Roles of electrostatic interaction in proteins

Bound ion effects: Using machine learning method to study the kinesin Ncd's binding with microtubule

Drosophila Ncd proteins are motor proteins that play important roles in spindle organization. Ncd and the tubulin dimer are highly charged. Thus, it is crucial to investigate Ncd-tubulin dimer interactions in the presence of ions, especially ions that are bound or restricted at the Ncd-tubulin dimer binding interfaces. To consider the ion effects, widely used implicit solvent models treat ions implicitly in the continuous solvent environment without focusing on the individual ions' effects. But highly charged biomolecules such as the Ncd and tubulin dimer may capture some ions at highly charged regions as bound ions. Such bound ions are restricted to their binding sites; thus, they can be treated as part of the biomolecules. By applying multiscale computational methods, including the machine-learning-based Hybridizing Ions Treatment-2 program, molecular dynamics simulations, DelPhi, and DelPhiForce, we studied the interaction between the Ncd motor domain and the tubulin dimer using a hybrid solvent model, which considers the bound ions explicitly and the other ions implicitly in the solvent environment. To identify the importance of treating bound ions explicitly, we also performed calculations using the implicit solvent model without considering the individual bound ions. We found that the calculations of the electrostatic features differ significantly between those of the hybrid solvent model and the pure implicit solvent model. The analyses show that treating bound ions at highly charged regions explicitly is crucial for electrostatic calculations. This work proposes a machine-learning-based approach to handle the bound ions using the hybrid solvent model. Such an approach is not only capable of handling kinesin-tubulin complexes but is also appropriate for other highly charged biomolecules, such as DNA/RNA, viral capsid proteins, etc.

A Hydroxylamine-Mediated Amidination of Lysine Residues That Retains the Protein's Positive Charge

Lysine-specific peptide and protein modification strategies are widely used to study charge-related functions and applications. However, these strategies often result in the loss of the positive charge on lysine, significantly impacting the charge-related properties of proteins. Herein, we report a strategy to preserve the positive charge and selectively convert amines in lysine side chains to amidines using nitriles and hydroxylamine under aqueous conditions. Various unprotected peptides and proteins were successfully modified with a high conversion rate. Moreover, the reactive amidine moiety and derived modification site enable subsequent secondary modifications. Notably, positive charges were retained during the modification. Therefore, positive charge-related protein properties, such as liquid-liquid phase separation behaviour of α-synuclein, were not affected. This strategy was subsequently applied to a lysine rich protein to develop an amidine-containing coacervate DNA complex with outstanding mechanical properties. Overall, our innovative strategy provides a new avenue to explore the characteristics of positively charged proteins.

Analytic Gradients for the Electrostatic Embedding QM/MM Model in Periodic Boundary Conditions Using Particle-Mesh Ewald Sums and Electrostatic Potential Fitted Charge Operators

Long-range electrostatic effects are fundamental for describing chemical reactivity in the condensed phase. Here, we present the methodology of an efficient quantum mechanical/molecular mechanical (QM/MM) model in periodic boundary conditions (PBC) compatible with QM/MM boundaries at chemical bonds. The method combines electrostatic potential fitted charge operators and electrostatic potentials derived from the smooth particle-mesh Ewald (PME) sum approach. The total energy and its analytic first derivatives with respect to QM, MM, and lattice vectors allow QM/MM molecular dynamics (MD) in the most common thermodynamic ensembles. We demonstrate the robustness of the method by performing a QM/MM MD equilibration of methanol in water. We simulate the cis/trans isomerization free-energy profiles in water of proline amino acid and a proline-containing oligopeptide, showing a correct description of the reaction barrier. Our PBC-compatible QM/MM model can efficiently be used to study the chemical reactivity in the condensed phase and enzymatic catalysis.

