Water follows polar and nonpolar protein surface domains

Using salted egg white in steamed bread: Impact on functional and structural characteristics

Steamed bread has long been an important part of Chinese cuisine. This study investigated the effects of salted egg white (SEW) (5, 10, 15, and 20% w/w) on the quality of steamed breads. Findings revealed that SEW notably enhanced the bread's volume and texture, with a 20% inclusion significantly boosting water retention and rheological properties, albeit reducing bread's lightness. In addition, the H-bond absorption band intensity in the Fourier transform infrared spectroscopy (FTIR) analysis showed increased peak intensities with higher SEW levels, indicative of protein structure alterations. X-ray diffraction confirmed the presence of an amylose-lipid complex. Scanning electron microscope (SEM) and Confocal laser scanning microscope (CLSM) imaging depicted a smooth, consistent protein network with SEW addition. Consumer sensory evaluation responded favourably to the SEW15 steamed bread, suggesting its potential for food industry application. Overall, the study considers SEW an effective ingredient for improving steamed bread quality.

Computation of Overhauser dynamic nuclear polarization processes reveals fundamental correlation between water dynamics, structure, and solvent restructuring entropy

Hydration water dynamics, structure, and thermodynamics are crucially important to understand and predict water-mediated properties at molecular interfaces. Yet experimentally and directly quantifying water behavior locally near interfaces at the sub-nanometer scale is challenging, especially at interfaces submerged in biological solutions. Overhauser dynamic nuclear polarization (ODNP) experiments measure equilibrium hydration water dynamics within 8-15 angstroms of a nitroxide spin probe on instantaneous timescales (10 picoseconds to nanoseconds), making ODNP a powerful tool for probing local water dynamics in the vicinity of the spin probe. As with other spectroscopic techniques, concurrent computational analysis is necessary to gain access to detailed molecular level information about the dynamic, structural, and thermodynamic properties of water from experimental ODNP data. We chose a model system that can systematically tune the dynamics of water, a water-glycerol mixture with compositions ranging from 0 to 0.3 mole fraction glycerol. We demonstrate the ability of molecular dynamics (MD) simulations to compute ODNP spectroscopic quantities, and show that translational, rotational, and hydrogen bonding dynamics of hydration water align strongly with spectroscopic ODNP parameters. Moreover, MD simulations show tight correlations between the dynamic properties of water that ODNP captures and the structural and thermodynamic behavior of water. Hence, experimental ODNP readouts of varying water dynamics suggest changes in local structural and thermodynamic hydration water properties.

Protein Interface Regulating the Inserting Process of Imidazole Ionic Liquids into the Cell Membrane

Ionic liquids (ILs) have shown promising potential in membrane protein extraction; however, the underlying mechanism remains unclear. Herein, we employed GPU-accelerated molecular dynamics (MD) simulations to investigate the dynamic insertion process of ILs into cell membranes containing membrane proteins. Our findings reveal that ILs spontaneously insert into the membrane, and the presence of membrane proteins significantly decelerates the rate of IL insertion into the membrane. Specifically, the relationship between the insertion rate and inserting free energy exhibits non-monotonic changes, which can be attributed to interfacial effects. The protein-water interface acts as trap for free ions and ionic clusters, while free ions preferentially insert into the membrane from the protein-lipid interface, which limits the insertion rate due to its narrowness. Thus, the insertion rate is governed by a combination of the free energy and interfacial effects. These findings provide valuable insights into the interfacial effects of protein-lipid bilayers and have implications for various biochemical-related applications.

Controlled adsorption of multiple bioactive proteins enables targeted mast cell nanotherapy

Protein adsorption onto nanomaterials often results in denaturation and loss of bioactivity. Controlling the adsorption process to maintain the protein structure and function has potential for a range of applications. Here we report that self-assembled poly(propylene sulfone) (PPSU) nanoparticles support the controlled formation of multicomponent enzyme and antibody coatings and maintain their bioactivity. Simulations indicate that hydrophobic patches on protein surfaces induce a site-specific dipole relaxation of PPSU assemblies to non-covalently anchor the proteins without disrupting the protein hydrogen bonding or structure. As a proof of concept, a nanotherapy employing multiple mast-cell-targeted antibodies for preventing anaphylaxis is demonstrated in a humanized mouse model. PPSU nanoparticles displaying an optimized ratio of co-adsorbed anti-Siglec-6 and anti-FcεRIα antibodies effectively inhibit mast cell activation and degranulation, preventing anaphylaxis. Protein immobilization on PPSU surfaces provides a simple and rapid platform for the development of targeted protein nanomedicines.

Deciphering the structure of a distinctive trimodular cellulosomal licheninase (RfGH16_21), a family 16 glycoside hydrolase from Ruminococcus flavefaciens by computational and experimental methods

In order to know the insights of a unique naturally existing trimodular licheninase from GH16 family, sub-family 21 (RfGH16_21) from Ruminococcus flavefaciens, its structure was modeled to understand its functional relations to reveal information regarding modifying the enzyme for improved properties with enhanced catalytic efficiency. Homology modeling revealed three tandem repeats of β-jelly roll like folds linked by natural linkers. Catalytic pockets and the catalytically important amino acids in each tandem repeat of RfGH16_21 determined by multiple sequence alignment and structure superposition with its homologues indicated that two Glu residues are involved in a retaining-type of catalytic mechanism. Sequential molecular docking revealed maximum binding energy with mixed linked cellotriose showing that cellotriose is the lowest oligomeric hydrolysed product formed by the catalytic action of endo-β-1,3-1,4-glucanase. Molecular dynamic (MD) simulation of RfGH16_21-cellotriose complex confirmed the structural specificity of catalytic residues and increased stability of enzyme in presence of ligand as compared to simulated RfGH16_21 alone. The binding affinity of cellotriose towards the three tandem repeats of RfGH16_21 was also confirmed by calculating total binding Gibbs free energy, i.e. -100.8 ± 2.6 KJ/mol, by using g_mmpbsa tool. The stability of the protein was determined by protein melting analysis that showed Ca2+ and Mg2+ ions imparted structural stability to RfGH16_21. Dynamic light scattering analysis of RfGH16_21 showed monodispersity and hydrodynamic radius of 4.0 nm at 2.0 mg/mL protein concentration, which was comparable with the radius of gyration of 3.2 nm determined by MD simulation showing the protein to be in monomeric form.Communicated by Ramaswamy H. Sarma.

Transformations in crystals of DNA-functionalized nanoparticles by electrolytes

Colloidal crystals have applications in water treatments, including water purification and desalination technologies. It is, therefore, important to understand the interactions between colloids as a function of electrolyte concentration. We study the assembly of DNA-grafted gold nanoparticles immersed in concentrated electrolyte solutions. Increasing the concentration of divalent Ca2+ ions leads to the condensation of nanoparticles into face-centered-cubic (FCC) crystals at low electrolyte concentrations. As the electrolyte concentration increases, the system undergoes a phase change to body-centered-cubic (BCC) crystals. This phase change occurs as the interparticle distance decreases. Molecular dynamics analysis suggests that the interparticle interactions change from strongly repulsive to short-range attractive as the divalent-electrolyte concentration increases. A thermodynamic analysis suggests that increasing the salt concentration leads to significant dehydration of the nanoparticle environment. We conjecture that the intercolloid attractive interactions and dehydrated states favour the BCC structure. Our results gain insight into salting out of colloids such as proteins as the concentration of salt increases in the solution.

