Physical Chemistry Chemical Physics

High-flux and ultralow energy consumption transport of biological and artificial ion channels has been widely reported [1-22]. However, there is a precondition for such transport: Ultralow energy-consumption rapid ion dehydration; its mechanism is a remaining challenge. Here, we demonstrate that a K+ ion can transfer from the hydration water outside KcsA channel to the water bound in the channel without its hydration water accompanying, i.e., a tunneling-like motion, which provides a basis for the ultralow energy-consumption ion dehydration. In our molecular dynamics simulations, a KcsA channel was divided into three regions: Cavity-1, Cavity-2 and filter. As a hydrated K+ ion moves from Cavity-1 to Cavity-2, there occurs a resonant energy transfer to the ion from the filter-confined coherently oscillating ions, leading to a tunneling-like motion of the ion from the Cavity-1 water to Cavity-2 water with no hydration shell accompanying and no influence on the Cavity-2 water. As the hydrated K+ ion further moves from Cavity-2 to KcsA filter, the ion adjusts its hydration-shell water structure to coherence-resonantly couples with the filter-confined ions, leading to another tunneling-like ion motion to reach complete dehydration. Such two processes cause directionally rapid ion dehydration of KcsA channel, as a basis for the high flux of channel. Our findings provide an understanding of the dehydration dynamics in biological channels and its relationship with the high flux of ultralow energy-consumption, potentially promoting the development of artificial membranes design.

For the cofactor-free 1-H-3-hydroxy-4-oxoquinaldine-2,4-dioxygenase (HOD), the dioxygen (O2) dependent steps are rate-limiting along with a spin state crossover to the singlet spin state. Here, the primary triplet O2 molecule activation on the 2-methyl-3-hydroxy-4(1H)-quinolone (MHQ) is investigated, and the catalytic role of the intersystem crossing effects is highlighted by directly comparing results from the Born-Oppenheimer dynamics and non-adiabatic surface hopping dynamics. This work confirms non-adiabatic dynamical effects are essential to modulate the O2 activation on the substrate MHQ. The time scale of the equilibration and conversion from triplet to singlet state should be in the range of a few hundreds of femtoseconds. We hope this work provides us a fresh look at the underlying physics of dioxygen activation reactions involving more than one spin state.

The Breast Cancer Associated Protein 1 (BRCA1) is a human tumor suppressor protein that commonly functions as ubiquitin ligase enzyme (E3) in the ubiquitination of the C-terminal H2A. BRCA1 enhances ubiquitin ligase activity by forming a heterodimeric complex with the BRCA1 Associated Ring Domain Protein (BARD1). The BRCA1/BARD1 complex works in concert with the ubiquitin-conjugating enzyme (UbcH5c or E2) to ubiquitinate one of the five lysines of the H2A C-terminal, ultimately promoting the repair of double-stranded DNA breaks. The mutations in the BRCA1-UbcH5c portion of the E3-E2 complex have been linked to breast and ovarian cancer. However, the mechanism of BRCA1/BARD1-UbcH5c complex ubiquitination at H2A is poorly understood, and the ubiquitination of exact lysine is debated. In this study, we sought to expand on the current research on H2A ubiquitination by using all-atom molecular dynamics simulations to model the BRCA1/BARD1-UbcH5c complex with the human ubiquitin protein (Ub). The Ub protein covalently bonds to the active site of E2, resulting in diminished flexibility of the E3-E2 complex with respect to the nucleosome core particle. The results of this study suggest a possible contribution of H3 in determining the preferred orientation of E2-Ub with respect to the H2A C-terminal lysines.

