Protein Conformational Changes Research Articles

REVIEW ON PROTEIN FOOTPRINTING AS A TOOL IN STRUCTURAL BIOLOGY

Structural characterization of proteins is fundamental for understanding their functions and interactions within cellular environments. Protein footprinting has emerged as a powerful and versatile technique in structural biology, providing valuable insights into protein structure, dynamics, and conformational changes. This study comprehensively explores the principles, methodologies, and applications of protein footprinting as an indispensable tool in structural biology. Protein footprinting encompasses a range of innovative techniques, including hydroxyl radical footprinting, mass spectrometry-based footprinting, and chemical footprinting, each offering unique advantages for probing different aspects of protein structure. The study elucidates the underlying principles of these methods, discussing the mechanisms by which protein-footprinting agents interact with amino acid residues and elucidate structural details. The application of protein footprinting in studying protein-protein interactions, ligand binding, and conformational changes is highlighted through a detailed examination of key studies and experimental approaches. The review emphasizes the versatility of protein footprinting in investigating diverse protein systems, from small globular proteins to large multi-subunit complexes. Furthermore, the integration of protein footprinting with other structural biology techniques, such as X-ray crystallography, NMR spectroscopy, and cryo-electron microscopy, is explored to showcase the complementary nature of these approaches in achieving a comprehensive understanding of protein structure and function. The study addresses recent advancements and technological innovations in protein footprinting methodologies, including advancements in mass spectrometry instrumentation and data analysis strategies. Additionally, it discusses challenges associated with the technique, such as data interpretation and accessibility, and proposes future directions for overcoming these hurdles. Protein footprinting stands as a valuable tool in the structural biologist’s arsenal, providing unique perspectives on protein structure and dynamics. As the field continues to evolve, with ongoing refinements in methodologies and expanded applications, protein footprinting is poised to play a pivotal role in unraveling the complexities of biological macromolecules. This study serves as a comprehensive resource for researchers and practitioners seeking an in-depth understanding of protein footprinting and its contributions to advancing structural biology.

Identification of potential inhibitor molecule against MabA protein of Mycobacterium leprae by integrated in silico approach

Leprosy is one of the chronic diseases with which humanity has struggled globally for millennia. The potent anti-leprosy medications rifampicin, clofazimine and dapsone, among others, are used to treat leprosy. Nevertheless, even in regions of the world where these drugs have been successfully implemented, resistance continues to be observed. Due to the problems with the current treatments, this disease should be fought at every level of society with new drugs. The purpose of this research was to identify natural candidates with the ability to inhibit MabA (gene-fabG1) with fewer negative effects. The work was accomplished through molecular docking, followed by a dynamic investigation of protein-ligand, which play a significant role in the design of pharmaceuticals. After modelling the protein structure with MODELLER 9.21v, AutoDock Vina was used to perform molecular docking with 13 3 D anti-leprosy medicines and a zinc library to determine the optimal protein-ligand interaction. In addition, the docking result was filtered based on binding energy, ADMET characteristics, PASS analysis and the most crucial binding residues. The ZINC08101051 chemical compound was prioritized for further study. Using an all-atom 100 ns MD simulation, the binding pattern and conformational changes in protein upon ligand binding were studied. Recommendation for subsequent validation based on deviation, fluctuation, gyration and hydrogen bond analysis, followed by main component and free energy landscape. Communicated by Ramaswamy H. Sarma

Directed evolution of linker helix as an efficient strategy for engineering LysR-type transcriptional regulators as whole-cell biosensors