The 75-99 C-Terminal Peptide of URG7 Protein Promotes α-Synuclein Disaggregation

Up Regulation Gene seven (URG7) is the pseudogene 2 of the transporter ABCC6. The translated URG7 protein is localized with its single transmembrane α-helix in the endoplasmic reticulum (ER) membrane, orienting the N- and C-terminal regions in the lumen and cytoplasm, respectively, and it plays a crucial role in the folding of ER proteins. Previously, the C-terminal region of URG7 (PU, residues 75-99) has been shown to modify the aggregation state of α-synuclein in the lysate of HepG2 cells. PU analogs were synthesized, and their anti-aggregation potential was tested in vitro on α-synuclein obtained using recombinant DNA technology. Circular dichroism (CD), differential scanning calorimetry (DSC), Fourier-transform infrared (FTIR) spectroscopy, and microscopic techniques were used to assess the sample's behavior. The results show that the peptides studied by themselves are prone to clathrate-like structure formation of variable stability. Aggregation of α-synuclein is accompanied by desolvation of its peptide chain and an increase in intermolecular β-sheets. The PU analogs all interact with α-synuclein aggregates and those possessing the most stable clathrate-like structures have the highest disaggregating effect. These findings suggest that the C-terminal region of URG7 may have a role in interacting and modulating α-synuclein structures and could be used to generate interesting therapeutic candidates as disaggregators of α-synuclein.

D-Ring Modifications of Tetracyclines Determine Their Ability to Induce Resistance Genes in the Environment

The widespread utilization of tetracyclines (TCs) in agriculture and medicine has led to the borderless spread of tetracycline resistance in humans, animals, and the environment, posing huge risks to both the ecosystem and human society. Changes in the functional group modifications resulted in a higher bacteriostatic efficacy of the new generation of TCs, but their effect on the emergence and evolution of antibiotic resistance genes (ARGs) is not yet known. To this end, four TCs from three generations were chosen to compare their structural effects on influencing the evolution of ARGs in soil microbial communities. The findings revealed that low-generation TCs, such as tetracycline and oxytetracycline, exhibited a greater propensity to stimulate the production and proliferation of ARGs than did high-generation tigecycline. Molecular docking analysis demonstrated that modifications of the D-ring functional group determined the binding capacity of TCs to the substrate-binding pocket of transcriptional regulators and efflux pumps mainly involved in drug resistance. This can be further evidenced by reverse transcription-quantitative polymerase chain reaction quantification and intracellular antibiotic accumulation assessment. This study sheds light on the mechanism of the structural effect of antibiotic-induced ARG production from the perspective of compound-protein binding, therefore providing theoretical support for controlling the dissemination of antibiotic resistance.

Role of Exchange Cations and Layer Charge on the Dynamics of Confined Water

Describing the dynamic behavior of water confined in clay minerals is a fascinating challenge and crucial in many research areas, ranging from materials science and geotechnical engineering to environmental sustainability. Water is the most abundant resource on Earth, and the high reactivity of naturally occurring hydrous clay minerals used since prehistoric times for a variety of applications means that water-clay interaction is a ubiquitous phenomenon in nature. We have attempted to experimentally distinguish the rotational dynamics and translational diffusion of two distinct populations of interlayer water, confined and ultraconfined, in the sodium (Na) forms of two smectite clay minerals, montmorillonite (Mt) and hectorite (Ht). Samples hydrated at a pseudo one-layer hydration (1LH) state under ambient conditions were studied with quasi-elastic neutron scattering (QENS) between 150 and 300 K. Using a simplified revised jump-diffusion and rotation-diffusion model (srJRM), we observed that while interlayer water near the ditrigonal cavity in Ht forms strong H-bonds to both adjacent surface O and structural OH, H-bonding of other more prevalent interlayer water with the surface O is weaker compared to Mt, inducing a higher temperature for dynamical changes of confined water. Given the lower layer charge and faster dynamics observed for Ht compared to Mt, we consider this strong evidence confirming the influence of the interlayer cation and surfaces on confined water dynamics.

Corner Engineering: Tailoring Enzymes for Enhanced Resistance and Thermostability in Deep Eutectic Solvents

Deep eutectic solvents (DESs), heralded for their synthesis simplicity, economic viability, and reduced volatility and flammability, have found increasing application in biocatalysis. However, challenges persist due to a frequent diminution in enzyme activity and stability. Herein, we developed a general protein engineering strategy, termed corner engineering, to acquire DES-resistant and thermostable enzymes via precise tailoring of the transition region in enzyme structure. Employing Bacillus subtilis lipase A (BSLA) as a model, we delineated the engineering process, yielding five multi-DESs resistant variants with highly improved thermostability, such as K88E/N89 K exhibited up to a 10.0-fold catalytic efficiency (kcat /KM ) increase in 30 % (v/v) choline chloride (ChCl): acetamide and 4.1-fold in 95 % (v/v) ChCl: ethylene glycol accompanying 6.7-fold thermal resistance improvement than wild type at ≈50 °C. The generality of the optimized approach was validated by two extra industrial enzymes, endo-β-1,4-glucanase PvCel5A (used for biofuel production) and esterase Bs2Est (used for plastics degradation). The molecular investigations revealed that increased water molecules at substrate binding cleft and finetuned helix formation at the corner region are two dominant determinants governing elevated resistance and thermostability. This study, coupling corner engineering with obtained molecular insights, illuminates enzyme-DES interaction patterns and fosters the rational design of more DES-resistant and thermostable enzymes in biocatalysis and biotransformation.

Osmolyte induced protein stabilization: modulation of associated water dynamics might be a key factor

The mechanism of protein stabilization by osmolytes remains one of the most important and long-standing puzzles. The traditional explanation of osmolyte-induced stability through the preferential exclusion of osmolytes from the protein surface has been seriously challenged by the observations like the concentration-dependent reversal of osmolyte-induced stabilization/destabilization. The more modern explanation of protein stabilization/destabilization by osmolytes considers an indirect effect due to osmolyte-induced distortion of the water structure. It provides a general mechanism, but there are numerous examples of protein-specific effects, i.e., a particular osmolyte might stabilize one protein, but destabilize the other, that could not be rationalized through such an explanation. Herein, we hypothesized that osmolyte-induced modulation of associated water might be a critical factor in controlling protein stability in such a medium. Taking different osmolytes and papain as a protein, we proved that our proposal could explain protein stability in osmolyte media. Stabilizing osmolytes rigidify associated water structures around the protein, whereas destabilizing osmolytes make them flexible. The strong correlation between the stability and the associated water dynamics, and the fact that such dynamics are very much protein specific, established the importance of considering the modulation of associated water structures in explaining the osmolyte-induced stabilization/destabilization of proteins. More interestingly, we took another protein, bromelain, for which a traditionally stabilizing osmolyte, sucrose, acts as a stabilizer at higher concentrations but as a destabilizer at lower concentrations. Our proposal successfully explains such observations, which is probably impossible by any known mechanisms. We believe this report will trigger much research in this area.

Equilibria in the aqueous system of cobalt(II) based on 2-picolinehydroxamic acid and N-(2-hydroxybenzyl)phenylalanine and its ability to inhibit the propagation of cancer cells

Mixed-ligand complexes of cobalt(II) with two bioligands, viz. 2-picolinehydroxamic acid and the reduced Schiff base N-(2-hydroxybenzyl)phenylalanine, were studied in aqueous solution by potentiometry and UV-Vis spectroscopic analysis. The coordination mode of the complexes and their stability were determined and compared to their parent species. Stacking interactions between the rings present in the ligands influence the stability of the complexes. Also, UV-Vis spectroscopy revealed that the stacking interactions affected the intercalation of DNA and mixed-ligand complexes. The in vitro anticancer activity of the free ligand 2-picolinehydroxamic acid and the complexes was tested against cervical and gastric human adenocarcinoma epithelial cell lines. At concentrations of 0.06 and 0.11 mM, the mixed-ligand structures showed the ability to reduce gastric cancer cells with no inhibitory effect on mouse fibroblasts. The cytotoxic effect was accompanied by damage to the cell nuclei, which may confirm that the complexes demonstrate effective binding to DNA. No determination of minimal inhibitory and bactericidal/fungicidal concentrations against the test organisms was possible at higher complex concentrations due to precipitation.

