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Two photocleavable disulfide-bridged tetrapeptides [cyclo(Boc-Cys-Pro-Aib-Cys-OMe) and cyclo(Boc-Cys-Pro-Phe-Cys-OMe)] which provide insight into cyclic peptide dynamics are reported.

Observation of coherent vibrational dynamics in a hydrogen bond obtained by femtosecond nonlinear measurements in mid-infrared spectral range is reported. The result provide experimental evidence in the time domain for the anharmonic coupling of slow and fast vibrational motions in hydrogen bond.

Stimulated photon echo experiments were used to study the amide I band region of globular peptides, apamin and a cyclic pentapeptide.

The time-resolved femtosecond spectroscopy in conjunction with nonequilibrium molecular dynamics (MD) simulations was used to study the energy transport in a short helical peptide in chloroform solution. A simple harmonic model of heat transport adopted on the bases of results showed that the heat diffusivity decreased significantly at temperatures initially reached by high-energy excitation.

The potential of transient two-dimensional (2D) infrared spectroscopy is demonstrated to resolve the vibrational bands hidden in conventional pump-probe spectra of the thioxopeptide Boc-Ala-Gly([double bond]S)-Ala-Aib-OMe. Different types of transient cross-peak signals are seen and their information is discussed by comparing with model spectra.

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. Results support a mechanism by which isomerization takes place via one common intermediate state independent of electronic excitation energy and initial conformation.

Thio amino acids can be infused into the essence of peptides without excessively disturbing their structure. The photoisomerization of the trans form of N-methylthioacetamide as a model conformational photoswtich is examined.

Ultrafast two-dimensional infrared spectroscopy (2D-IR) is a promising tool to investigate molecular structure. The investigation of this conformational transition of a photoswitchable cyclic peptide by transient 2D-IR spectroscopy (T2D-IR) is done.

Transient 2D infrared (two-dimensional infrared), (T2D-IR), snapshots of the peptide ensemble taken during the transition from the cis to the trans configuration are presented. The results suggest that the homogenous to the total width of the amide-I band changes during the course of the conformational transition.

Ultrafast two-dimensional infrared spectroscopy (2D IR) has been advanced in recent years toward measuring signals from only a monolayer of sample molecules at solid-liquid and solid-gas interfaces. A series of experimental methods has been introduced, which in the chronological order of development are 2D sumfrequency-generation (2D SFG), transmission 2D IR, and reflection 2D IR, the latter in either internal, attenuated total reflection (ATR), or external reflection configuration. The different variants of 2D vibrational spectroscopy are based on either the even-order or the odd-order nonlinear susceptibility, and all allow resolving similar molecular temporal and spectral information. In this review, we introduce the basic principles of the different methods of 2D vibrational spectroscopy at surfaces along with a balanced overview on the technological aspects as well as benefits and shortcomings. We furthermore discuss the current scope of applications for 2D vibrational surface spectroscopy, which spans an impressively broad range of samples from biological molecules to heterogeneous catalysts. The emphasis is on the ultrafast structural dynamics of molecules at interfaces, environmental interactions, and intermolecular interactions. We furthermore consider important recent technological developments of 2D vibrational surface spectroscopy, which employ (i) surface enhancement, (ii) methods for studying electrochemical interfaces, and (iii) extensions for resolving nonequilibrium processes (transient 2D IR). A detailed outlook is finally given regarding important future applications and technological developments of 2D vibrational surface spectroscopy. [ABSTRACT FROM AUTHOR]

A study was conducted to analyze the utlrafast response of the modes in the 1600-1700 cm(super -1) region of N-methylacetamide and three small globular peptides. Femtosecond infrared pump probe and dynamic hole burning experiments were carried out to examine the ultrafast response. Experimental results indicated that population equilibration was slower than vibrational relaxation. Findings also showed that vibrational relaxation was faster on the low-frequency side than on the high-frequency side of the amide I band.

We present two-dimensional infrared (2D IR) spectra of the OD stretch vibration of isotope diluted water (HOD/H2O) from ambient conditions (293 K) down to the metastable supercooled regime (260 K). We observe that spectral diffusion slows down from 700 fs to 2.6 ps as we lower the temperature. A comparison between measurements performed at the magic angle with those at parallel polarization shows that the 2D IR line shape is affected by the frequency-dependent anisotropy decay in the case of parallel polarization, altering the extracted correlation decay. A fit within the framework of an Arrhenius law reveals an activation energy of Ea = 6.2 ± 0.2 kcal/mol and a pre-exponential factor of 1/A = 0.02 ± 0.01 fs. Alternatively, a power law fit results in an exponent γ = 2.2 and a singularity temperature Ts = 221 K. We tentatively conclude that the power law provides the better physical picture to describe the dynamics of liquid water around the freezing point. [ABSTRACT FROM AUTHOR]

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 ∼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. [ABSTRACT FROM AUTHOR]

Cyanobacteriochromes are bistable photoreceptor proteins with desirable photochemical properties for biotechnological applications, such as optogenetics or fluorescence microscopy. Here, we investigate Slr1393-g3, a cyanobacteriochrome that reversibly photoswitches between a red-absorbing (Pr) and green-absorbing (Pg) form. We applied advanced IR spectroscopic methods to track the sequence of intermediates during the photocycle over many orders of magnitude in time. In the conversion from Pg to Pr, we have revealed a new intermediate with distinct spectroscopic features in the IR, which precedes Pr formation using transient IR spectroscopy. In addition, stationary and transient 2D IR experiments measured the vibrational couplings between different groups of the chromophore and the protein in these intermediate states, as well as their structural disorder. Anharmonic QM/MM calculations predict spectra in good agreement with experimental 2D IR spectra of the initial and final states of the photocycle. They facilitate the assignment of the IR spectra that serve as a basis for the interpretation of the spectroscopic results and suggest structural changes of the intermediates along the photocycle.

The dynamics of peptide-protein binding and unbinding of a variant of the RNase S system has been investigated. To initiate the process, a photoswitchable azobenzene moiety has been covalently linked to the S-peptide, thereby switching its binding affinity to the S-protein. Transient fluorescence quenching was measured with the help of a time-resolved fluorometer, which has been specifically designed for these experiments and is based on inexpensive light-emitting diodes and laser diodes only. One mutant shows on-off behavior with no specific binding detectable in one of the states of the photoswitch. Unbinding is faster by at least 2 orders of magnitude, compared to that of other variants of the RNase S system. We conclude that unbinding is essentially barrier-less in that case, revealing the intrinsic dynamics of the unbinding event, which occurs on a time scale of a few hundred microseconds in a strongly stretched-exponential manner.

While much is known about different allosteric regulation mechanisms, the nature of the allosteric signal and the time scale on which it propagates remains elusive. The PDZ3 domain from postsynaptic density-95 protein is a small protein domain with a terminal third α-helix, i.e., the α3-helix, which is known to be allosterically active. By cross-linking the allosteric helix with an azobenzene moiety, we obtained a photocontrollable PDZ3 variant. Photoswitching triggers its allosteric transition, resulting in a change in binding affinity of a peptide to the remote binding pocket. Using time-resolved infrared and UV/vis spectroscopy, we follow the allosteric signal transduction and reconstruct the timeline in which the allosteric signal propagates through the protein within 200 ns.