N-glycomic profiling of capsid proteins from Adeno-Associated Virus serotypes

Adeno-associated virus (AAV) vector has become the leading platform for gene delivery. Each serotype exhibits a different tissue tropism, immunogenicity, and in vivo transduction performance. Therefore, selecting the most suitable AAV serotype is critical for efficient gene delivery to target cells or tissues. Genome divergence among different serotypes is due mainly to the hypervariable regions of the AAV capsid proteins. However, the heterogeneity of capsid glycosylation is largely unexplored. In the present study, the N-glycosylation profiles of capsid proteins of AAV serotypes 1 to 9 have been systemically characterized and compared using a previously developed high-throughput and high-sensitivity N-glycan profiling platform. The results showed that all 9 investigated AAV serotypes were glycosylated, with comparable profiles. The most conspicuous feature was the high abundance mannosylated N-glycans, including FM3, M5, M6, M7, M8, and M9, that dominated the chromatograms within a range of 74 to 83%. Another feature was the relatively lower abundance of fucosylated and sialylated N-glycan structures, in the range of 23%-40% and 10%-17%, respectively. However, the exact N-glycan composition differed. These differences may be utilized to identify potential structural relationships between the 9 AAV serotypes. The current research lays the foundation for gaining better understanding of the importance of N-glycans on the AAV capsid surface that may play a significant role in tissue tropism, interaction with cell surface receptors, cellular uptake, and intracellular processing.

Biophysical chemistry behind sickle cell anemia and the mechanism of voxelotor action

Sickle cell anemia disease has been a great challenge to the world in the present situation. It occurs only due to the polymerization of sickle hemoglobin (HbS) having Pro-Val-Glu typed mutation, while the polymerization does not occur in normal hemoglobin (HbA) having Pro-Glu-Glu peptides. It is also well confirmed that the oxygenated HbS (OHbS) does not participate in the polymerization, while the deoxygenated HbS (dHbS) does, which causes the shape of red blood cells sickled. After polymerization, the blood has a low oxygen affinity. Keeping this fact into consideration, only those drugs are being synthesized that stabilize the OHbS structure so that the polymerization of HbS can be stopped. The literature data showed no systematic description of the changes occurring during the OHbS conversion to dHbS before polymerization. Hence, an innovative reasonable study between HbA and HbS, when they convert into their deoxygenated forms, was done computationally. In this evaluation, physiochemical parameters in HbA/HbS before and after deoxygenation were studied and compared deeply. The computationally collected data was used to understand the abnormal behaviour of dHbS arising due to the replacement of Glu6 with Val6. Consequently, during the presented computational study, the changes occurring in HbS were found opposite/abnormal as compared to HbA after the deoxygenation of both. The mechanism of Voxelotor (GBT-440) action to stop the HbS polymerization was also explained with the help of computationally collected data. Besides, a comparative study between GBT-440 and another suggested drug was also done to know their antisickling strength. Additionally, the effect of pH, CO, CO2, and 2,3-diphosphoglycerate (2,3-DPG) on HbS structure was also studied computationally.

An extensive ion-pair/hydrogen-bond network contributes to the thermostability of the MutL ATPase domain from Aquifex aeolicus

Proteins from hyperthermophiles often contain a large number of ionic interactions. Close examination of the previously determined crystal structure of the ATPase domain of MutL from a hyperthermophile, Aquifex aeolicus, revealed that the domain contains a continuous ion-pair/hydrogen-bond network consisting of 11 charged amino acid residues on a β-sheet. Mutations were introduced to disrupt the network, showing that the more extensively the network was disrupted, the greater the thermostability of the protein was decreased. Based on urea denaturation analysis, a thermodynamic parameter, energy for the conformational stability, was evaluated, which indicated that amino acid residues in the network contributed additively to the protein stability. A continuous network rather than a cluster of isolated interactions would pay less entropic penalty upon fixing the side chains to make the same number of ion pairs/hydrogen bonds, which might contribute more favorably to the structural formation of thermostable proteins.

