Nonbonded Atomic Contacts Drive Ultrafast Helix Motions in Myoglobin

Application of simultaneous ultrasonic curing on pork (Longissimus dorsi): Mass transport of NaCl, physical characteristics, and microstructure

This study aimed to investigate the effect of ultrasound curing with various working modes and frequency combinations, including mono-, dual- and tri-frequency, on the content of NaCl and tenderness of pork loins (Longissimus dorsi). The physical qualities, myoglobin, moisture migration, distribution, and microstructure of pork were also evaluated. The results displayed that the NaCl content of samples cured by simultaneous ultrasound (100 W/L) working mode with a frequency combination of 20, 40, and 60 kHz was higher than that of other ultrasound working modes. The effect of ultrasonic brining was significantly better than the static curing when the saline solution was >35 mL. In addition, the samples cured by simultaneous ultrasound had better physical qualities, including more pickling absorptivity, less cooking loss, and lower hardness, tenderness, and chewiness value. The intensity of lightness was reduced, although redness and yellowness remained unaltered compared to static curing. The myoglobin content decreased drastically without changing the oxygenation level, and the relaxation time of T_2b and T₂₁ was delayed. The microstructure indicated that the ultrasonic treatment could promote changes in meat texture. Overall, the simultaneous ultrasound at various frequencies could efficiently accelerate NaCl penetration and improve pork quality.

Time-resolved spectroscopic mapping of vibrational energy flow in proteins: Understanding thermal diffusion at the nanoscale

Vibrational energy exchange between various degrees of freedom is critical to barrier-crossing processes in proteins. Hemeproteins are well suited for studying vibrational energy exchange in proteins because the heme group is an efficient photothermal converter. The released energy by heme following photoexcitation shows migration in a protein moiety on a picosecond timescale, which is observed using time-resolved ultraviolet resonance Raman spectroscopy. The anti-Stokes ultraviolet resonance Raman intensity of a tryptophan residue is an excellent probe for the vibrational energy in proteins, allowing the mapping of energy flow with the spatial resolution of a single amino acid residue. This Perspective provides an overview of studies on vibrational energy flow in proteins, including future perspectives for both methodologies and applications.

Contact-Mediated Retinal-Opsin Coupling Enables Proton Pumping in Gloeobacter Rhodopsin

When a chromophore embedded in a photoreceptive protein undergoes a reaction upon photoexcitation, the photoreaction triggers structural changes in the protein moiety that are necessary for the function of the protein. It is thus essential to elucidate the coupling between the chromophore and protein moiety to understand the functional mechanism for photoreceptive proteins, but the mechanism by which this coupling occurs remains poorly understood. Here, we show that nonbonded atomic contacts play an essential role in driving functionally important structural changes following photoisomerization of the chromophore in Gloeobacter rhodopsin (GR). Time-resolved ultraviolet resonance Raman spectroscopy revealed that the substitution of Trp222, which contacts with methyl groups of the retinal chromophore, with a Phe residue reduced the extent of structural change. The proton-pumping activity of the GR mutant was as small as 9% of that of the wild type. Time-resolved visible absorption and resonance Raman spectra showed that the photocycle of the mutant proceeded to the L intermediate following the all-trans to 13-cis photoisomerization step but did not result in the deprotonation of the chromophore. The present results demonstrate that the atomic contacts between the chromophore and the Trp222 side chain induce the structural changes necessary for proton transfer. The requirement for dense atomic packing in a protein structure for the efficient propagation of structural changes through a coupling mechanism is discussed.

Prediction of Allosteric Communication Pathways in Proteins

MOTIVATION

Allostery in proteins is an essential phenomenon in biological processes. In this paper, we present a computational model to predict paths of maximum information transfer between active and allosteric sites. In this information theoretic study, we use mutual information as the measure of information transfer, where transition probability of information from one residue to its contacting neighbors is proportional to the magnitude of mutual information between the two residues. Starting from a given residue and using a Hidden Markov Model, we successively determine the neighboring residues that eventually lead to a path of optimum information transfer. The Gaussian approximation of mutual information between residue pairs is adopted. The limits of validity of this approximation are discussed in terms of a nonlinear theory of mutual information and its reduction to the Gaussian form.