Whole-cell biosensors based on transcriptional regulators are powerful tools for rapid measurement, high-throughput screening, dynamic metabolic regulation, etc. To optimize the biosensing performance of transcriptional regulator, its effector-binding domain is commonly engineered. However, this strategy is encumbered by the limitation of diversifying such a large domain and the risk of affecting effector specificity. Molecular dynamics simulation of effector binding of LysG (an LysR-type transcriptional regulator, LTTR) suggests the crucial role of the short linker helix (LH) connecting effector- and DNA-binding domains in protein conformational change. Directed evolution of LH efficiently produced LysG variants with extended operational range and unaltered effector specificity. The whole-cell biosensor based on the best LysGE58V variant outperformed the wild-type LysG in enzyme high-throughput screening and dynamic regulation of l-lysine biosynthetic pathway. LH mutations are suggested to affect DNA binding and facilitate transcriptional activation upon effector binding. LH engineering was also successfully applied to optimize another LTTR BenM for biosensing. Since LTTRs represent the largest family of prokaryotic transcriptional regulators with highly conserved structures, LH engineering is an efficient and universal strategy for development and optimization of whole-cell biosensors.

Fourier Transform Infrared Spectroscopy Reveals Molecular Changes in Blood Vessels of Rats Treated with Pentadecapeptide BPC 157.

Recently, it was found that when confronted with major vessel occlusion and vascular failure, stable gastric pentadecapeptide BPC 157 therapy might rapidly functionally improve minor vessels to take over the function of disabled major vessels, reorganize blood flow, and compensate failed vessel function. We focused on the BPC 157 therapy effect obtained by giving 10 ng/kg ip to rats 5 min before sacrifice on the rat thoracic aorta, which we assessed with Fourier transform infrared spectroscopy (FTIR) 90 min thereafter. We applied a principal component analysis (PCA). The PCA model showed, with a clear distinction being mostly due to the PC1 score, differences between the spectra of BPC 157- and saline-treated rats. The comparison of the averaged spectra of these two groups with their differential spectrum and PC loadings allowed us to identify the parts of the FTIR spectra that contributed the most to the spectral separation of the two observed groups. The PC1 loadings and the differential spectrum showed that the main bands affecting the separation were the amid I band around 1650 cm-1, the amid II band around 1540 cm-1, and the vibrational band around 1744 cm-1. Fitting the spectral range between 1450 and 1800 cm-1 showed changes in protein conformation and confirmed the appearance of the vibrational band at 1744 cm-1. Controls had a substantially more intense vibrational band at 1744 cm-1. These spectral results showed the cells from saline-treated (control) rats to be in the early stage of cell death, while the samples from BPC 157-rats were protected. Thus, BPC 157 therapy changed the lipid contents and protein secondary structure conformation, with a rapid effect on vessels, within a short time upon application.

Computing committors via Mahalanobis diffusion maps with enhanced sampling data.

The study of phenomena such as protein folding and conformational changes in molecules is a central theme in chemical physics. Molecular dynamics (MD) simulation is the primary tool for the study of transition processes in biomolecules, but it is hampered by a huge timescale gap between the processes of interest and atomic vibrations that dictate the time step size. Therefore, it is imperative to combine MD simulations with other techniques in order to quantify the transition processes taking place on large timescales. In this work, the diffusion map with Mahalanobis kernel, a meshless approach for approximating the Backward Kolmogorov Operator (BKO) in collective variables, is upgraded to incorporate standard enhanced sampling techniques, such as metadynamics. The resulting algorithm, which we call the target measure Mahalanobis diffusion map (tm-mmap), is suitable for a moderate number of collective variables in which one can approximate the diffusion tensor and free energy. Imposing appropriate boundary conditions allows use of the approximated BKO to solve for the committor function and utilization of transition path theory to find the reactive current delineating the transition channels and the transition rate. The proposed algorithm, tm-mmap, is tested on the two-dimensional Moro-Cardin two-well system with position-dependent diffusion coefficient and on alanine dipeptide in two collective variables where the committor, the reactive current, and the transition rate are compared to those computed by the finite element method (FEM). Finally, tm-mmap is applied to alanine dipeptide in four collective variables where the use of finite elements is infeasible.