Raman Fingerprints of SARS-CoV-2 Omicron Subvariants: Molecular Roots of Virological Characteristics and Evolutionary Directions

The latest RNA genomic mutation of SARS-CoV-2 virus, termed the Omicron variant, has generated a stream of highly contagious and antibody-resistant strains, which in turn led to classifying Omicron as a variant of concern. We systematically collected Raman spectra from six Omicron subvariants available in Japan (i.e., BA.1.18, BA.2, BA.4, BA.5, XE, and BA.2.75) and applied machine-learning algorithms to decrypt their structural characteristics at the molecular scale. Unique Raman fingerprints of sulfur-containing amino acid rotamers, RNA purines and pyrimidines, tyrosine phenol ring configurations, and secondary protein structures clearly differentiated the six Omicron subvariants. These spectral characteristics, which were linked to infectiousness, transmissibility, and propensity for immune evasion, revealed evolutionary motifs to be compared with the outputs of genomic studies. The availability of a Raman "metabolomic snapshot", which was then translated into a barcode to enable a prompt subvariant identification, opened the way to rationalize in real-time SARS-CoV-2 activity and variability. As a proof of concept, we applied the Raman barcode procedure to a nasal swab sample retrieved from a SARS-CoV-2 patient and identified its Omicron subvariant by coupling a commercially available magnetic bead technology with our newly developed Raman analyses.

Low-Entropy Hydration Shells at the Spike RBD's Binding Site May Reveal the Contagiousness of SARS-CoV-2 Variants

The infectivity of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is primarily determined by the binding affinity between the receptor-binding domain (RBD) of the spike protein and the angiotensin-converting enzyme 2 (ACE2) receptor. Here, through screening off pseudo hydrophilic groups on protein surfaces, the distribution of low-entropy regions on hydration shells of the ACE2 receptor and the RBDs of multiple SARS-CoV-2 variants was demonstrated. Shape matching between the low-entropy hydration shells of multiple SARS-CoV-2 variants and the ACE2 receptor has been identified as a mechanism that drives hydrophobic attraction between the RBDs and the ACE2 receptor, which estimates the binding affinity. Low-entropy regions of the hydration shells, which play important roles in determining the binding of other viruses and their receptors, are demonstrated. The RBD-ACE2 binding is thus found to be guided by hydrophobic collapse between the shape-matched low-entropy regions of the hydration shells of the proteins. A measure of the low-entropy status of the hydration shells can be estimated by calculating genuine hydrophilic groups within the binding sites. An important indicator of the contagiousness of SARS-CoV-2 variants is the low-entropy level of its hydration shells at the spike protein binding site.

Biochemical characterisation of a novel broad pH spectrum subtilisin from Fictibacillus arsenicus DSM 15822T

Subtilisins from microbial sources, especially from the Bacillaceae family, are of particular interest for biotechnological applications and serve the currently growing enzyme market as efficient and novel biocatalysts. Biotechnological applications include use in detergents, cosmetics, leather processing, wastewater treatment and pharmaceuticals. To identify a possible candidate for the enzyme market, here we cloned the gene of the subtilisin SPFA from Fictibacillus arsenicus DSM 15822T (obtained through a data mining-based search) and expressed it in Bacillus subtilis DB104. After production and purification, the protease showed a molecular mass of 27.57 kDa and a pI of 5.8. SPFA displayed hydrolytic activity at a temperature optimum of 80 °C and a very broad pH optimum between 8.5 and 11.5, with high activity up to pH 12.5. SPFA displayed no NaCl dependence but a high NaCl tolerance, with decreasing activity up to concentrations of 5 m NaCl. The stability enhanced with increasing NaCl concentration. Based on its substrate preference for 10 synthetic peptide 4-nitroanilide substrates with three or four amino acids and its phylogenetic classification, SPFA can be assigned to the subgroup of true subtilisins. Moreover, SPFA exhibited high tolerance to 5% (w/v) SDS and 5% H2 O2 (v/v). The biochemical properties of SPFA, especially its tolerance of remarkably high pH, SDS and H2 O2 , suggest it has potential for biotechnological applications.

The role of glycerol-water mixtures in the stability of FKBP12-rapalog-FRB complexes

The thermodynamic and biophysical implications of the introduction of a co-solvent during protein-ligand binding remain elusive. Using ternary complexes of 12-kDa FK506 binding protein (FKBP12), FKBP-rapamycin binding (FRB) domain of the mammalian/mechanistic target of rapamycin (mTOR) kinase, and rapamycin analogs (rapalogs) in glycerol-water mixtures, the influence of solvent composition on ligand binding dynamics was explored. The pharmaceutical potential of rapalogs and the utility of glycerol as a co-solvent in drug delivery applications were critical in deciding the system to be studied. Consolidation of existing studies on rapamycin modification was first performed to strategically design a new rapalog called T1. The results from 100-ns dual-boost Gaussian accelerated molecular dynamics simulations showed that protein stability was induced in the presence of glycerol. Reweighting of the trajectories revealed that the glycerol-rich solvent system lowers the energy barrier in the conformational space of the protein while also preserving native contacts between the ligand and the residues in the binding site. Calculated binding free energies using MM/GBSA also showed that electrostatic energy and polar contribution of solvation energy are heavily influenced by the changes in solvation. Glycerol molecules are preferentially excluded through electrostatic interactions from the solvation shell which induce complex stability as seen in existing experiments. Hence, using glycerol as a co-solvent in rapamycin delivery has a significant role in maintaining stability. In addition, compound T1 is a potential mTORC1-selective inhibitor with strong affinity for the FKBP12-FRB complex. This study aims to provide insights on the design of new rapalogs, and the applicability of glycerol as co-solvent for FKBP12-rapalog-FRB complexes.

P176S Mutation Rewires Electrostatic Interactions That Alter Maspin Functionality

Maspin is known to regress tumors by inhibiting angiogenesis; however, its roles have been reported to be context- and sequence-dependent. Various proteins and cofactors bind to maspin, possibly explaining its conflicting roles. Moreover, polymorphic forms of maspin have also been linked to tumor regression and survival; for instance, maspin with Ser at 176 (maspin-S176) promotes tumors, while maspin with Pro at 176 (maspin-P176) has opposing roles in cancer pathogenesis. With the help of long molecular dynamics simulations, a possible link between polymorphic forms and tumor progression has been established. First, maspin is dynamically stable with either amino acid at the 176 position. Second, differential contacts have been observed among various regions; third, these contacts have significantly altered the electrostatic energetics of various residues; finally, these altered electrostatics of maspin-S176 and maspin-P176 rewire the polar contacts that abolished the allosteric control of the protein. By combining these factors, the altered electrostatics substantially affect the localization and preference of maspin-binding partners, thus culminating in a different maspin-protein(cofactor)-interaction landscape that may have been manifested in previous conflicting reports. Here, the underlying reason has been highlighted and discussed, which may be helpful for better therapeutic manipulation.

Solvation thermodynamics from cavity shapes of amino acids

According to common physical chemistry wisdom, the solvent cavities hosting a solute are tightly sewn around it, practically coinciding with its van der Waals surface. Solvation entropy is primarily determined by the surface and the volume of the cavity while enthalpy is determined by the solute-solvent interaction. In this work, we challenge this picture, demonstrating by molecular dynamics simulations that the cavities surrounding the 20 amino acids deviate significantly from the molecular surface. Strikingly, the shape of the cavity alone can be used to predict the solvation free energy, entropy, enthalpy, and hydrophobicity. Solute-solvent interactions involving the different chemical moieties of the amino acid, determine indirectly the cavity shape, and the properties of the branches but do not have to be taken explicitly into account in the prediction model.

