydration ͉ femtosecond dynamics ͉ intraprotein electron transfer ͉ sited-directed mutation P rotein dynamics is a complex process and evolves on a multidimensional energy landscape with various interactions and conformations over wide time scales (1-7). To understand such complex dynamics, we need to dissect the process into elementary steps and determine their relevant time scales. Many elementary reactions even occur on a similar time scale (8) and different methods are often integrated to separate each reaction channel and thus elucidate their molecular mechanisms (5, 9-13). Here, we report our direct studies of complex protein dynamics at the active site in human thioredoxin (hTrx). Using site-directed mutagenesis and femtosecond-resolved fluorescence spectroscopy, we break down the complex dynamics into four elementary processes: one solvent relaxation dynamics and three electron-transfer (ET) reactions. Fig. 1 shows the x-ray structure of oxidized hTrx at a 2.1-Å resolution (14). hTrx, an enzyme catalyzing dithiol-disulfide exchanges with substrate proteins, is a compact globular protein with a central core of five strands of ␤-pleated sheet surrounded by four ␣ helices. The active site of hTrx consists of a highly conserved sequence W31-C-G-P-C-K36 that forms a protruding part of the structure between the second ␤ strand and the second ␣ helix. The enzyme contains only a single tryptophan (W31), locate...

show abstract

Section: Discussionsupporting

confidence: 92%

“…Under this perturbation, the response can result from both the surrounding water molecules and the protein (polar/charged residues and backbone) (45). Within 7 Å from W31, there is only one charged residue, D60, at 3.59 Å, which forms a hydrogen bond between O of the carboxyl group and N of the indole ring (Fig.…”

Section: Figmentioning

confidence: 99%

Dissection of complex protein dynamics in human thioredoxin

Wang

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

View full text Add to dashboard Cite

show abstract

“…Solvation becomes faster. This was also observed by Singer et al 12,50 The slowest component above ~100ps disappears when the amino acid side chains are not fluctuating. This indicates the role of amino acid side chain fluctuations in a substantial retardation of solvation timescales.…”

Section: B Solvation Dynamics Of Tryptophan: Effect Of Adjacent Charsupporting

confidence: 81%

“…50 Zhong et al showed that charged/polar residues as well as the side-chain fluctuations play a major role in slowness. 15,44,50 It is straightforward to understand the reason of fastness on freezing side chain motion because a slow component is removed from time dependence of solvation energy. However, the role of water molecules inside the PHL in slowing down the dynamics and their relative contribution is not properly addressed.…”

Section: (I) What Are the Prevailing Factors Responsible For The Slowmentioning

confidence: 99%

Origin of diverse time scales in the protein hydration layer solvation dynamics: A simulation study

Mondal

Mukherjee

Bagchi

2017

The Journal of Chemical Physics

View full text Add to dashboard Cite

“…Thus, the comparable time scale, stabilization energy, and solvation speed indicate that both sites have the similar polar environment and initial ultrafast response. The second relaxation in tens of picoseconds reflects the coupled water-protein motions, a collective rearrangement of the local configuration (19,20,39). Although both sites have a similar time scale of approximately 20 ps, the At(6-4)-Wt has a stabilization energy of 471 cm −1 , about ten times larger than that of EcPhr-Wt, leading to a significantly larger solvation speed.…”

Section: Resultsmentioning

confidence: 99%

Ultrafast solvation dynamics at binding and active sites of photolyases

Chang

Guo

Kao

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

View full text Add to dashboard Cite

Dynamic solvation at binding and active sites is critical to protein recognition and enzyme catalysis. We report here the complete characterization of ultrafast solvation dynamics at the recognition site of photoantenna molecule and at the active site of cofactor/ substrate in enzyme photolyase by examining femtosecondresolved fluorescence dynamics and the entire emission spectra. With direct use of intrinsic antenna and cofactor chromophores, we observed the local environment relaxation on the time scales from a few picoseconds to nearly a nanosecond. Unlike conventional solvation where the Stokes shift is apparent, we observed obvious spectral shape changes with the minor, small, and large spectral shifts in three function sites. These emission profile changes directly reflect the modulation of chromophore's excited states by locally constrained protein and trapped-water collective motions. Such heterogeneous dynamics continuously tune local configurations to optimize photolyase's function through resonance energy transfer from the antenna to the cofactor for energy efficiency and then electron transfer between the cofactor and the substrate for repair of damaged DNA. Such unusual solvation and synergetic dynamics should be general in function sites of proteins.function-site solvation | ultrafast dynamics | spectral tuning | protein rigidity and flexibility | femtosecond-resolved emission spectra D ynamic solvation in binding and active sites plays a critical role in protein recognition and enzyme reaction, and such local motions optimize spatial configurations and minimize energetic pathways (1-11). These dynamics involve local constrained protein and trapped-water motions within angstrom distance and occur on ultrafast time scales (6,7,10,11). Typically, extrinsic dye molecules or synthetic amino acids were used as local optical probes to label function sites, and the local relaxations were observed, ranging from femtoseconds to nanoseconds (5,(12)(13)(14). Such labeling of bulky dye molecules usually induces significant local perturbations, and direct characterization with intrinsic chromophores in proteins eliminates those interferences and reveals intact environment responses (4, 7, 15-21), as recently examined in green fluorescence proteins (21). We have recently studied a series of flavoproteins using intrinsic flavin molecule as the optical probe (10, 22, 23) and especially found the important functional role of local solvation in photolyase (10).Photolyase, a flavoprotein and a photoenzyme, repairs damaged DNA caused by UV irradiation. Two types of structurally similar photolyases are specific for two major UV-induced DNA lesions of cyclobutane pyrimidine dimer (CPD) and (6-4) photoproduct (24). The CPD photolyase contains two noncovalently bound chromophores, a pterin molecule in the form of methenyltetrahydrofolate (MTHF) in the binding site as the photoantenna for energy efficiency and a fully reduced flavin adenine dinucleotide (FADH − ) at the active site as the catalytic cofactor for repair of d...

show abstract

Hydration Dynamics and Time Scales of Coupled Water−Protein Fluctuations

Cited by 235 publications

References 71 publications

Dissection of complex protein dynamics in human thioredoxin

Dissection of complex protein dynamics in human thioredoxin

Origin of diverse time scales in the protein hydration layer solvation dynamics: A simulation study

Ultrafast solvation dynamics at binding and active sites of photolyases

Contact Info

Product

Resources

About