Molecular characterization of capsaicin binding interactions with ovalbumin and casein

Capsaicin (CAP) rich diets may help with a variety of human pathophysiological conditions; however, CAP administration is difficult due to its high pungency and limited water solubility. This study comprehensively explored the mechanism of CAP binding with ovalbumin (OVA) and casein (CAS) by multi-spectroscopic, thermodynamics, and molecular docking simulation at pH 7.4, as well as the prospect of employing these food proteins as CAP carriers. The findings demonstrated that CAP could interact with OVA/CAS and increase their fluorescence intensity, which was followed by specific protein conformational changes. According to the ITC data, the interaction between CAP and OVA/CAS proceeded spontaneously, with hydrogen bonding and hydrophobic interactions governing the binding process. The binding constant Ka for the CAP-OVA and CAP-CAS complexes was determined by ITC to be 1.07 ± 0.21 ⅹ 105 M−1 and 2.22 ± 0.14 ⅹ 105 M−1, respectively. Molecular docking analysis further indicated the existence of a high affinity CAP binding site on OVA and CAS, supporting the experimental findings. Moreover, the data demonstrated that CAP binding interactions with these proteins led to the formation of complexes with about 97% CAP encapsulation efficiency, contributing to a synergistic enhancement in their antioxidant activity. Therefore, this study implies that OVA and CAS have great potential for being utilized as edible delivery vehicles for lipophilic bioactive molecules such as CAP.

Oxidized cellulose nanofibrils-based surimi gel enhancing additives: Interactions, performance and mechanisms

Surimi-based products with preferred textural properties and high nutritional value are fashionable throughout the market. Enhancing surimi gel characteristics is of key importance for enabling the following processing and warranting the end-product quality, but challenging due to the lack of energy- and performance-efficient processes and the elusive mechanisms underpinned such enhancements. Focusing on enhancing surimi gel properties by introducing sustainable additives, we successfully explore functionalized cellulose nanofibrils as a textural enhancer in surimi gels and establish a new model to expound the interaction mechanisms. Firstly, TEMPO-mediated oxidation prior to homogenization harvests functionalized cellulose nanofibrils with unique fibrillary shape, uniform nano-size, high surface hydrophilicity and activated -COO - groups, highly suited for the additive use in surimi gels (Monto et al., 2021). Secondly, the innovative application of oxidized cellulose nanofibrils at a remarkably low concentrations (0.1 g/100 g surimi) greatly improve the whiteness, microstructure, water holding capacity, gel strength and thermal stability of the surimi gels, through a synergistic effect of matrix-reinforcing, water binding and entrapping, covalent interactions (disulfide bonds, amide bonds), non-covalent interactions (hydrogen bonds, ionic bonds) and favorable protein conformational changes within the network. Next, a new mechanism model toward the high-performance surimi gels is concluded to better elucidate the interactions between oxidized cellulose nanofibrils and myosin molecules. We expect that this work can provide guidelines on designing novel and high-quality cellulose-additive foods and understanding the roles of food additives in meat gel systems, for advancing the applications of new additives and gelation mechanisms in the food industry. • A low cellulose nanofibrils (TCN) addition (0.1%) greatly improves surimi gel properties. • Deliberately activated COO − groups at TCN surface facilitates cellulose-myosin interactions. • Improved water holding capacity due to surface hydrophicility, water binding and entrapping. • Enhanced gel strength due to newly introduced ionic bonds, hydrogen bonds and physical entanglement. • A new mechanism model illustrating cellulose-protein interactions is established.

