Biomedical subjects

Peter Hamm

Publications and source records attributed to Peter Hamm.

15 recordsLinked to original sources

PubMed2006

Watching hydrogen-bond dynamics in a beta-turn by transient two-dimensional infrared spectroscopy.

X-ray crystallography and nuclear magnetic resonance measurements provide us with atomically resolved structures of an ever-growing number of biomolecules. These static structural snapshots are important to our understanding of biomolecular function, but real biomolecules are dynamic entities that often exploit conformational changes and transient molecular interactions to perform their tasks. Nuclear magnetic resonance methods can follow such structural changes, but only on millisecond timescales under non-equilibrium conditions. Time-resolved X-ray crystallography has recently been used to monitor the photodissociation of CO from myoglobin on a subnanosecond timescale, yet remains challenging to apply more widely. In contrast, two-dimensional infrared spectroscopy, which maps vibrational coupling between molecular groups and hence their relative positions and orientations, is now routinely used to study equilibrium processes on picosecond timescales. Here we show that the extension of this method into the non-equilibrium regime allows us to observe in real time in a short peptide the weakening of an intramolecular hydrogen bond and concomitant opening of a beta-turn. We find that the rate of this process is two orders of magnitude faster than the 'folding speed limit' established for contact formation between protein side chains.

Computer Simulation↗

PubMed2006

Time-resolved IR spectroscopy of N-methylthioacetamide: trans-->cis isomerization upon n-pi and pi-pi excitation and cis-->trans photoreaction.

Time-resolved infrared spectroscopy was used to study the photoisomerization of N-Methylthioacetamide (NMTAA) in D2O in both the cis-->trans and the trans-->cis direction upon selective excitation of the n-pi (S1) and pi-pi (S2) electronic transitions. While isomerization and the return to the ground state takes place on two distinct time scales ( cis isomerization is 30-40%, independent of the electronic state excited, while the cis-->trans isomerization proceeds with a 60-70% quantum efficiency. These results support a mechanism by which isomerization takes place via one common intermediate state independent of electronic excitation energy and initial conformation.

Isomerism↗

PubMed2006

The infrared-driven cis-trans isomerization of HONO. II: Vibrational relaxation and slow isomerization channel.

In a recent paper [R. Schanz et al., J. Chem. Phys. 122, 044509 (2005)], we investigated the IR-driven cis-trans isomerization of HONO in a Kr matrix with the help of femtosecond IR spectroscopy. We found that isomerization occurs on a 20 ps time scale, however, with a cis-->trans quantum yield of only 10% that is significantly below the value reported in the literature (close to 100%). At the same time, we concluded that vibrational energy has not completely dissipated out of the molecule at the maximum delay time we reached in this study (500 ps). In order to verify whether additional, slower reaction channels exist, we extend the study here to delay times up to 100 ns. At a temperature of 32 K, we indeed find an additional isomerization channel on a 2 ns timescale, which increases the total cis-->trans quantum yield to approximately 30%. The trans-->cis quantum yield is approximately 7%. There is still a discrepancy between the quantum yields we observe and the literature values, however, we provide experimental evidence that this discrepancy is due to the different temperatures of our study. Vibrational cooling occurs on a 20 ns time scale, and cascades in a highly nonstatistical manner through one single normal mode (most likely the ONO bending mode nu(5)). Intermolecular energy dissipation into the rare gas matrix is more efficient than intramolecular vibrational energy redistribution and the matrix environment can certainly not be considered a weak perturbation.

Journal Article↗

PubMed2006

Three-dimensional-IR spectroscopy: beyond the two-point frequency fluctuation correlation function.

Three-dimensional-IR spectroscopy is proposed as a new spectroscopic technique that is sensitive to three-point frequency fluctuation correlation functions. This will be important when the statistics of the underlying stochastic process is non-Gaussian, and hence when the system does not follow the linear response hypothesis. Furthermore, a very general classification of nonlinear spectroscopy in terms of higher order frequency fluctuation correlation functions is introduced, according to which certain moments of a multidimensional spectrum are related to certain frequency fluctuation correlation functions. The classification is rigorous in the so-called inhomogeneous limit, but remains valid approximately also when motional narrowing becomes important. The work also puts a recent paper [J. Bredenbeck et al., Phys. Rev. Lett. 95, 083201 (2005)] onto solid theoretical grounds, where we have shown for the first time that fifth-order spectroscopy--in this case transient two-dimensional spectroscopy--is indeed sensitive to the three-point frequency fluctuation correlation function.

Journal Article↗

PubMed2005

Solvation beyond the linear response regime.

Transient two-dimensional infrared spectroscopy (2D-IR) on a charge transfer model system is used as a nonlinear probe of solvation dynamics. Unlike what is expected in the linear response case, nonequilibrium relaxation and equilibrium spectral diffusion occur on different time scales. Transient 2D-IR spectroscopy is shown to be sensitive to higher order frequency fluctuation correlation functions, and provides evidence for a coupling between commonly observed fast and slow solvation processes.