Spatial Layouts of Low-Entropy Hydration Shells Guide Protein Binding

Protein-protein binding enables orderly biological self-organization and is therefore considered a miracle of nature. Protein‒protein binding is driven by electrostatic forces, hydrogen bonding, van der Waals force, and hydrophobic interactions. Among these physical forces, only hydrophobic interactions can be considered long-range intermolecular attractions between proteins due to the electrostatic shielding of surrounding water molecules. Low-entropy hydration shells around proteins drive hydrophobic attraction among them that essentially coordinate protein‒protein binding. Here, an innovative method is developed for identifying low-entropy regions of hydration shells of proteins by screening off pseudohydrophilic groups on protein surfaces and revealing that large low-entropy regions of the hydration shells typically cover the binding sites of individual proteins. According to an analysis of determined protein complex structures, shape matching between a large low-entropy hydration shell region of a protein and that of its partner at the binding sites is revealed as a universal law. Protein‒protein binding is thus found to be mainly guided by hydrophobic collapse between the shape-matched low-entropy hydration shells that is verified by bioinformatics analyses of hundreds of structures of protein complexes, which cover four test systems. A simple algorithm is proposed to accurately predict protein binding sites.

Hofmeister Series: From Aqueous Solution of Biomolecules to Single Cells and Nanovesicles

Hofmeister effects play a critical role in numerous physicochemical and biological phenomena, including the solubility and/or accumulation of proteins, the activities of enzymes, ion transport in biochannels, the structure of lipid bilayers, and the dynamics of vesicle opening and exocytosis. This minireview focuses on how ionic specificity affects the physicochemical properties of biomolecules to regulate cellular exocytosis, vesicular content, and nanovesicle opening. We summarize recent progress in further understanding Hofmeister effects on biomacromolecules and their applications in biological systems. These important steps have increased our understanding of the Hofmeister effects on cellular exocytosis, vesicular content, and nanovesicle opening. Increasing evidence is firmly establishing that the ions along the Hofmeister series play an important role in living organisms that has often been ignored.

Structural features of interfacial water predict the hydrophobicity of chemically heterogeneous surfaces

The hydrophobicity of an interface determines the magnitude of hydrophobic interactions that drive numerous biological and industrial processes. Chemically heterogeneous interfaces are abundant in these contexts; examples include the surfaces of proteins, functionalized nanomaterials, and polymeric materials. While the hydrophobicity of nonpolar solutes can be predicted and related to the structure of interfacial water molecules, predicting the hydrophobicity of chemically heterogeneous interfaces remains a challenge because of the complex, non-additive contributions to hydrophobicity that depend on the chemical identity and nanoscale spatial arrangements of polar and nonpolar groups. In this work, we utilize atomistic molecular dynamics simulations in conjunction with enhanced sampling and data-centric analysis techniques to quantitatively relate changes in interfacial water structure to the hydration free energy (a thermodynamically well-defined descriptor of hydrophobicity) of chemically heterogeneous interfaces. We analyze a large data set of 58 self-assembled monolayers (SAMs) composed of ligands with nonpolar and polar end groups of different chemical identity (amine, amide, and hydroxyl) in five mole fractions, two spatial patterns, and with scaled partial charges. We find that only five features of interfacial water structure are required to accurately predict hydration free energies. Examination of these features reveals mechanistic insights into the interfacial hydrogen bonding behaviors that distinguish different surface compositions and patterns. This analysis also identifies the probability of highly coordinated water structures as a unique signature of hydrophobicity. These insights provide a physical basis to understand the hydrophobicity of chemically heterogeneous interfaces and connect hydrophobicity to experimentally accessible perturbations of interfacial water structure.

Equilibria of complexes in the aqueous cobalt(II)-N-(2-hydroxybenzyl)phenylalanine system and their biological activity compared to analogous Schiff base structures

Due to their excellent prospects in biological applications, Schiff bases and their complexes are a source of continuing interest. The present study examines the formation of four cobalt(II) complexes with the reduced Schiff base N-(2-hydroxybenzyl)phenylalanine (PhAlaSal) in alkaline aqueous solution by pH-metry. UV-Vis and ESI-MS studies confirmed the model of proposed species. Kinetic analysis indicated that the single- and bi-ligand cobalt(II) complexes transitioned from octahedral to tetrahedral structures. The Schiff base and its complexes detected under physiological pH were tested for antimicrobial abilities and compared with analogous structures of the Schiff base derivative, N-(2-hydroxybenzyl)alanine (AlaSal). The ability of these structures to influence cell growth was tested on L929 mouse fibroblasts and on cervix and gastric adenocarcinoma cancer cell lines. N-(2-hydroxybenzyl)phenylalanine demonstrates greater antimicrobial efficacy than N-(2-hydroxybenzyl)alanine but also higher cytotoxicity; however, it is nonetheless effective against cancer cells. In turn, AlaSal demonstrates low cytotoxicity for fibroblasts and high cytotoxicity for gastric adenocarcinoma epithelial cells at bacteriostatic concentration for Helicobacter pylori and Candida strains. The presence of these microorganisms in the gastric milieu supports the development of gastritis and gastric cancer; AlaSal therapy may be simultaneously effective against both. Due to their cytotoxicity, Schiff base complexes are not suitable for use against fungal and bacterial infections, but may effectively prevent cancer cell growth.

Data availability

Data will be made available on request.

Bioactive multi-protein adsorption enables targeted mast cell nanotherapy

Proteins readily and often irreversibly adsorb to nanomaterial surfaces, resulting in denaturation and loss of bioactivity1,2. Controlling this process to preserve protein structure and function has remained an elusive goal that would enhance the fabrication and biocompatibility of protein-based bioactive nanomaterials3-7. Here, we demonstrate that poly(propylene sulfone) (PPSU)8 nanoparticles support the controlled formation of multi-component enzyme and antibody coatings while maintaining their bioactivity. Simulations indicate that hydrophobic patches9 on protein surfaces induce site-specific dipole relaxation on PPSU surfaces to noncovalently anchor proteins without disrupting hydrogen bonding or protein structure. As proof-of-concept, a nanotherapy for enhanced antibody-based targeting of mast cells and inhibition of anaphylaxis3,4 is demonstrated in a humanized mouse model. The ratio of co-adsorbed anti-Siglec-610,11 and anti-FcεRIα antibodies is systematically optimized to effectively inhibit mast cell activation and degranulation. Protein immobilization on PPSU surfaces therefore provides a simple and rapid platform for the development of targeted nanomedicines.

Regulation of the Inevitable Water-Responsivity of Silk Fibroin Biopolymer by Polar Amino Acid Activation

In nature, water is vital for maintaining homeostasis. Particularly, organisms (e.g., plant leaf, bird feather) exploit water fluidics for motions. Hydration-adaptive crystallization is the representative water-responsive actuation of biopolymers. This crystallization has inspired the development of intelligent human-robot interfaces. At the same time, it hinders the consistent adhesion of tissue adhesive. As hydration-adaptive crystallization is inevitable, the on-demand control of crystallization is desirable in the innovative biopolymeric biomedical systems. To this end, this study developed an amino acid-based technology to artificially up- or down-regulate the inevitable crystallization of silk fibroin. A case II diffusion model was constructed, and it revealed that the activity of polar amino acid is related to crystallization kinetics. Furthermore, the water dynamics study suggested that active amino acid stabilizes crystallization-triggering water molecules. As a proof-of-concept, we verified that a 30% increase in the activity of serine resulted in a 50% decrease in the crystallization rate. Furthermore, the active amino acid-based suppression of hydration-adaptive crystallization enabled the silk fibroin to keep its robust adhesion (approximately 160 kJ m^-3) by reducing the water-induced loss of adhesive force. The proposed silk fibroin was demonstrated as a stable tissue adhesive applied on ex vivo porcine mandible tissue. This amino acid-based regulation of hydration-adaptive crystallization will pioneer next-generation biopolymer-based healthcare.