Novel trehalose-based excipients for stabilizing nebulized anti-SARS-CoV-2 antibody

COVID-19 is caused by the infection of the lungs by SARS-CoV-2. Monoclonal antibodies, such as sotrovimab, showed great efficiency in neutralizing the virus before its internalization by lung epithelial cells. However, parenteral routes are still the preferred route of administration, even for local infections, which requires injection of high doses of antibody to reach efficacious concentrations in the lungs. Lung administration of antibodies would be more relevant requiring lower doses, thus reducing the costs and the side effects. But aerosolization of therapeutic proteins is very challenging, as the different processes available are harsh and trigger protein aggregation and conformational changes. This decreases the efficiency of the treatment, and can increase its immunogenicity.To address those issues, we developed a series of new excipients composed of a trehalose core, a succinyl side chain and a hydrophobic carbon chain (from 8 to 16 carbons). Succinylation increased the solubility of the excipients, allowing their use at relevant concentrations for protein stabilization. In particular, the excipient with 16 carbons (C16TreSuc) used at 5.6 mM was able to preserve colloidal stability and antigen-binding ability of sotrovimab during the nebulization process. It could also be used as a cryoprotectant, allowing storage of sotrovimab in a lyophilized form during weeks. Finally, we demonstrated that C16TreSuc could be used as an excipient to stabilize antibodies for the treatment against COVID-19, by in vitro and in vivo assays. The presence of C16TreSuc during nebulization preserved the neutralization capacity of sotrovimab against SARS-CoV-2 in vitro; an increase of its efficacy was even observed, compared to the non-nebulized control. The in vivo study also showed the wide distribution of sotrovimab in mice lungs, after nebulization with 5.6 mM of excipient.This work brings a solution to stabilize therapeutic proteins during storage and nebulization, making pulmonary immunotherapy possible in the treatment of COVID-19 and other lung diseases.

The recovery effect of Vitamin C on structural alterations due to Streptozotocin-Induced diabetes in rat testicular tissues

Type I Diabetes is a multisystem disease that causes alterations in carbohydrate, protein, and fat metabolisms due to hyperglycemia. It has an extensive pathology, especially the mechanism involving oxidative stress is still complex. Type I diabetes is correlated with increased formation of free radicals and decreased levels of antioxidant potential. Vitamin C (Vit C) is a powerful antioxidant that participates in antioxidant defense, protecting lipid membranes and proteins from oxidative damage by donating electrons to free radicals.The effect of type I diabetes and the recovery role of Vit C on the structure and composition of the biomolecular content of testicular tissue is still unknown. Therefore, the current study aimed to investigate the alterations in the biomolecules of rat testes due to Streptozotocin (STZ)-induced type I diabetes using Attenuated Total Reflectance (ATR)-Fourier Transform Infrared (FTIR) spectroscopy and histological staining. The results revealed that the biomolecular structure and composition of testicular tissue are highly affected due to the development of diabetes. We obtained decreased saturation levels and increased unsaturation index in the lipids indicating the presence of lipid peroxidation in the diabetic state. The elevated lipid peroxidation levels have been implicated in the pathogenesis of naturally occurring and chemically induced diabetes. On the other hand, the protein content of diabetic rat testicular tissue was shown to decrease considerably, indicating an increase in proteolysis processes. Supporting the ratio of protein structural and conformational change, protein secondary structural components were also found to alter substantially in the diabetic state. Diabetes was also shown to lead to a decrease in the content of nucleic acids compared to proteins. These diabetes-induced alterations were found to be substantially recovered with the administration of Vit C. Although different doses and administration types of Vit C have been reported in the literature, there is no consensus yet. Therefore, we used three different doses of Vit C in our study as high (100 mg/kg/day), medium (50 mg/kg/day) and low (15 mg/kg/day) doses intraperitoneally in the present study, and the medium dose was found to be the most effective in the recovery from the diabetes-induced structural damages on rat testicular tissue. Vit C may have a therapeutic effect to be used as a complementary therapy in the treatment of diabetes.