Journal Article↗

PubMed2005

Active phase stabilization in Fourier-transform two-dimensional infrared spectroscopy.

A scheme for active phase stabilization and absolute positioning in Fourier-transform two-dimensional (2D) IR spectroscopy is presented. The position accuracy is better than 20 nm(rms) corresponding to lambda/250 at 5 microm, which significantly improves the quality of Fourier-transform 2D IR spectra. Phase stabilization is added to a standard photon echo setup in a way that does not impair the flexibility of the experiment and the control over IR pulse parameters.

Journal Article↗

PubMed2005

Restricted rotational motion of CO in a protein internal cavity: evidence for nonseparating correlation functions from IR pump-probe spectroscopy.

The strongly restricted orientational motion of CO molecules trapped in the Xe4 internal cavity of myoglobin mutant L29W-S108L is investigated by polarization-dependent mid-infrared pump-probe spectroscopy at cryogenic temperatures. Following an ultrafast initial decay, the signal anisotropy reaches an asymptotic value that is significantly larger than the prediction from the well-known relation [see text], based on previously established potential parameters. This discrepancy is explained by showing that the full four-point correlation function describing third-order spectroscopy [see text] does not factorize in systems where its fast decay is dominated by restricted reorientation of the transition dipole moments.

Animals↗

PubMed2005

Alpha-helix formation in a photoswitchable peptide tracked from picoseconds to microseconds by time-resolved IR spectroscopy.

Photo-triggered alpha-helix formation of a 16-residue peptide featuring a built-in conformational photoswitch is monitored by time-resolved IR spectroscopy. An experimental approach with 2-ps time resolution and a scanning range up to 30 micros is used to cover all time scales of the peptide dynamics. Experiments are carried out at different temperatures between 281 and 322 K. We observe single-exponential kinetics of the amide I' band at 322 K on a time scale comparable to a recent temperature-jump folding experiment. When lowering the temperature, the kinetics become slower and nonexponential. The transition is strongly activated. Spectrally dispersed IR measurements provide multiple spectroscopic probes simultaneously in one experiment by resolving the amide I' band, isotope-labeled amino acid residues, and side chains. We find differing relaxation dynamics at different spectral positions.

Amino Acid Sequence↗

PubMed2005

A femtosecond study of the infrared-driven cis-trans isomerization of nitrous acid (HONO).

We investigate the dynamics and mechanism of the IR-driven cis-trans isomerization of nitrous acid (HONO) in a low-temperature krypton matrix applying ultrafast time resolved IR spectroscopy. After excitation of the OH-stretching mode the trans HONO state decays biexponentially on a 8 and 260 ps time scale. The initially excited cis HONO state decays on a 20 ps time scale. Cis HONO isomerizes with 10% quantum yield on a 20 ps time scale to trans HONO. The quantum yield we observe is significantly smaller than the previously reported 100%, which could imply that additional, much slower reaction channels exist. We furthermore developed a four-dimensional model of the system, which includes the three proton intramolecular degrees of freedom of HONO fully quantum mechanically and one intermolecular translational degree of freedom of the molecule in the crystal cage. We find that cis-trans isomerization necessarily is accompanied by a translation of the molecule as a whole in the crystal cage. The translational degree of freedom tunes the intramolecular proton states of HONO with respect to each other. When resonances occur, the proton states might couple and transfer population. We suggest a possible reaction pathway, where the cis OH-stretch excited state first couples to a high cis torsional mode, which then may transfer almost instantaneously to the trans side. The model qualitatively explains all experimental observations.

Journal Article↗

PubMed2004

Double-resonance versus pulsed Fourier transform two-dimensional infrared spectroscopy: an experimental and theoretical comparison.

In this study we focus on the differences and analogies of two experimental implementations of two-dimensional infrared (2D-IR) spectroscopy: double-resonance or dynamic hole burning 2D-IR spectroscopy and pulsed Fourier transform or heterodyne detected photon echo spectroscopy. A comparison is done theoretically as well as experimentally by contrasting data obtained from both methods. As an example we have studied the strongly coupled asymmetric and symmetric carbonyl stretching vibrations of dicarbonylacetylacetonato rhodium dissolved in hexane. Both methods yield the same peaks in a 2D-IR spectrum. Within certain approximations we derive an analytic expression which shows that the 2D-IR spectra are broadened in one frequency dimension in the double-resonance experiment by convolution with the pump pulse spectral width, while the spectral resolution in the other frequency direction is the same in both cases.

Journal Article↗

PubMed2004

Transient two-dimensional infrared spectroscopy: exploring the polarization dependence.

