Simulation of the Amide I Infrared Spectrum in Photoinduced Peptide Folding/Unfolding Transitions

Thermodynamic Evolution of a Metamorphic Protein: A Theoretical-Computational Study of Human Lymphotactin

Metamorphic, or fold-switching, proteins feature different folds that are physiologically relevant. The human chemokine XCL1 (or Lymphotactin) is a metamorphic protein that features two native states, an [Formula: see text] and an all[Formula: see text] fold, which have similar stability at physiological condition. Here, extended molecular dynamics (MD) simulations, principal component analysis of atomic fluctuations and thermodynamic modeling based on both the configurational volume and free energy landscape, are used to obtain a detailed characterization of the conformational thermodynamics of human Lymphotactin and of one of its ancestors (as was previously obtained by genetic reconstruction). Comparison of our computational results with the available experimental data show that the MD-based thermodynamics can explain the experimentally observed variation of the conformational equilibrium between the two proteins. In particular, our computational data provide an interpretation of the thermodynamic evolution in this protein, revealing the relevance of the configurational entropy and of the shape of the free energy landscape within the essential space (i.e., the space defined by the generalized internal coordinates providing the largest, typically non-Gaussian, structural fluctuations).

Evidence for a high pKa of an aspartic acid residue in the active site of CALB by a fully atomistic multiscale approach

Candida antarctica Lipase B (CALB) is a paradigm for the family of lipases. At pH 7, the optimal pH for catalysis, the protonation state of an aspartic acid of the active site (Asp134) could not be conclusively assigned. In fact, the pK_a estimate provided by a widely used computational tool, namely PropKa, that predicts pKa values of ionizable groups in proteins based on the crystallographic structure, is only slightly above 7 (pKa = 7.25). This, along with the lack of an experimental evaluation, makes the assignment of its protonation state at neutral pH challenging. Here, we calculate the pK_a of Asp134 by means of a fully atomistic multiscale computational approach based on classical molecular dynamics (MD) simulation and the perturbed matrix method (PMM), namely the MD-PMM approach. MD-PMM is able to take into account the dynamics of the system and, at the same time, to treat the deprotonation step at the quantum level. The calculations provide a pK_a value of 8.9 ± 1.1, hence suggesting that Asp134 in CALB should be protonated at neutral, and even at slightly basic, pH.

A computational insight into the relationship between side chain IR line shapes and local environment in fibril-like structures

Infrared spectroscopy is a widely used technique to characterize protein structures and protein mediated processes. While the amide I band provides information on proteins' secondary structure, amino acid side chains are used as infrared probes for the investigation of protein reactions and local properties. In this paper, we use a hybrid quantum mechanical/classical molecular dynamical approach based on the perturbed matrix method to compute the infrared band due to the C=O stretching mode of amide-containing side chains. We calculate, at first, the infrared band of zwitterionic glutamine in water and obtain results in very good agreement with the experimental data. Then, we compute the signal arising from glutamine side chains in a microcrystal of the yeast prion Sup35-derived peptide, GNNQQNY, with a fibrillar structure. The infrared bands obtained by selective isotopic labeling of the two glutamine residues, Q4 and Q5, of each peptide were experimentally used to investigate the local hydration in the fibrillar microcrystal. The experimental spectra of the two glutamine residues, which experience different hydration environments, feature different spectral signals that are well reproduced by the corresponding calculated spectra. In addition, the analysis of the simulated spectra clarifies the molecular origin of the experimentally observed spectroscopic differences that arise from the different local electric field experienced by the two glutamine residues, which is, in turn, determined by a different hydrogen bonding pattern.

Modeling amino-acid side chain infrared spectra: the case of carboxylic residues

Infrared (IR) spectroscopy is commonly utilized for the investigation of protein structures and protein-mediated processes.