Protein aggregate formations are essential processes to regulate biochemical networks in the cell, while anomalously formed aggregates such as amyloid fibrils cause serious neuronal diseases. It has been discussed for a quarter century that protein crowding milieus, such as micelle-like aggregates, promote the formation of growth nuclei, fibril-growth competent aggregates which trigger rapid growth of pathogenic amyloid fibrils, but the mechanisms are still elusive, in particular at microscopic level. In this study, we examined the long-standing problem by employing atomistic molecular dynamics simulations for amyloid {beta}(1-42) (A{beta}42), the paradigmatic amyloid-forming peptide. First, we constructed an atomistic model of A{beta}42 growth nuclei in A{beta}42 aggregate milieu, the pentameric A{beta}42 protomer dimer surrounded by 40 A{beta}42 monomers. Next, we simulated A{beta}42 monomer dissociation from the A{beta}42 growth nuclei and examined the effect of A{beta}42 aggregate milieu on the process. A{beta}42 aggregates spatially restrict A{beta}42 monomer dissociation pathways, while such spatial restriction itself does not significantly suppress A{beta}42 monomer dissociation from the growth nuclei. Rather, A{beta}42 aggregate milieus thermodynamically stabilize an A{beta}42 monomer binding to the growth edge by making atomic contacts with the monomer and contributes to stable formation of growth nuclei. A part of the aggregate milieu anchors dissociating monomer to the remaining part of growth nuclei, suggesting cooperative suppression of A{beta}42 monomer dissociation from A{beta}42 growth nuclei. Since the A{beta}42 aggregate milieu does not take a micelle-like configuration, we here discuss a new mechanism for stable formation of A{beta}42 growth nuclei in the presence of aggregate milieu.

Circadian rhythm by Cyanobacteria is one of the simplest biological clocks: the clock consists of only three proteins, KaiA, KaiB and KaiC. Their oligomers, KaiA dimer (A2), KaiB tetramer (B4) and KaiC hexamer (C6) oscillate an association- disassociation cycle with 24hr period. In a widely accepted model, the oscillation process is as follows. From the viewpoint of a base unit (C6), C6 homo-oligomer [->] A2C6 complex [->] B6C6 complex [->] AnB6C6 complex (n[≤]12) [->]C6 homo-oligomer. In this study, Small-Angle X-ray Scattering, Contrast Matching-Small-Angle Neutron Scattering, Analytical Ultracentrifuge and phosphorylation-analysis PAGE measurements were performed to reveal the kinetics not only of KaiC hexamer but also of all components in a working Kai clock. The complementary analysis disclosed that the oscillation is not the single process as the widely accepted model but composed with synchronized multiple association-dissociation reactions between components. Namely, there are various reactions between components, which proceed simultaneously, in a working Kai-clock.

The most common age-related neurodegenerative disorder, Alzheimers disease, is clinically characterized by continuous neuronal loss resulting in loss of memory and dementia with no cure to date. Amyloid-{beta} (A{beta}) aggregates and tau protein are believed to be the causative agents of this pathogenesis. In the present study, we have investigated the effect of the Pro-Drug peptide (PDp) and its metabolites (-aspartyl & {beta}-aspartyl) on the A{beta} aggregates using atomistic molecular dynamics simulations. One of the key findings in our work is in the presence of -aspartyl as a ligand, the salt bridges which hold the N-terminals together are completely disrupted, thus setting the N-terminals free and exposed entirely to the solvent which can make the aggregation of A{beta} less severe. The efficiency of the ligands, which are responsible for the disruption of A{beta}, depends on the alignment and strength of the repulsive interactions. Besides repulsive interactions, we found that there is a need for hydrogen bonding, which acts as a support for the ligand to stay in the vicinity of the aggregate. Moreover, we have noticed that one of the metabolites, namely {beta}-aspartyl, formed more hydrogen bonds with the aggregate than the other ligands and had a different mode of action with the chains of A{beta} due to its unique flexible kink in the backbone.

In this work, the combined influence of urea and KI on protein native structure is quantitatively investigated through the comparative molecular dynamics simulations on the structural dynamics of a polypeptide of TRPZIP4 in a series of urea/KI mixed solutions (urea concentration: 4M, KI salt concentration: 0M-6M). The observed enhanced denaturing ability of urea/KI mixture can be explained by direct interactions of urea/K+/water towards protein (electrostatic and vdW interactions from urea and electrostatic interactions from K+ and water) and indirect influence of KI on the strengthened interaction of urea towards protein backbone and side-chain. The latter indirect influence is fulfilled through the weakening of hydrogen bonding network among urea and water by the appearance of K+-water and I--urea interactions. As a result, the denaturing ability enhancement of urea and KI mixed solution is induced by the collaborative behavior of urea and KI salt.