CSAlign and CSAlign-Dock: Structure alignment of ligands considering full flexibility and application to protein–ligand docking

Structure prediction of protein–ligand complexes, called protein–ligand docking, is a critical computational technique that can be used to understand the underlying principle behind the protein functions at the atomic level and to design new molecules regulating the functions. Protein-ligand docking methods have been employed in structure-based drug discovery for hit discovery and lead optimization. One of the important technical challenges in protein–ligand docking is to account for protein conformational changes induced by ligand binding. A small change such as a single side-chain rotation upon ligand binding can hinder accurate docking. Here we report an increase in docking performance achieved by structure alignment to known complex structures. First, a fully flexible compound-to-compound alignment method CSAlign is developed by global optimization of a shape score. Next, the alignment method is combined with a docking algorithm to dock a new ligand to a target protein when a reference protein–ligand complex structure is available. This alignment-based docking method, called CSAlign-Dock, showed superior performance to ab initio docking methods in cross-docking benchmark tests. Both CSAlign and CSAlign-Dock are freely available as a web server at https://galaxy.seoklab.org/csalign.

Adenylate Kinase-Catalyzed Reactions of AMP in Pieces: Specificity for Catalysis at the Nucleoside Activator and Dianion Catalytic Sites.

The pressure to optimize the enzymatic rate acceleration for adenylate kinase (AK)-catalyzed phosphoryl transfer has led to the evolution of an induced-fit mechanism, where the binding energy from interactions between the protein and substrate adenosyl group is utilized to drive a protein conformational change that activates the enzyme for catalysis. The adenine group of adenosine contributes 11.8 kcal mol-1 to the total ≥14.7 kcal mol-1 adenosine stabilization of the transition state for AK-catalyzed phosphoryl transfer to AMP. The relative third-order rate constants for activation of adenylate kinase, by the C-5 truncated adenosine 1-(β-d-erythrofuranosyl)adenine (EA), for catalysis of phosphoryl transfer from ATP to phosphite dianion (HP, kcat/KHPKAct = 260 M-2 s-1), fluorophosphate (47 M-2 s-1), and phosphate (9.6 M-2 s-1), show that substitution of -F for -H and of -OH for -H at HP results, respectively, in decreases in the reactivity of AK for catalysis of phosphoryl transfer due to polar and steric effects of the -F and -OH substituents. The addition of a 5'-CH2OH to the EA activator results in a 3.0 kcal mol-1 destabilization of the transition state for AK-activated phosphoryl transfer to HP due to a steric effect. This is smaller than the 8.3 kcal mol-1 steric effect of the 5'-CH2OH substituent at OMP on HP-activated OMPDC-catalyzed decarboxylation of 1-(β-d-erythrofuranosyl)orotate. The 2'-OH ribosyl substituent shows significant interactions with the transition states for AK-catalyzed phosphoryl transfer from ATP to AMP and for adenosine-activated AK-catalyzed phosphoryl transfer from ATP to HP.

Exploring the binding mechanism of pumpkin seed protein and apigenin: Spectroscopic analysis, molecular docking and molecular dynamics simulation

Apigenin is a vital flavonoid that has attracted considerable attention in recent years due to its potent health benefits. Pumpkin seed protein (PSP) is a valuable by-product after pumpkin seed processing. However, the non-covalent interaction mechanism between apigenin and PSP remains to be explored. Here, the structural and conformational changes and molecular mechanisms underlying their interaction were investigated using multi-spectroscopic analysis integrated with molecular simulation approaches. The experimental results indicated that apigenin statically quenched the intrinsic fluorescence of PSP, indicating that the interaction between them did occur. Thermodynamic analysis and computational simulation results showed that the driving forces between apigenin and PSP were the hydrophobic interactions that predominated. The binding of apigenin resulted in changes in the conformation, microenvironment, and surface hydrophobicity of PSP. Furthermore, it was revealed by molecular docking and molecular dynamic (MD) simulations that apigenin maintained binding stability in the hydrophobic pockets of the protein through its interaction with several key residues. Additionally, it was found that the movement strength and directions of individual resides were altered after apigenin binding, which is the molecular basis of protein structural and conformational changes induced by apigenin. This study may provide theoretical evidence for the potential application of PSP and apigenin complex products in the food industry.