Identification of novel biallelic variants in BMP15 in two siblings with premature ovarian insufficiency

BACKGROUND

Premature ovarian insufficiency (POI) occurs in women before the age of 40 years, accompanied by amenorrhea, hypoestrogenism, hypergonadotropinism, and infertility. The pathology of POI is complex and the molecular genetic mechanisms are poorly understood. Bone morphogenetic protein 15 (BMP15) plays a crucial role in oocyte maturation and follicular development through the activation of granulosa cells. Dysfunction of BMP15 causes ovarian dysgenesis and is related to POI. Identifying pathogenic variants contributes to revealing genetic mechanisms and making clinical diagnoses of POI.

METHODS

The study involved two sisters diagnosed with POI. Whole-exome sequencing (WES) was performed to identify causative genes. Sanger sequencing was used to validate the mutations in patients with POI and members of the family with no clinical signs or symptoms. The effect of the novel mutations on the BMP15 structure was analyzed by PSIPRED. By over-expressing wild-type (WT) or mutant BMP15 plasmids in vitro, a functional study of the BMP15 mutant was conducted by real-time qPCR and western blotting. Through cocultivation with HEK293T cells, the effects of secreted BMP15 WT and variants on granulosa cell proliferation and apoptosis were detected through a cell counting kit-8 assay and flow cytometric analysis.

RESULTS

We identified biallelic variants in BMP15, c.791G > A (p. R264Q) and c.1076C > T (p. P359L), in two siblings with POI. Both sisters carried the same biallelic variants, while the other female members of their family carried only one of them. Structural prediction showed that the variants have not affected the secondary structure of BMP15 but may change the conformation of water molecules around protein surfaces and thermal stability of BMP15. Real-time qPCR showed no significant difference in mRNA levels among WT and the two variants. Western blotting indicated a reduction in BMP15 expression with the c.791G > A and c.1076C > T variants compared to WT. Moreover, mutants 791G > A and 1076C > T impaired the function of secreted BMP15 in promoting granulosa cell proliferation and suppressing cell apoptosis caused by reactive oxygen species.

CONCLUSIONS

This study identified novel biallelic variants, c.791G > A and c.1076C > T, of BMP15 in two siblings with POI. Both missense variants reduced the level of the BMP15 protein and impaired the function of BMP15 in promoting granulosa cell proliferation in vitro. Taken together, our findings provide a novel molecular genetic basis and potential pathogenesis of BMP15 variants in POI.

The Role of Surface Chemistry in the Orientational Behavior of Water at an Interface

Molecular dynamics studies have demonstrated that molecular water at an interface, with either a gas or a solid, displays anisotropic orientational behavior in contrast to its bulk counterpart. This effect has been recently implicated in the like-charge attraction problem for colloidal particles in solution. Here, negatively charged particles in solution display a long-ranged attraction where continuum electrostatic theory predicts monotonically repulsive interactions, particularly in solutions with monovalent salt ions at low ionic strength. Anisotropic orientational behavior of solvent molecules at an interface gives rise to an excess interfacial electrical potential which we suggest generates an additional solvation contribution to the total free energy that is traditionally overlooked in continuum descriptions of interparticle interactions in solution. In the present investigation we perform molecular dynamics simulation based calculations of the interfacial potential using realistic surface models representing various chemistries as well as different solvents. Similar to previous work that focused on simple model surfaces constructed by using oxygen atoms, we find that solvents at more realistic model surfaces exhibit substantial anisotropic orientational behavior. We explore the dependence of the interfacial solvation potential on surface properties such as surface group chemistry and group density at silica and carboxylated polystyrene interfaces. For water, we note surprisingly good agreement between results obtained for a simple O-atom wall and more complex surface models, suggesting a general qualitative consistency of the interfacial solvation effect for surfaces in contact with water. In contrast, for an aprotic solvent such as DMSO, surface chemistry appears to exert a stronger influence on the sign and magnitude of the interfacial solvation potential. The study carries broad implications for molecular-scale interactions and may find relevance in explaining a range of phenomena in soft-matter physics and cell biology.

Exonic splicing code and protein binding sites for calcium

Auxilliary splicing sequences in exons, known as enhancers (ESEs) and silencers (ESSs), have been subject to strong selection pressures at the RNA and protein level. The protein component of this splicing code is substantial, recently estimated at ∼50% of the total information within ESEs, but remains poorly understood. The ESE/ESS profiles were previously associated with the Irving-Williams (I-W) stability series for divalent metals, suggesting that the ESE/ESS evolution was shaped by metal binding sites. Here, we have examined splicing activities of exonic sequences that encode protein binding sites for Ca2+, a weak binder in the I-W affinity order. We found that predicted exon inclusion levels for the EF-hand motifs and for Ca2+-binding residues in nonEF-hand proteins were higher than for average exons. For canonical EF-hands, the increase was centred on the EF-hand chelation loop and, in particular, on Ca2+-coordinating residues, with a 1>12>3∼5>9 hierarchy in the 12-codon loop consensus and usage bias at codons 1 and 12. The same hierarchy but a lower increase was observed for noncanonical EF-hands, except for S100 proteins. EF-hand loops preferentially accumulated exon splits in two clusters, one located in their N-terminal halves and the other around codon 12. Using splicing assays and published crosslinking and immunoprecipitation data, we identify candidate trans-acting factors that preferentially bind conserved GA-rich motifs encoding negatively charged amino acids in the loops. Together, these data provide evidence for the high capacity of codons for Ca2+-coordinating residues to be retained in mature transcripts, facilitating their exon-level expansion during eukaryotic evolution.

Polar Substitutions on the Surface of a Lipase Substantially Improve Tolerance in Organic Solvents

Biocatalysis in organic solvents (OSs) enables more efficient routes to the synthesis of various valuable chemicals. However, OSs often reduce enzymatic activity, which limits the use of enzymes in OSs. Herein, we report a comprehensive understanding of interactions between surface polar substitutions and DMSO by integrating molecular dynamics (MD) simulations of 45 variants from Bacillus subtilis lipase A (BSLA) and substitution landscape into a "BSLA-SSM" library. By systematically analyzing 39 structural-, solvation-, and interaction energy-based observables, we discovered that hydration shell maintenance, DMSO reduction, and decreased local flexibility simultaneously govern the stability of polar variants in OS. Moreover, the fingerprints of 1631 polar-related variants in three OSs demonstrated that substituting aromatic to polar amino acid(s) hold great potential to highly improve OSs resistance. Hence, surface polar engineering is a powerful strategy to generate OS-tolerant lipases and other enzymes, thereby adapting the catalyst to the desired reaction and process with OSs.

The FUSION protein crystallization screen

The success and speed of atomic structure determination of biological macromolecules by X-ray crystallography depends critically on the availability of diffraction-quality crystals. However, the process of screening crystallization conditions often consumes large amounts of sample and time. An innovative protein crystallization screen formulation called FUSION has been developed to help with the production of useful crystals. The concept behind the formulation of FUSION was to combine the most efficient components from the three MORPHEUS screens into a single screen using a systematic approach. The resulting formulation integrates 96 unique combinations of crystallization additives. Most of these additives are small molecules and ions frequently found in crystal structures of the Protein Data Bank (PDB), where they bind proteins and complexes. The efficiency of FUSION is demonstrated by obtaining high yields of diffraction-quality crystals for seven different test proteins. In the process, two crystal forms not currently in the PDB for the proteins α-amylase and avidin were discovered.