Microbial rhodopsin, an important photoreceptor protein, has been widely used in several fields, such as optogenetics, biotechnology, and biodevices etc. However, current microbial rhodopsins are all transmembrane proteins, which both complicates the investigation on the photoreaction mechanism and limits their further applications. Therefore, a suitable mimic for microbial rhodopsin can not only provide a better model for understanding the mechanism, but also can extend the applications. The human protein CRABPII turns out to be a good template for design mimics on rhodopsin, due to the convenience in synthesis and the stability after mutations. Recently, Geiger et al. designed a new CRABPII-based mimic M1-L121E on microbial rhodopsin with the correct 13-cis (13C) isomerization after irritation. However, it still remains a question how similar it is compared with the natural microbial rhodopsin, in particular in the aspect of the photoreaction dynamics. In this article, we investigated the excited-state dynamics of this mimic by measuring its transient absorption spectra. Our results reveal that there are two components in the solution of mimic M1-L121E at PH=8, known as protonated Schiff base (PSB) and unprotonated Schiff base (USB) states. In both states, the photoreaction process from 13-cis (13C) to all-trans (AT) is faster than that from the inverse direction. In addition, the photoreaction process in PSB state is faster than that in the USB state. In the end, we compared the isomerization time of the PSB state with the properties of the microbial rhodopsin, and confirmed that the mimic M1-L121E indeed captures the main feature of the rhodopsin and is a good model of microbial rhodopsin in the photoreaction dynamics. However, our results also reveal significant differences in the excited-state dynamics of the mimic relative to the natural microbial rhodopsin, including the slower PSB isomerization rates in both 13C-AT and AT-13C directions, as well as the unusual USB photoreaction dynamics at PH=8. Such unique properties have not been observed in the natural rhodopsin, which could further deepen the understanding in photoreaction mechanism of the photosensitive proteins.

Molecular dynamics (MD) has become a popular simulation tool in recent years. However, its application is often limited by a timescale problem, due to its femtosecond-level integration timestep. To address this challenge, various enhanced sampling methods have been developed to accelerate system dynamics. Here, we introduce a novel enhanced sampling approach: Kinetically Accelerated Molecular Dynamics (KAMD). By combining the atomic-level accuracy of MD with the diffusive behavior of Brownian dynamics (BD), KAMD significantly improves sampling efficiency on domain/motif level while preserving equilibrium properties. We showed that KAMD is particularly effective in simulating two types of processes: large-scale conformational changes and ligand unbinding events.

The guanine exchange factor SOS1 is a crucial node into the positive feedback regulation of the KRAS signaling pathway. Currently, the regulation of KRAS-SOS1 interactions and KRAS downstream effector proteins has become a new hotspot in the development of KRAS-driven cancer therapies. However, the detailed dynamic mechanisms of SOS1-catalyzed GDP extraction and the impact of KRAS mutations remain unknown. Herein, the main mechanisms of GDP extraction from KRAS oncogenes by means of the guanine exchange factor SOS1 are disclosed and described with full details at the atomic-level. For GDP-bound wild-type KRAS, four amino acids (Lys811, Glu812, Lys939 and Glu942) responsible for the catalytic function of SOS1 were identified. With the occurrence of KRAS-G12D mutation, the GDP extraction rate is significantly increased. The molecular interactions behind this phenomenon have been subsequently identified being mainly hydrogen bonding interactions between the mutated residue Asp12 and a positively charged pocket located at the intrinsically disordered region807-818 and composed by Ser807, Trp809, Thr810 and Lys811. Our findings provide new insights into the SOS1-KRAS interactions and facilitate the development of related anti-cancer strategies based on the blockage of the above described mechanisms.