We present a general expression for the polarization dependence of transient two-dimensional IR spectroscopy (T2D-IR), a technique designed to measure 2D-IR spectra of transient species. T2D-IR is a UV pump narrowband-IR-pump broadband-IR-probe experiment of fifth order in the laser field which involves up to three different transition dipole moments. The UV pulse adds an additional degree of freedom in polarization as compared to 2D-IR spectroscopy and increases the versatility of signal manipulation and the potential structural information content of the signals. The polarization conditions leading to a maximum of structural information are discussed. Important special cases of polarization conditions are formulated. The application of polarization selectivity is demonstrated for different types of T2D-IR experiments on photo triggered metal-to-ligand charge transfer in the model system [Re(CO)(3)(dmbpy)Cl].

Journal Article↗

PubMed2004

A fast photoswitch for minimally perturbed peptides: investigation of the trans-->cis photoisomerization of N-methylthioacetamide.

Thio amino acids can be integrated into the backbone of peptides without significantly perturbing their structure. In this contribution we use ultrafast infrared and visible spectroscopy as well as state-of-the-art ab initio computations to investigate the photoisomerization of the trans form of N-methylthioacetamide (NMTAA) as a model conformational photoswitch. Following the S2 excitation of trans-NMTAA in water, the return of the molecule into the trans ground state and the formation of the cis isomer is observed on a dual time scale, with a fast component of 8-9 ps and a slow time constant of approximately 250 ps. On both time scales the probability of isomerization to the cis form is found to be 30-40%, independently of excitation wavelength. Ab initio CASPT2//CASSCF photochemical reaction path calculations indicate that, in vacuo, the trans-->cis isomerization event takes place on the S1 and/or T1 triplet potential energy surfaces and is controlled by very small energy barriers, in agreement with the experimentally observed picosecond time scale. Furthermore, the calculations identify one S2/S1 and four nearly isoenergetic S1/S0 conical intersection decay channels. In line with the observed isomerization probability, only one of the S1/S0 conical intersections yields the cis conformation upon S1-->S0 decay. A substantially equivalent excited-state relaxation results from four T1/S0 intersystem crossing points.

Kinetics↗

PubMed2004

Labeling vibrations by light: ultrafast transient 2D-IR spectroscopy tracks vibrational modes during photoinduced charge transfer.

We report on a novel ultrafast two-dimensional infrared laser experiment that correlates vibrational bands of reactant and product of a photoreaction. The possibilities of this technique are demonstrated for the metal-to-ligand charge transfer (MLCT) in [Re(CO)3Cl(dmbpy)] (dmbpy = 4,4'-dimethyl-2,2'bipyridine) where we correlated the CO vibrational modes of the ground state and the MLCT state. A distinct vibrational mode is excited in the electronic ground state by an infrared laser pulse. This vibrational label survives the subsequent electronic excitation and can be followed in the excited electronic state. It is shown that the order of the vibrational energy levels is not preserved when exciting the molecule as was commonly assumed in the literature.

Journal Article↗

PubMed2004

Time-resolved visible and infrared study of the cyano complexes of myoglobin and of hemoglobin I from Lucina pectinata.

The dynamics of the ferric CN complexes of the heme proteins Myoglobin and Hemoglobin I from the clam Lucina pectinata upon Soret band excitation is monitored using infrared and broad band visible pump-probe spectroscopy. The transient response in the UV-vis spectral region does not depend on the heme pocket environment and is very similar to that known for ferrous proteins. The main feature is an instantaneous, broad, short-lived absorption signal that develops into a narrower red-shifted Soret band. Significant transient absorption is also observed in the 360-390 nm range. At all probe wavelengths the signal decays to zero with a longest time constant of 3.6 ps. The infrared data on MbCN reveal a bleaching of the C triple bond N stretch vibration of the heme-bound ligand, and the formation of a five-times weaker transient absorption band, 28 cm(-1) lower in energy, within the time resolution of the experiment. The MbC triple bond N stretch vibration provides a direct measure for the return of population to the ligated electronic (and vibrational) ground state with a 3-4 ps time constant. In addition, the CN-stretch frequency is sensitive to the excitation of low frequency heme modes, and yields independent information about vibrational cooling, which occurs on the same timescale.

Animals↗

PubMed2003

Picosecond conformational transition and equilibration of a cyclic peptide.

Ultrafast IR spectroscopy is used to monitor the nonequilibrium backbone dynamics of a cyclic peptide in the amide I vibrational range with picosecond time resolution. A conformational change is induced by means of a photoswitch integrated into the peptide backbone. Although the main conformational change of the backbone is completed after only 20 ps, the subsequent equilibration in the new region of conformational space continues for times >16 ns. Relaxation and equilibration processes of the peptide backbone occur on a discrete hierarchy of time scales. Albeit possessing only a few conformational degrees of freedom compared with a protein, the peptide behaves highly nontrivially and provides insights into the complexity of fast protein folding.

Peptides, Cyclic↗