Functional enzyme-polymer complexes

SignificanceThe use of biological enzyme catalysts could have huge ramifications for chemical industries. However, these enzymes are often inactive in nonbiological conditions, such as high temperatures, present in industrial settings. Here, we show that the enzyme PETase (polyethylene terephthalate [PET]), with potential application in plastic recycling, is stabilized at elevated temperature through complexation with random copolymers. We demonstrate this through simulations and experiments on different types of substrates. Our simulations also provide strategies for designing more enzymatically active complexes by altering polymer composition and enzyme charge distribution.

How do interfaces alter the dynamics of supercooled water?

The structure of liquid water in the proximity of an interface can deviate significantly from that of bulk water, with surface-induced structural perturbations typically converging to bulk values at about ∼1 nm from the interface. While these structural changes are well established it is, in contrast, less clear how an interface perturbs the dynamics of water molecules within the liquid. Here, through an extensive set of molecular dynamics simulations of supercooled bulk and interfacial water films and nano-droplets, we observe the formation of persistent, spatially extended dynamical domains in which the average mobility varies as a function of the distance from the interface. This is in stark contrast with the dynamical heterogeneity observed in bulk water, where these domains average out spatially over time. We also find that the dynamical response of water to an interface depends critically on the nature of the interface and on the choice of interface definition. Overall these results reveal a richness in the dynamics of interfacial water that opens up the prospect of tuning the dynamical response of water through specific modifications of the interface structure or confining material.

Specific Ion Effects in Lanthanide-Amphiphile Structures at the Air-Water Interface and Their Implications for Selective Separation

The use of surfactants to attract dissolved ions to water surfaces and interfaces is an essential step in both solvent-based and solvent-free separation processes. We have studied the interactions of lanthanide ions in the aqueous subphase with monolayers of dihexadecyl phosphate at air-water interfaces. With heavier lanthanides (atomic number Z ≥ 65) in the subphase, the floating layer can be compressed to an area/molecule of about half the molecular cross section, indicating bilayer formation. X-ray fluorescence and reflectivity data support this conclusion. In the presence of lighter lanthanides (Z < 65), only monolayers are observed. Subphase-concentration-dependent studies using Er³⁺ (heavier) and Nd³⁺ (lighter) lanthanides show a stepwise progression, with ions attaching to the monolayer only when the solution concentration is >3 × 10^-7 M. Above ∼10^-5 M, bilayers form but only in the presence of the heavier lanthanide. Grazing incidence X-ray diffraction shows evidence of lateral ion-ion correlations in the bilayer structure but not in monolayers. Explicit solvent all-atom molecular dynamics simulations confirm the elevated ion-ion correlation in the bilayer system. This bilayer structure isolates heavier lanthanides but not lighter lanthanides from an aqueous solution and is therefore a potential mechanism for the selective separation of heavier lanthanides.

Origin of Proteolytic Stability of Peptide-Brush Polymers as Globular Proteomimetics

Peptide-brush polymers (PBPs), wherein every side-chain of the polymers is peptidic, represent a new class of proteomimetic with unusually high proteolytic resistance while maintaining bioactivity. Here, we sought to determine the origin of this behavior and to assess its generality via a combined theory and experimental approach. A series of PBPs with various polymer backbone structures were prepared and examined for their proteolytic stability and bioactivity. We discovered that an increase in the hydrophobicity of the polymer backbones is predictive of an elevation in proteolytic stability of the side-chain peptides. Computer simulations, together with small-angle X-ray scattering (SAXS) analysis, revealed globular morphologies for these polymers, in which pendant peptides condense around hydrophobic synthetic polymer backbones driven by the hydrophobic effect. As the hydrophobicity of the polymer backbones increases, the extent of solvent exposure of peptide cleavage sites decreases, reducing their accessibility to proteolytic enzymes. This study provides insight into the important factors driving PBP aqueous-phase structures to behave as globular, synthetic polymer-based proteomimetics.

Enabling biocatalysis in high-concentration organic cosolvent by enzyme gate engineering

Biocatalysis in high-concentration organic solvents (OSs) offers many advantages, but realizing this process remains a huge challenge. An R-selective ω-amine transaminase variant (AcATA_M2 ) exhibited high activity toward 50 g/L pro-sitagliptin ketone 1-[1-piperidinyl]-4-[2,4,5-trifluorophenyl]-1,3-butanedione (PTfpB). However, AcATA_M2 displayed unsatisfactory organic-cosolvent resistance against high-concentration dimethyl sulfoxide (DMSO), which is required to enhance the solubility of the hydrophobic substrate PTfpB. Located in the substrate-binding tunnel, enzyme gates are structural elements that undergo reversible conformational transitions, thus affecting the accessibility of the binding pocket to solvent molecules. Depending on the conformation of the enzyme gates, one can define an open or closed conformation on which the enzyme activity in OSs may depend. To enhance the DMSO resistance of AcATA_M2 , we identified the beneficial residues at the "enzyme gate" region via computational analysis, alanine scanning, and site-saturation mutagenesis. Two beneficial variants, namely, AcATA_M2 ^F56D and AcATA_M2 ^F56V , not only displayed improved enzyme activity but also exhibited enhanced DMSO resistance (the half-life value increased from 25.71 to 42.49 h under 60% DMSO). Molecular dynamic simulations revealed that the increase in DMSO resistance was mainly caused by the decrease in the number of DMSO molecules in the substrate-binding pocket. Moreover, in the kilogram-scale experiment, the conversion of 80 g/L substrate was increased from 50% (AcATA_M2 ) to 85% (M2^F56D in 40% DMSO) with a high e.e. of >99% within 24 h.

Antifreeze proteins and their biomimetics for cell cryopreservation: Mechanism, function and application-A review

Cell-based therapy is a promising technology for intractable diseases and health care applications, in which cryopreservation has become an essential procedure to realize the production of therapeutic cells. Ice recrystallization is the major factor that affects the post-thaw viability of cells. As a typical series of biomacromolecules with ice recrystallization inhibition (IRI) activity, antifreeze proteins (AFPs) have been employed in cell cryopreservation. Meanwhile, synthesized materials with IRI activity have emerged in the name of biomimetics of AFPs to expand their availability and practicality. However, fabrication of AFPs mimetics is in a chaotic period. There remains little commonality among different AFPs mimetics, then it is difficult to set guidelines on their design. With no doubt, a comprehensive understanding on the antifreezing mechanism of AFPs in molecular level will enable us to rebuild the function of AFPs, and provide convenience to clarify the relationship between structure and function of these early stage biomimetics. In this review, we would discuss those previously reported biomimetics to summarize their structure characteristics concerning the IRI activity and attempt to develop a roadmap for guiding the design of novel AFPs mimetics.