The functions of DNA and RNA rely on their deformations. When stretched, both DNA and RNA duplexes change their twist angles through twist-stretch coupling. The coupling is negative for DNA but positive for RNA, which is not yet completely understood. Here, our magnetic tweezers experiments show that the coupling of RNA reverses from positive to negative by multivalent cations. Combining with the previously reported tension-induced negative-to-positive coupling-reversal of DNA, we propose a unified mechanism of the couplings of both RNA and DNA based on molecular dynamics simulations. Two deformation pathways are competing when stretched: shrinking the radius causes positive couplings but widening the major groove causes negative couplings. For RNA whose major groove is clamped by multivalent cations and canonical DNA, their radii shrink when stretched, thus exhibiting positive couplings. For elongated DNA whose radius already shrinks to the minimum and canonical RNA, their major grooves are widened when stretched, thus exhibiting negative coupling.

Molecular switching plays a critical role in biological and displaying systems. Here we demonstrate the first use of peptides to operate molecular switches of donor-acceptor Stenhouse adducts (DASAs), a series of negative photochromes that are highly promising for applications ranging from smart material to biological systems. Fluorescence imaging proved A{beta}40 species could make SHA-2 more stable in the linear configuration than without peptide and decrease the rate of molecular switching. According to molecular dynamics simulation, SHA-2 bound to protein resulted in substantial changes in the tertiary structure of A{beta}40 monomer with the region of Glu22-Ala30 partially unfolded and being more exposed to water. This structural change is likely to impede the aggregation of A{beta}40, as evidenced by fluorescence and ProteoStat(R) aggresome detection experiments. SHA-2 is able to inhibit the aggregation of A{beta}40 by producing the off-pathway structures. These results open ample opportunities for optically addressable potential widely apply DASAs in the biological system based on this peptides-tailor process.

The dynamics of the aggregated light-harvesting complex (LHCII) associated with its antennae pigments can be crucial for a transition between light harvesting and dissipative states pivotal for non-photochemical quenching (NPQ). To this end, aggregation of chlorophyll-a (CLA) without the LHCII and pigment binding LHCII monomers in the plant thylakoid membranes have been investigated using coarse-grained molecular dynamics simulations at 293 K. Both CLA without the LHCII and pigment-binding LHCII monomers dynamically form and break dimers and higher-order aggregates in thylakoids within the simulation time. The contact lifetime and waiting time distributions of CLA dimers exhibit multiple time scales including most populated fast time scales and less populated slow time scales. The survival probability of CLA dimer in the absence of the LHCII follows a non-exponential decay with multiple residence time scales, leading to a time-dependent rate, unlike conventional rate theory. Such non-exponential decay of survival manifests the emergence of dynamic disorder in CLA without the LHCII resulting from the coupling between time scales of dimer formation and higher-order aggregates. The conformational fluctuations of the LHCII known for inter-CLA coupling variation occur on multiple time scales comparable to the LHCII dimer residence time scales leading to less probable but comparable and more probable slower inter-CLA fluctuations. This indicates the dynamic coupling in the LHCII conformations and their aggregates with the antennae pigments can result in dynamic disorder which will be highly relevant for the light-harvesting efficiency and regulation of NPQ. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/638782v1_ufig1.gif" ALT="Figure 1"> View larger version (57K): org.highwire.dtl.DTLVardef@5fd895org.highwire.dtl.DTLVardef@8456cforg.highwire.dtl.DTLVardef@5f5c69org.highwire.dtl.DTLVardef@abf6d0_HPS_FORMAT_FIGEXP M_FIG C_FIG