RESULTS

Predictions of the model are tested on six widely studied cases, CheY Bacterial Chemotaxis, B-cell Lymphoma extra-large Bcl-xL, Human proline isomerase cyclophilin A (CypA), Dihydrofolate reductase DHFR, HRas GTPase, and Caspase-1. The communication transmission rendering the propagation of local fluctuations from the active sites throughout the structure in multiple paths correlate well with the known experimental data. Distinct paths originating from the active site may likely represent a multi functionality such as involving more than one allosteric site and/or preexistence of some other functional states. Our model is computationally fast and simple, and can give allosteric communication pathways, which are crucial for the understanding and control of protein functionality.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Information Flow and Allosteric Communication in Proteins

Based on Schreiber's work on transfer entropy, a molecular theory of nonlinear information transfer in proteins is developed. The joint distribution function for residue fluctuations is expressed in terms of tensor Hermite polynomials which conveniently separate harmonic and nonlinear contributions to information transfer. The harmonic part of information transfer is expressed as the difference between time dependent and independent mutual information. Third order nonlinearities are discussed in detail. Amount and speed of information transfer between residues, important for understanding allosteric activity in proteins, are discussed. While mutual information shows the maximum amount of information that may be transferred between two residues, it does not explain the actual amount of transfer nor the transfer rate of information. For this, dynamic equations of the system are needed. The solution of the Langevin equation and molecular dynamics trajectories are used in the present work for this purpose. Allosteric communication in Human NAD-dependent isocitrate dehydrogenase is studied as an example. Calculations show that several paths contribute collectively to information transfer. Important residues on these paths are identified. Time resolved information transfer between these residues, their amplitudes and transfer rates, which are in agreement with time resolved ultraviolet resonance Raman measurements in general, are estimated. Estimated transfer rates are in the order of 1-20 megabits per second. Information transfer from third order contributions are one to two orders of magnitude smaller than the harmonic terms, showing that harmonic analysis is a good approximation to information transfer.

Concerted Motions and Molecular Function: What Physical Chemistry We Can Learn from Light-Driven Ion-Pumping Rhodopsins

Transmembrane ion gradients are generated and maintained by ion-pumping proteins in cells. Light-driven ion-pumping rhodopsins are retinal-containing proteins found in archaea, bacteria, and eukarya. Photoisomerization of the retinal chromophore induces structural changes in the protein, allowing the transport of ions in a particular direction. Understanding unidirectional ion transport by ion-pumping rhodopsins is an exciting challenge for biophysical chemistry. Concerted changes in ion-binding affinities of the ion-binding sites in proteins are key to unidirectional ion transport, as is the coupling between the chromophore and the protein moiety to drive the concerted motions regulating ion-binding affinities. The commonality of ion-pumping rhodopsin protein structures and the diversity of their ion-pumping functions suggest universal principles governing ion transport, which would be widely applicable to molecular systems. In this Perspective, I review the insights obtained from previous studies on rhodopsins and discuss future perspectives.

Changes in the structure and digestibility of myoglobin treated with sodium chloride

Myoglobin is a protein not easily broken down by digestive enzymes due to its rigid structure. This study evaluated the structural characteristics of myoglobin under various sodium chloride treatments (0.4-0.8 mol/L for 5-10 h) and the impacts on its digestibility using spectroscopic and molecular dynamics simulation techniques. Myoglobin digestibility was 40% following pepsin digestion and 60% after being sequentially digested by pepsin and trypsin. The α-helix content of myoglobin did not change significantly following sodium chloride treatment but hydrophobic amino acids were exposed and the binding of phenylalanine targeted by some digestive enzymes became more stable, leading to the reduced digestibility.