Electrostatic interactions of enzymes in non-aqueous conditions: insights from molecular dynamics simulations

Electrostatic interactions of enzymes and their effects on enzyme activity and stability are poorly understood in non-aqueous conditions. Here, we investigate the contribution of the electrostatic interactions on the stability and activity of enzymes in the non-aqueous environment using molecular dynamics simulations. Lipase was selected as active and lysozyme as inactive model enzymes in non-aqueous media. Hexane was used as a common non-aqueous solvent model. In agreement with the previous experiments, simulations show that lysozyme has more structural instabilities than lipase in hexane. The number of hydrogen bonds and salt bridges of both enzymes is dramatically increased in hexane. In contrast to the other opinions, we show that the increase of the electrostatic interactions in non-aqueous media is not so favorable for enzymatic function and stability. In this condition, the newly formed hydrogen bonds and salt bridges can partially denature the local structure of the enzymes. For lysozyme, the changes in electrostatic interactions occur in all domains including the active site cleft, which leads to enzyme inactivation and destabilization. Interestingly, most of the changes in electrostatic interactions of lipase occur far from the active site regions. Therefore, the active site entrance regions remain functional in hexane. The results of this study reveal how the changes in electrostatic interactions can affect enzyme stability and activity in non-aqueous conditions. Moreover, we show for the first time how some enzymes, such as lipase, remain active in a non-aqueous environment.Communicated by Ramaswamy H. Sarma.

Chicken Feather Protein Dispersant for Effective Crude Oil Dispersion in the Marine Environment

Various studies report that aside from the adverse impact of the crude oil on the marine environment, there is the likelihood that chemical dispersants used on the surface of water as oil-treating agents themselves possess a degree of toxicity, which have additional effects on the environment. To eliminate the subject of toxicity, there exist several materials in nature that have the ability to form good emulsions, and such products include protein molecules. In this study, chicken feathers which are known to contain ≥90% protein were used to formulate a novel dispersant to disperse crude oil in seawater (35 ppt). Protein from chicken feathers was extracted and synthesized into the chicken feather protein (CFP) dispersant using deionized water as a solvent. Emulsions formed from CFP-synthesized dispersants were stable over a considerably long period of time, whereas the droplet sizes of the emulsion formed were on the average very small in diameter, making droplet coalescence very slow. The CFP dispersants exhibited moderate surface and interfacial activity at normal seawater salinity. Using the US EPA's baffled flask test, at 800 and 1000 mg/ml CFP surfactant-to-oil ratios, dispersion effectiveness values of 56.92 and 68.64 vol % were obtained, respectively, which show that CFP has a great potential in crude oil dispersion. Moreover, the acute toxicity test performed on Nile tilapia showed that CFP was practically nontoxic with an LC50 value of more than 100 mg/L after 96 h of exposure. The results obtained showed that the CFP dispersant is environmentally friendly.

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.

Structure-based pathogenicity relationship identifier for predicting effects of single missense variants and discovery of higher-order cancer susceptibility clusters of mutations

We report the structure-based pathogenicity relationship identifier (SPRI), a novel computational tool for accurate evaluation of pathological effects of missense single mutations and prediction of higher-order spatially organized units of mutational clusters. SPRI can effectively extract properties determining pathogenicity encoded in protein structures, and can identify deleterious missense mutations of germ line origin associated with Mendelian diseases, as well as mutations of somatic origin associated with cancer drivers. It compares favorably to other methods in predicting deleterious mutations. Furthermore, SPRI can discover spatially organized pathogenic higher-order spatial clusters (patHOS) of deleterious mutations, including those of low recurrence, and can be used for discovery of candidate cancer driver genes and driver mutations. We further demonstrate that SPRI can take advantage of AlphaFold2 predicted structures and can be deployed for saturation mutation analysis of the whole human proteome.

AlphaFold, allosteric, and orthosteric drug discovery: Ways forward

Drug discovery is arguably a highly challenging and significant interdisciplinary aim. The stunning success of the artificial intelligence-powered AlphaFold, whose latest version is buttressed by an innovative machine-learning approach that integrates physical and biological knowledge about protein structures, raised drug discovery hopes that unsurprisingly, have not come to bear. Even though accurate, the models are rigid, including the drug pockets. AlphaFold's mixed performance poses the question of how its power can be harnessed in drug discovery. Here we discuss possible ways of going forward wielding its strengths, while bearing in mind what AlphaFold can and cannot do. For kinases and receptors, an input enriched in active (ON) state models can better AlphaFold's chance of rational drug design success.