SARS-CoV-2 Variants, RBD Mutations, Binding Affinity, and Antibody Escape

Since 2020, the receptor-binding domain (RBD) of the spike protein of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been constantly mutating, producing most of the notable missense mutations in the context of "variants of concern", probably in response to the vaccine-driven alteration of immune profiles of the human population. The Delta variant, in particular, has become the most prevalent variant of the epidemic, and it is spreading in countries with the highest vaccination rates, causing the world to face the risk of a new wave of the contagion. Understanding the physical mechanism responsible for the mutation-induced changes in the RBD's binding affinity, its transmissibility, and its capacity to escape vaccine-induced immunity is the "urgent challenge" in the development of preventive measures, vaccines, and therapeutic antibodies against the coronavirus disease 2019 (COVID-19) pandemic. In this study, entropy-enthalpy compensation and the Gibbs free energy change were used to analyze the impact of the RBD mutations on the binding affinity of SARS-CoV-2 variants with the receptor angiotensin converting enzyme 2 (ACE2) and existing antibodies. Through the analysis, we found that the existing mutations have already covered almost all possible detrimental mutations that could result in an increase of transmissibility, and that a possible mutation in amino-acid position 498 of the RBD can potentially enhance its binding affinity. A new calculation method for the binding energies of protein-protein complexes is proposed based on the entropy-enthalpy compensation rule. All known structures of RBD-antibody complexes and the RBD-ACE2 complex comply with the entropy-enthalpy compensation rule in providing the driving force behind the spontaneous protein-protein docking. The variant-induced risk of breakthrough infections in vaccinated people is attributed to the L452R mutation's reduction of the binding affinity of many antibodies. Mutations reversing the hydrophobic or hydrophilic performance of residues in the spike RBD potentially cause breakthrough infections of coronaviruses due to the changes in geometric complementarity in the entropy-enthalpy compensations between antibodies and the virus at the binding sites.

Unexpected inverse correlations and cooperativity in ion-pair phase transfer

Liquid/liquid extraction is one of the most widely used separation and purification methods, where a forefront of research is the study of transport mechanisms for solute partitioning and the relationships that these have to solution structure at the phase boundary. To date, organized surface features that include protrusions, water-fingers, and molecular hinges have been reported. Many of these equilibrium studies have focused upon small-molecule transport – yet the extent to which the complexity of the solute, and the competition between different solutes, influence transport mechanisms have not been explored. Here we report molecular dynamics simulations that demonstrate that a metal salt (LiNO₃) can be transported via a protrusion mechanism that is remarkably similar to that reported for H₂O by tri-butyl phosphate (TBP), a process that involves dimeric assemblies. Yet the LiNO₃ out-competes H₂O for a bridging position between the extracting TBP dimer, which in-turn changes the preferred transport pathway of H₂O. Examining the electrolyte concentration dependence on ion-pair transport unexpectedly reveals an inverse correlation with the extracting surfactant concentration. As [LiNO₃] increases, surface adsorbed TBP becomes a limiting reactant in correlation with an increased negative surface charge induced by excess interfacial NO₃⁻, however the rate of transport is enhanced. Within the highly dynamic interfacial environment, we hypothesize that this unique cooperative effect may be due to perturbed surface organization that either decreases the energy of formation of transporting protrusion motifs or makes it easier for these self-assembled species to disengage from the surface.

A forefront of research in separations science (specifically liquid–liquid extraction) is the study of transport mechanisms for solute partitioning, and the relationships that these have to solution structure at the phase boundary.

A Modeling-Based Design to Engineering Protein Hydrogels with Random Copolymers

Protein enzymes have shown great potential in numerous technological applications. However, the design of supporting materials is needed to preserve protein functionality outside their native environment. Direct enzyme-polymer self-assembly offers a promising alternative to immobilize proteins in an aqueous solution, achieving higher control of their stability and enzymatic activity in industrial applications. Herein, we propose a modeling-based design to engineering hydrogels of cytochrome P450 and of PETase with styrene/2-vinylpyridine (2VP) random copolymers. By tuning the copolymer fraction of polar groups and of charged groups via quaternization of 2VP for coassembly with cytochrome P450 and via sulfonation of styrene for coassembly with PETase, we provide quantitative guidelines to select either a protein-polymer hydrogel structure or a single-protein encapsulation. The results highlight that, regardless of the protein surface domains, the presence of polar interactions and hydration effects promote the formation of a more elongated enzyme-polymer complex, suggesting a membrane-like coassembly. On the other hand, the effectiveness of a single-protein encapsulation is reached by decreasing the fraction of polar groups and by increasing the charge fraction up to 15%. Our computational analysis demonstrates that the enzyme-polymer assemblies are first promoted by the hydrophobic interactions which lead the protein nonpolar residues to achieve the maximum coverage and to play the role of the most robust contact points. The mechanisms of coassembly are unveiled in the light of both protein and polymer physical-chemistry, providing bioconjugate phase diagrams for the optimal material design.

The driving force for co-translational protein folding is weaker in the ribosome vestibule due to greater water ordering

Interactions between the ribosome and nascent chain can destabilize folded domains in the ribosome exit tunnel's vestibule, the last 3 nm of the exit tunnel where tertiary folding can occur. Here, we test if a contribution to this destabilization is a weakening of hydrophobic association, the driving force for protein folding. Using all-atom molecular dynamics simulations, we calculate the potential-of-mean force between two methane molecules along the center line of the ribosome exit tunnel and in bulk solution. Associated methanes, we find, are half as stable in the ribosome's vestibule as compared to bulk solution, demonstrating that the hydrophobic effect is weakened by the presence of the ribosome. This decreased stability arises from a decrease in the amount of water entropy gained upon the association of the methanes. And this decreased entropy gain originates from water molecules being more ordered in the vestibule as compared to bulk solution. Therefore, the hydrophobic effect is weaker in the vestibule because waters released from the first solvation shell of methanes upon association do not gain as much entropy in the vestibule as they do upon release in bulk solution. These findings mean that nascent proteins pass through a ribosome vestibule environment that can destabilize folded structures, which has the potential to influence co-translational protein folding pathways, energetics, and kinetics.

Entropy-Enthalpy Compensations Fold Proteins in Precise Ways

Exploring the protein-folding problem has been a longstanding challenge in molecular biology and biophysics. Intramolecular hydrogen (H)-bonds play an extremely important role in stabilizing protein structures. To form these intramolecular H-bonds, nascent unfolded polypeptide chains need to escape from hydrogen bonding with surrounding polar water molecules under the solution conditions that require entropy-enthalpy compensations, according to the Gibbs free energy equation and the change in enthalpy. Here, by analyzing the spatial layout of the side-chains of amino acid residues in experimentally determined protein structures, we reveal a protein-folding mechanism based on the entropy-enthalpy compensations that initially driven by laterally hydrophobic collapse among the side-chains of adjacent residues in the sequences of unfolded protein chains. This hydrophobic collapse promotes the formation of the H-bonds within the polypeptide backbone structures through the entropy-enthalpy compensation mechanism, enabling secondary structures and tertiary structures to fold reproducibly following explicit physical folding codes and forces. The temperature dependence of protein folding is thus attributed to the environment dependence of the conformational Gibbs free energy equation. The folding codes and forces in the amino acid sequence that dictate the formation of β-strands and α-helices can be deciphered with great accuracy through evaluation of the hydrophobic interactions among neighboring side-chains of an unfolded polypeptide from a β-strand-like thermodynamic metastable state. The folding of protein quaternary structures is found to be guided by the entropy-enthalpy compensations in between the docking sites of protein subunits according to the Gibbs free energy equation that is verified by bioinformatics analyses of a dozen structures of dimers. Protein folding is therefore guided by multistage entropy-enthalpy compensations of the system of polypeptide chains and water molecules under the solution conditions.

Hydration of methemoglobin studied by in silico modeling and dielectric spectroscopy

The hemoglobin concentration of 35 g/dl of human red blood cells is close to the solubility threshold. Using microwave dielectric spectroscopy, we have assessed the amount of water associated with hydration shells of methemoglobin as a function of its concentration in the presence or absence of ions. We estimated water-hemoglobin interactions to interpret the obtained data. Within the concentration range of 5-10 g/dl of methemoglobin, ions play an important role in defining the free-to-bound water ratio competing with hemoglobin to recruit water molecules for the hydration shell. At higher concentrations, hemoglobin is a major contributor to the recruitment of water to its hydration shell. Furthermore, the amount of bound water does not change as the hemoglobin concentration is increased from 15 to 30 g/dl, remaining at the level of ∼20% of the total intracellular water pool. The theoretical evaluation of the ratio of free and bound water for the hemoglobin concentration in the absence of ions corresponds with the experimental results and shows that the methemoglobin molecule binds about 1400 water molecules. These observations suggest that within the concentration range close to the physiological one, hemoglobin molecules are so close to each other that their hydration shells interact. In this case, the orientation of the hemoglobin molecules is most likely not stochastic, but rather supports partial neutralization of positive and negative charges at the protein surface. Furthermore, deformation of the red blood cell shape results in the rearrangement of these structures.