Engineering a Conformationally Switchable Artificial Metalloprotein.

Many naturally occurring metalloenzymes are gated by rate-limiting conformational changes, and there exists a critical interplay between macroscopic structural rearrangements of the protein and subatomic changes affecting the electronic structure of embedded metallocofactors. Despite this connection, most artificial metalloproteins (ArMs) are prepared in structurally rigid protein hosts. To better model the natural mechanisms of metalloprotein reactivity, we have developed conformationally switchable ArMs (swArMs) that undergo a large-scale structural rearrangement upon allosteric effector binding. The swArMs reported here contain a Co(dmgH)2(X) cofactor (dmgH = dimethylglyoxime and X = N3-, H3C-, and iPr-). We used UV-vis absorbance and energy-dispersive X-ray fluorescence spectroscopies, along with protein assays, and mass spectrometry to show that these metallocofactors are installed site-specifically and stoichiometrically via direct Co-S cysteine ligation within the Escherichia coli glutamine binding protein (GlnBP). Structural characterization by single-crystal X-ray diffraction unveils the precise positioning and microenvironment of the metallocofactor within the protein fold. Fluorescence, circular dichroism, and infrared spectroscopies, along with isothermal titration calorimetry, reveal that allosteric Gln binding drives a large-scale protein conformational change. In swArMs containing a Co(dmgH)2(CH3) cofactor, we show that the protein stabilizes the otherwise labile Co-S bond relative to the free complex. Kinetics studies performed as a function of temperature and pH reveal that the protein conformational change accelerates this bond dissociation in a pH-dependent fashion. We present swArMs as a robust platform for investigating the interplay between allostery and metallocofactor regulation.

In silico and docking studies on the binding activities of Keap1 of antioxidant compounds in non-oilseed legumes

We used in silico methods to predict the physiochemical and pharmacological characteristics, toxicity, and biological activities of the screened compounds. All compounds showed positive results while calculating their physiochemical and pharmacokinetic descriptors. Using the Prediction of Activity Spectra for Substances (PASS) software on compounds form non-oilseed legumes, we identified compounds (mainly 4 polyphenol compounds) with anti-infective, anti-eczematic, antimutagenic, muco-membranous protector, fibrinolytic, anticarcinogenic, hepato-protectant, cardio-protectant, antioxidant, and astringent effect. PASS predicted HO-1 expression enhancing and free radical scavenging properties for gallic acid, coumaric acid, catechin, and epicatechin. Data about validation protocols for molecular docking of ligand IVV to Keap1 was performed by root mean square deviation (RMSD) value is used to validate docking protocol and representation mainly for analyzing stability of protein and predicting conformational changes of protein. Molecular docking is a powerful technique for studies of receptor-ligand interaction and has led to the discovery of Keap1-Nrf2 small molecule inhibitors. Keap1 inhibits the degradation of Nrf2. Our results suggest that screened compounds from non-oilseed legumes can effectively interact with the Keap1 binding site and dissociate Keap1 and Nrf2. The screened compounds from non-oilseed legumes that displayed high binding affinities with Keap1 are promising new Nrf2 activators. We performed molecular docking to identify the molecular interactions of gallic acid, catechin, and epicatechin with Keap1. Non-oilseed legumes plant is a natural source of potent antioxidant that may prevent diseases and could be potentially used as functional food, nutraceuticals, and drugs.

Cold-induced calreticulin OsCRT3 conformational changes promote OsCIPK7 binding and temperature sensing in rice.