Proton circuits within biological membranes are at the heart of natural bioenergetic systems, whereas different biological membranes are characterized by different lipid compositions. In this study, we investigate how the composition of mixed lipid membranes influences the proton transfer (PT) properties of the membrane by following the excited-state PT (ESPT) process from a tethered probe to the membrane with time-scales and length-scales of PT that are relevant to bioenergetic systems. Two processes can happen during ESPT: the initial PT from the probe to the membrane at short timescales, followed by diffusion of dissociated protons around the probe on the membrane, and the possible geminate recombination with the probe at longer timescales. Here, we use membranes that are composed of mixtures of phosphatidylcholine (PC) and phosphatidic acid (PA). We show that the changes in the ESPT properties are not monotonous with the concentration of the lipid mixture; at low concentration of PA in PC, we find that the membrane is a poor proton acceptor. Molecular dynamics simulations indicate that at this certain lipid mixture, the membrane has the least defects (more structured and unflawed). Accordingly, we suggest that defects can be an important factor in facilitating PT. We further show that the composition of the membrane affects the geminate proton diffusion around the probe, whereas, on a time-scale of tens of nanoseconds, the dissociated proton is mostly lateral restricted to the membrane plane in PA membranes, while in PC, the diffusion is less restricted by the membrane.

Quasi-elastic neutron scattering (QENS) is a powerful technique to study protein dynamics. In general, QENS measurements are carried out in D2O solvent whereas functional studies of proteins are conducted in H2O solvent. Therefore, to link the QENS studies with the functional studies and then to understand the molecular basis of protein functions in detail, it is important to investigate the effects of solvent isotopic change on dynamical parameters obtained by QENS. For this purpose, in this study, MD simulations were carried out on hen egg white lysozyme, a well-folded and characterized protein, in H2O and in D2O. The dynamical parameters were extracted from the QENS spectra calculated from the MD trajectories. It was found that isotopic effects depend on energy resolutions and that at the energy resolutions that recent QENS studies often employ, the local dynamical behavior of proteins characterized in D2O more or less reflects that in H2O.

Zeaxanthin (Zea) is a key component in the energy-dependent, rapidly reversible, non-photochemical quenching process (qE) that regulates photosynthetic light harvesting. Previous transient absorption (TA) studies suggested that Zea can participate in direct quenching via Chlorophyll (Chl) to Zea energy transfer. However, the contamination of intrinsic exciton-exciton annihilation (EEA) makes the assignment of TA signal ambiguous. In this study, we present EEA-free TA data using Nicotiana benthamiana thylakoid membranes, including wild type and three NPQ mutants (npq1, npq4, and lut2) generated by CRISPR/Cas9 mutagenesis. Results show a strong correlation between excitation energy transfer from excited Chl Qy to Zea S1 and the xanthophyll cycle during qE activation. Notably, a Lut S1 signal is absent in the npq1 thylakoids which lack zeaxanthin. Additionally, the fifth-order response analysis shows a reduction in the exciton diffusion length (LD) from 55 {+/-} 5 nm to 38 {+/-} 3 nm under high light illumination, consistent with the reduced range of exciton motion being a key aspect of plants response to excess light.

Polyampholyte gel is a perfect physics model to mimic condensed state of proteins. We have studied the hierarchical dynamics of polyampholyte gels by dynamic light scattering. In addition to the normal gel mode, which indicates the gel elasticity, we also discovered a new mode with a stretched exponential decay with the stretched exponent {beta} = 1/3, and a diffusive exponential decay, which indicates the coupled motion between counterion and the polyampholyte backbone. After dialysis to low salt concentration, the coupled motion of the counterion will go away, so that there are only two modes. Combined with a newly developed theory, we attribute this stretched exponential mode to hierarchical dynamics of the segments between two crosslinking junctions, whose segmental distribution obeys Poisson distribution. As salt concentration inside the gel increases, {beta} decreases from 0.38 to 0.33, which is consistent with theoretical results. The gel with the molar charge ratio R=1, which is at the charge balance point, has the highest value {beta} = 0.38. As long as R deviates further away from the charge balance point from either side, the {beta} values decrease. When the gel is 100% positive charged, their dynamic light scattering results will go back to that of the normal polyelectrolyte gels.