Structural and dynamical heterogeneity of water trapped inside Na+-pumping KR2 rhodopsin in the dark state

Photoisomerization in the retinal leads to a channel opening in rhodopsins that triggers translocation or pumping of ions/protons. Crystal structures of rhodopsins contain several structurally conserved water molecules. It has been suggested that water plays an active role in facilitating the ion pumping/translocation process by acting as a lubricant in these systems. In this paper, we systematically investigate the localization, structure, dynamics, and energetics of the water molecules along the channel for the resting/dark state of KR2 rhodopsin. By employing several microseconds long atomistic molecular dynamics simulation of this trans-membrane protein system, we demonstrate the presence of five distinct water containing pockets/cavities separated by gateways controlled by protein side-chains. There exists a strong hydrogen bonded network involving these buried water molecules and functionally important key residues. We present evidence of significant structural and dynamical heterogeneity in the water molecules present in these cavities, with very rare exchange between them. The exchange time scale of such buried water with the bulk has an extremely wide range, from tens of nanoseconds to >1.5 µs. The translational and rotational dynamics of buried water are found to be strongly dependent on the protein cavity size and local interactions with a classic signature of trapped diffusion and rotational anisotropy.

L-ARGININE AND L-GLUTAMIC ACID INCREASE THE CONTENT OF PROTEIN C IN THE EARLY STAGES OF ISOLATION FROM DONOR PLASMA

Current large-scale production of blood-derived pharmacological preparations is aimed at expanding the list of products and deeper extraction of target proteins especially at the pre-purification stage. In particular, this problem becomes critical for the isolation of proteins like protein C (PC), which is present in plasma in trace amounts. Aim. We aimed to improve the buffer composition to minimize the interaction of PC with other proteins and lipids that are inevitably present in the stock material. Methods. The content of protein C in plasma and its derivatives was assessed by the amidolytic activity to the chromogenic substrate S2366. A decrease in homologous impurities and plasma enrichment with protein C was provided by selective bulk adsorption on DEAE-cellulose. Results. Here we describe that an equimolar mixture of two amino acids (L-arginine and L-glutamic acid) essentially increased the content of protein C at the stage of cryo-depleted plasma pre-purification, including initial dilution and subsequent enrichment of plasma with protein C due to selective bulk adsorption on DEAE- cellulose. Additionally, it was revealed that solutions of these amino acids, when combined, inhibit the induced amidolytic activity of protein C and increase its solubility (in contrast to other plasma proteases). Conclusion. Pre-adding of a mixture of amino acids L-arginine and L-glutamic acid to cryo-depleted plasma significantly optimizes the pre-purification stage of protein C, providing a 5-fold increase in its yield after elution from DEAE-cellulose.

2H NMR study on temperature-dependent water dynamics in amino-acid functionalized silica nanopores

We prepare various amino-acid functionalized silica pores with diameters of ∼6 nm and study the temperature-dependent reorientation dynamics of water in these confinements. Specifically, we link basic Lys, neutral Ala, and acidic Glu to the inner surfaces and combine ²H nuclear magnetic resonance spin-lattice relaxation and line shape analyses to disentangle the rotational motions of the surfaces groups and the crystalline and liquid water fractions coexisting below partial freezing. Unlike the crystalline phase, the liquid phase shows reorientation dynamics, which strongly depends on the chemistry of the inner surfaces. The water reorientation is slowest for the Lys functionalization, followed by Ala and Glu and, finally, the native silica pores. In total, the rotational correlation times of water at the different surfaces vary by about two orders of magnitude, where this span is largely independent of the temperature in the range ∼200-250 K.

IsPETase Is a Novel Biocatalyst for Poly(ethylene terephthalate) (PET) Hydrolysis

Poly(ethylene terephthalate) (PET) is one of the most widely used synthetic polyesters, but also a major cause of plastic pollution. Because the chemical degradation of PET would be uneconomical and rather burdensome, considerable efforts have been devoted to exploring enzymatic processes for the disposal of PET waste. Many PET-hydrolyzing enzymes have been reported in recent decades, some of which demonstrate excellent potential for industrial applications. This review sets out to summarize the state of investigation into IsPETase, a cutinase-like enzyme from Ideonella sakaiensis possessing ability to degrade crystalline PET, and to gain further insight into the structure-function relationship of IsPETase. Benefiting from the continuing identification of novel cutinase-like proteins and growing availability of the engineered IsPETase, we may anticipate future developments in this type of enzyme would generate suitable biocatalyst for industrial use.

Mutational Pattern in Multiple Pulmonary Nodules Are Associated With Early Stage Lung Adenocarcinoma

The clinical significance of mutation in multiple pulmonary nodules is largely limited by single gene mutation-directed analysis and lack of validation of gene expression profiles. New analytic strategy is urgently needed for comprehensive understanding of genomic data in multiple pulmonary nodules. In this study, we performed whole exome sequencing in 16 multiple lung nodules and 5 adjacent normal tissues from 4 patients with multiple pulmonary nodules and decoded the mutation information from a perspective of cellular functions and signaling pathways. Mutated genes as well as mutation patterns shared in more than two lesions were identified and characterized. We found that the number of mutations or mutated genes and the extent of protein structural changes caused by different mutations is positively correlated with the degree of malignancy. Moreover, the mutated genes in the nodules are associated with the molecular functions or signaling pathways related to cell proliferation and survival. We showed a developing pattern of quantity (the number of mutations/mutated genes) and quality (the extent of protein structural changes) in multiple pulmonary nodules. The mutation and mutated genes in multiple pulmonary nodules are associated with cell proliferation and survival related signaling pathways. This study provides a new perspective for comprehension of genomic mutational data and might shed new light on deciphering molecular evolution of early stage lung adenocarcinoma.

Exploring the Cold-Adaptation Mechanism of Serine Hydroxymethyltransferase by Comparative Molecular Dynamics Simulations

Cold-adapted enzymes feature a lower thermostability and higher catalytic activity compared to their warm-active homologues, which are considered as a consequence of increased flexibility of their molecular structures. The complexity of the (thermo)stability-flexibility-activity relationship makes it difficult to define the strategies and formulate a general theory for enzyme cold adaptation. Here, the psychrophilic serine hydroxymethyltransferase (pSHMT) from Psychromonas ingrahamii and its mesophilic counterpart, mSHMT from Escherichia coli, were subjected to μs-scale multiple-replica molecular dynamics (MD) simulations to explore the cold-adaptation mechanism of the dimeric SHMT. The comparative analyses of MD trajectories reveal that pSHMT exhibits larger structural fluctuations and inter-monomer positional movements, a higher global flexibility, and considerably enhanced local flexibility involving the surface loops and active sites. The largest-amplitude motion mode of pSHMT describes the trends of inter-monomer dissociation and enlargement of the active-site cavity, whereas that of mSHMT characterizes the opposite trends. Based on the comparison of the calculated structural parameters and constructed free energy landscapes (FELs) between the two enzymes, we discuss in-depth the physicochemical principles underlying the stability-flexibility-activity relationships and conclude that (i) pSHMT adopts the global-flexibility mechanism to adapt to the cold environment and, (ii) optimizing the protein-solvent interactions and loosening the inter-monomer association are the main strategies for pSHMT to enhance its flexibility.