Unusually low temperatures caused by global climate change adversely affect rice production. Sensing cold to trigger signal network is a key base for improvement of chilling tolerance trait. Here, we report that Oryza sativa Calreticulin 3 (OsCRT3) localized at the endoplasmic reticulum (ER) exhibits conformational changes under cold stress, thereby enhancing its interaction with CBL-interacting protein kinase 7 (OsCIPK7) to sense cold. Phenotypic analyses of OsCRT3 knock-out mutants and transgenic overexpression lines demonstrate that OsCRT3 is a positive regulator in chilling tolerance. OsCRT3 localizes at the ER and mediates increases in cytosolic calcium levels under cold stress. Notably, cold stress triggers secondary structural changes of OsCRT3 and enhances its binding affinity with OsCIPK7, which finally boosts its kinase activity. Moreover, Calcineurin B-like protein 7 (OsCBL7) and OsCBL8 interact with OsCIPK7 specifically on the plasma membrane. Taken together, our results thus identify a cold-sensing mechanism that simultaneously conveys cold-induced protein conformational change, enhances kinase activity, and Ca2+ signal generation to facilitate chilling tolerance in rice.

Structural dynamics of the N-terminal SH2 domain of PI3K in its free and CD28-bound states.

Protein conformational changes with fluctuations are fundamental aspects of protein-protein interactions (PPIs); understanding these motions is required for the rational design of PPI-regulating compounds. Src homology 2 (SH2) domains are commonly found in adapter proteins involved in signal transduction and specifically bind to consensus motifs of proteins containing phosphorylated tyrosine (pY). Here, we analysed the interaction between the N-terminal SH2 domain (nSH2) of the regulatory subunit in phosphoinositide 3-kinase (PI3K) and the cytoplasmic region of the T-cell co-receptor, CD28, using NMR and molecular dynamics (MD) simulations. First, we assigned the backbone signals of nSH2 on 1 H-15 N heteronuclear single quantum coherence spectra in the absence or presence of the CD28 phosphopeptide, SDpYMNMTPRRPG. Chemical shift perturbation experiments revealed allosteric changes at the BC loop and the C-terminal region of nSH2 upon CD28 binding. NMR relaxation experiments showed a conformational exchange associated with CD28 binding in these regions. The conformational stabilisation of the C-terminal region correlated with the regulation of PI3K catalytic function. Further, using 19 F- and 31 P-labelled CD28 phosphopeptide, we analysed the structural dynamics of CD28 and demonstrated that the aromatic ring of the pY residue fluctuated between multiple conformations upon nSH2 binding. Our MD simulations largely explained the NMR results and the structural dynamics of nSH2 and CD28 in both bound and unbound states. Notably, in addition to its major conformation, we detected a minor conformation of nSH2 in the CD28 bound state that may explain the allosteric conformational change in the BC loop.

The Effects of Ethanol and Rutin on the Structure and Gel Properties of Whey Protein Isolate and Related Mechanisms

The effects of different levels of rutin (0, 0.05%, 0.1%, 0.2% and 0.3% w/v) and ethanol on the structure and gel properties of whey protein isolate (WPI) were examined. The results showed that the addition of ethanol promoted the gel formation of WPI. The addition of rutin increased the gel strength of WPI and maintained the water-holding capacity of the gel. Ethanol caused an increase in thiol content and surface hydrophobicity, but rutin decreased the thiol content and surface hydrophobicity of WPI. The particle size, viscosity and viscoelasticity of WPI increased at rutin levels of 0.2% and 0.3%, indicating that rutin caused cross-linking and aggregation of WPI, but rutin had no significant effect on the zeta-potential, indicating that electrostatic interactions were not the main force causing the changes in protein conformation and gel properties. Ethanol and rutin improved the gel properties of WPI possibly by inducing cross-linking of WPIs via hydrophobic and covalent interactions.

Anxiolytic effect of YangshenDingzhi granules: Integrated network pharmacology and hippocampal metabolomics.