Theoretical-computational modeling of charge transfer and intersystem crossing reactions in complex chemical systems

In this paper we present a theoretical-computational methodology specifically aimed at describing processes involving internal conversion or intersystem crossing, from atomistic (semiclassical) simulations and, hence, very suitable for treating complex atomic-molecular systems. The core of the presented approach is the evaluation of the diabatic perturbed energy surfaces of a portion of the whole system, treated at the quantum level and therefore preventively selected, in semi-classical interaction with the atomic-molecular environment. Subsequently, the estimation of the coupling between the diabatic surfaces and the inclusion of the obtained observables within a properly designed kinetic model allows the reconstruction of the whole phenomenology directly comparable to the experimental (typically kinetic) data. Application to two systems has demonstrated that the proposed approach can represent a valuable tool, somewhat complementary to other methods based on explicit quantum-dynamical approaches, for the theoretical-computational investigations of large and complex atomic-molecular systems.

On the nature of solvatochromic effect: The riboflavin absorption spectrum as a case study

We present here the calculation of the absorption spectrum of riboflavin in acetonitrile and dimethyl sulfoxide using a hybrid quantum/classical approach, namely the perturbed matrix method, based on quantum mechanical calculations and molecular dynamics simulations. The calculated spectra are compared to the absorption spectrum of riboflavin previously calculated in water and to the experimental spectra obtained in all three solvents. The experimentally observed variations in the absorption spectra upon change of the solvent environment are well reproduced by the calculated spectra. In addition, the nature of the excited states of riboflavin interacting with different solvents is investigated, showing that environment effects determine a recombination of the gas-phase electronic states and that such a recombination is strongly affected by the polarity of the solvent inducing significant changes in the absorption spectra.

Parallel folding pathways of Fip35 WW domain explained by infrared spectra and their computer simulation

We present a calculation of the amide I' infrared (IR) spectra of the folded, unfolded, and intermediate states of the WW domain Fip35, a model system for β-sheet folding. Using an all-atom molecular dynamics simulation in which multiple folding and unfolding events take place we identify six conformational states and then apply perturbed matrix method quantum-mechanical calculations to determine their amide I' IR spectra. Our analysis focuses on two states previously identified as Fip35 folding intermediates and suggests that a three-stranded core similar to the folded state core is the main source of the spectroscopic differences between the two intermediates. In particular, we propose a hypothesis for why folding via one of these intermediates was not experimentally observed by IR T-jump.

Influence of Glu/Arg, Asp/Arg, and Glu/Lys Salt Bridges on α-Helical Stability and Folding Kinetics

Using a combination of ultraviolet circular dichroism, temperature-jump transient-infrared spectroscopy, and molecular dynamics simulations, we investigate the effect of salt bridges between different types of charged amino-acid residue pairs on α-helix folding. We determine the stability and the folding and unfolding rates of 12 alanine-based α-helical peptides, each of which has a nearly identical composition containing three pairs of positively and negatively charged residues (either Glu(-)/Arg(+), Asp(-)/Arg(+), or Glu(-)/Lys(+)). Within each set of peptides, the distance and order of the oppositely charged residues in the peptide sequence differ, such that they have different capabilities of forming salt bridges. Our results indicate that stabilizing salt bridges (in which the interacting residues are spaced and ordered such that they favor helix formation) speed up α-helix formation by up to 50% and slow down the unfolding of the α-helix, whereas salt bridges with an unfavorable geometry have the opposite effect. Comparing the peptides with different types of charge pairs, we observe that salt bridges between side chains of Glu(-) and Arg(+) are most favorable for the speed of folding, probably because of the larger conformational space of the salt-bridging Glu(-)/Arg(+) rotamer pairs compared to Asp(-)/Arg(+) and Glu(-)/Lys(+). We speculate that the observed impact of salt bridges on the folding kinetics might explain why some proteins contain salt bridges that do not stabilize the final, folded conformation.

Prospects of high-resolution resonant X-ray inelastic scattering studies on solid materials, liquids and gases at diffraction-limited storage rings

The spectroscopic technique of resonant inelastic X-ray scattering (RIXS) will particularly profit from immensely improved brilliance of diffraction-limited storage rings (DLSRs). In RIXS one measures the intensities of excitations as a function of energy and momentum transfer. DLSRs will allow for pushing the achievable energy resolution, signal intensity and the sampled spot size to new limits. With RIXS one nowadays probes a broad range of electronic systems reaching from simple molecules to complex materials displaying phenomena like peculiar magnetism, two-dimensional electron gases, superconductivity, photovoltaic energy conversion and heterogeneous catalysis. In this article the types of improved RIXS studies that will become possible with X-ray beams from DLSRs are envisioned.