Temozolomide is an efficient small-molecule drug mostly employed for the treatment of glioblastoma, a tumor attacking both the spinal cord and the brain. Understanding the interactions of temozolomide with different lipids at the brain cell membrane can help elucidate how temozolomide permeates through cell membranes and its membrane-crossing ability. In the present work, we have constructed a simplified brain plasma membrane model to explore temozolomides microscopic structure and dynamics by means of all-atom microsecond scale molecular dynamics simulations. The preferential location of temozolomide is at the solvent-aqueous fluid surrounding the brain membrane, but it can access the interface with the membrane regularly, eventually binding to lipids of the choline and cerebroside classes. The free energy barriers of temozolomide related to brain-like plasma membrane crossing were investigated by adaptive biasing force methods, revealing values ranging from 18.5 to 66.5 kcal/mol at temperatures of 323 K and 310 K, respectively. Our results suggest that temozolomide cannot cross the membrane by pure diffusion at the normal human body temperature but that rising the temperature significantly increases the probability of barrier crossing. This fact is mainly due to the crucial role played by cholesterol and lipids of the cerebroside class. The findings reported in this work can be used to optimize the molecular design of temozolomide and to develop new analogs with better pharmacokinetic properties. Author summaryGlioblastoma is a devastating tumor affecting the brain and spinal cord, which has in the FDA-approved drug temozolomide its main clinical treatment. The present study explores how temozolomide interacts with several lipids in brain-like cell membranes. Our findings show that at normal body temperature temozolomide cannot cross the membrane by pure diffusion, but that higher temperatures significantly enhance its ability to cross the membrane by reducing the free energy barriers. Temozolomide interacts differently with several lipids and sterols depending on the temperature, which affects its permeability. This implies that temozolomide will cross the outer layer of the brain membrane only with the help of driving agents, such as intermembrane proteins. Our research suggests that temozolomide may be more effective at higher temperatures and cancer patients with fever might need a lower dose. Importantly, cholesterol plays a key role in blocking temozolomide from crossing brain-like membranes, so reducing dietary intake of cholesterol and cerebroside lipids could help modify brain cell membranes, making it easier for temozolomide to target cancer cells effectively and potentially reducing side effects.

Respiratory viruses, carried through airborne microdroplets, frequently adhere to surfaces, including plastics and metals. However, our understanding of the interactions between viruses and materials remains limited, particularly in scenarios involving polarizable surfaces. Here, we investigate the role of receptor-binding domain (RBD) mutations on the adsorption of SARS-CoV-2 to hydrophobic and hydrophilic surfaces employing molecular simulations. To contextualize our findings, we contrast the interactions on inanimate surfaces with those on native-biological interfaces, specifically the ACE2 receptor. Notably, we identify a twofold increase in structural deformations for the proteins receptor binding motif onto the inanimate surfaces, indicative of enhanced shock-absorbing mechanisms. Furthermore, the distribution of amino acids (landing-footprints) on the inanimate surface reveals a distinct regional asymmetry relative to the biological interface. In spite of the H-bonds formed at the hydrophilic substrate, the simulations consistently show a higher number of contacts and interfacial area with the hydrophobic surface, with the WT RBD adsorbed more strongly than the delta or omicron RBDs. In contrast, the adsorption of delta and omicron to hydrophilic surfaces was characterized by a distinctive hopping-pattern. The novel shock-absorbing mechanisms identified in the virus adsorption on inanimate surfaces could lead current experimental efforts in the design of virucidal surfaces.

The extracellular lipid matrix in the stratum corneum (SC) is crucial for generating a skin barrier (permeability) function. The lipid matrix contains three major components; ceramides, cholesterol, and free fatty acids. The broad diversity of ceramides depends on their molecular structures (e.g., hydroxylations and chain lengths) and plays a critical role in maintaining the structural integrity of the lipid matrix. Although recent studies identified a new subclass of ceramide, 1-O-acylceramide NP (CerENP), its precise role in the lipid matrix of SC is still elusive. Herein, we investigate the role of CerENP on the structure and permeability of the SC by molecular dynamics simulations. Our results suggest that the CerENP molecules induce a denser lipid matrix in the lateral dimension in the long periodicity phase model with a bilayer-slab- bilayer structure. Moreover, ethanol permeability analysis indicates that CerENP can suppress molecular permeability through the lipid matrix. This study provides insight into the role of a new subclass of ceramide in the SC, which can lead to our better understanding of skin organization and disease-related barrier dysfunction.