Anxiety disorder is one of the most common mental diseases. It is mainly characterized by a sudden, recurring but indescribable panic, fear, tension and/or anxiety. Yangshendingzhi granules (YSDZ) are widely used in the treatment of anxiety disorders, but its active ingredients and underlying mechanisms are not yet clear. This study integrates network pharmacology and metabolomics to investigate the potential mechanism of action of YSDZ in a rat model of anxiety. First, potential active ingredients and targets were screened by network pharmacology. Then, predictions were verified by molecular docking, molecular dynamics and western blotting. Metabolomics was used to identify differential metabolites and metabolic pathways. All results were integrated for a comprehensive analysis. Network pharmacology analysis found that Carotene, β-sitosterol, quercetin, Stigmasterol, and kaempferol in YSDZ exert anxiolytic effects mainly by acting on IL1β, GABRA1, PTGS1, ESR1, and TNF targets. Molecular docking results showed that all the affinities were lower than -5kcal/mol, and the average affinities were -7.7764kcal/mol. Molecular dynamics simulation results showed that RMSD was lower than 2.5 A, and the overall conformational changes of proteins were small, indicating that the small molecules formed stable complexes with proteins. The results of animal experiments showed that YSDZ exerts anxiolytic effects by regulating GABRA1 and TNF-α, ameliorating pathological damage in hippocampal CA1, and regulating metabolic pathways such as thiamine, cysteine and methionine metabolism, lysine biosynthesis and degradation. Altogether, we reveal multiple mechanisms through which YSDZ exerts its anti-anxiety effects, which may provide a reference for its clinical application and drug development.

Long-range allostery mediates the regulation of plasminogen activator inhibitor-1 by cell adhesion factor vitronectin

The serpin plasminogen activator inhibitor 1 (PAI-1) spontaneously undergoes a massive structural change from a metastable and active conformation, with a solvent-accessible reactive center loop (RCL), to a stable, inactive, or latent conformation, with the RCL inserted into the central β-sheet. Physiologically, conversion to the latent state is regulated by the binding of vitronectin, which hinders the latency transition rate approximately twofold. The molecular mechanisms leading to this rate change are unclear. Here, we investigated the effects of vitronectin on the PAI-1 latency transition using all-atom path sampling simulations in explicit solvent. In simulated latency transitions of free PAI-1, the RCL is quite mobile as is the gate, the region that impedes RCL access to the central β-sheet. This mobility allows the formation of a transient salt bridge that facilitates the transition; this finding rationalizes existing mutagenesis results. Vitronectin binding reduces RCL and gate mobility by allosterically rigidifying structural elements over 40Å away from the binding site, thus blocking transition to the latent conformation. The effects of vitronectin are propagated by a network of dynamically correlated residues including a number of conserved sites that were previously identified as important for PAI-1 stability. Simulations also revealed a transient pocket populated only in the vitronectin-bound state, corresponding to a cryptic drug-binding site identified by crystallography. Overall, these results shed new light on PAI-1 latency transition regulation by vitronectin and illustrate the potential of path sampling simulations for understanding functional protein conformational changes and for facilitating drug discovery.

Binary-FRET reveals transient excited-state structure associated with activity-dependent CaMKII - NR2B binding and adaptation

Synaptic functions are mediated and modulated by a coordinated choreography of protein conformational changes and interactions in response to intracellular calcium dynamics. Time-lapse Förster resonance energy transfer can be used to study the dynamics of both conformational changes and protein-protein interactions simultaneously under physiological conditions if two resonance energy transfer reactions can be multiplexed. Binary-FRET is a technique developed to independently monitor the dynamics of calcium-calmodulin dependent protein kinase-II catalytic-domain pair separation in the holoenzyme, and its role in establishing activity-dependent holoenzyme affinity for the NR2B binding fragment of the N-methyl-D-aspartate receptor. Here we show that a transient excited-state intermediate exists where paired catalytic-domains in the holoenzyme first separate prior to subsequent NR2B association. Additionally, at non-saturating free calcium concentrations, our multiplexed approach reveals that the holoenzyme exhibits a biochemical form of plasticity, calcium dependent adaptation of T-site ligand binding affinity.