Fragment-Based Calculations of Enzymatic Thermochemistry Require Dielectric Boundary Conditions

Electronic structure calculations on enzymes require hundreds of atoms to obtain converged results, but fragment-based approximations offer a cost-effective solution. We present calculations on enzyme models containing 500-600 atoms using the many-body expansion, comparing to benchmarks in which the entire enzyme-substrate complex is described at the same level of density functional theory. When the amino acid fragments contain ionic side chains, the many-body expansion oscillates under vacuum boundary conditions but rapid convergence is restored using low-dielectric boundary conditions. This implies that full-system calculations in the gas phase are inappropriate benchmarks for assessing errors in fragment-based approximations. A three-body protocol retains sub-kilocalorie per mole fidelity with respect to a supersystem calculation, as does a two-body calculation combined with a full-system correction at a low-cost level of theory. These protocols pave the way for application of high-level quantum chemistry to large systems via rigorous, ab initio treatment of many-body polarization.

Practical considerations for the measurement of near-surface electrostatics based on solvent paramagnetic relaxation enhancements

Electrostatic interactions can play important roles in regulating various biological processes. Quantifying surface electrostatics of biomolecules is, therefore, of significant interest. Recent advances in solution NMR spectroscopy have enabled site-specific measurements of de novo near-surface electrostatic potentials (ϕ_ENS) based on a comparison of solvent paramagnetic relaxation enhancements generated from differently charged paramagnetic co-solutes with similar structures. Although the NMR-derived near-surface electrostatic potentials have been shown to agree with theoretical calculations in the context of folded proteins and nucleic acids, such benchmark comparisons may not always be possible, particularly in cases where high-resolution structural models are lacking, such as in the study of intrinsically disordered proteins. Cross-validation of ϕ_ENS potentials can be achieved by comparing values obtained using three pairs of paramagnetic co-solutes, each with a different net charge. Notably we have found cases where agreement of ϕ_ENS potentials between the three pairs is poor and herein we investigate the source of this discrepancy in some detail. We show that for the systems considered here ϕ_ENS potentials obtained from cationic and anionic co-solutes are accurate and that the use of paramagnetic co-solutes with different structures can be a viable option for validation, although the optimal choice of paramagnetic compounds depends on the system of interest.

Activated aggregation strategies to construct size-increasing nanoparticles for cancer therapy

The development of novel therapeutic strategies and modalities for tumors is still one of the important areas of current scientific research. Low permeability and short residence time of drugs in solid tumor areas are important reasons for the low efficiency of existing therapeutic strategies. Typically, nanoparticles with large size displayed enhanced residence time but low permeability. Therefore, to prolong the retention time of materials in solid tumors, size-increasing strategies have been developed to directly generate large-scale nanoparticles using small molecular compounds or increase the size of small nanoparticles in solid tumor areas. In this review, we summarize recently reported activatable aggregation systems that could be activated by cancer-related substances for cancer therapy and classify them by the mechanisms that lead to aggregation. In the end, we propose some potential challenges briefly from the view of our opinion. This article is categorized under: Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease.

A fortunate period of overlap with Prof. Haruki Nakamura

The author recounts a period of overlap with Prof. Haruki Nakamura that stretched from 2007 till the present day. Starting as a short-term research fellow in his laboratory, the author has also been a coauthor, academic colleague, and joint journal editorial board member of Prof. Nakamura.

Non-Ewald methods for evaluating the electrostatic interactions of charge systems: similarity and difference

In molecular simulations, it is essential to properly calculate the electrostatic interactions of particles in the physical system of interest. Here we consider a method called the non-Ewald method, which does not rely on the standard Ewald method with periodic boundary conditions, but instead relies on the cutoff-based techniques. We focus on the physicochemical and mathematical conceptual aspects of the method in order to gain a deeper understanding of the simulation methodology. In particular, we take into account the reaction field (RF) method, the isotropic periodic sum (IPS) method, and the zero-multipole summation method (ZMM). These cutoff-based methods are based on different physical ideas and are completely distinguishable in their underlying concepts. The RF and IPS methods are "additive" methods that incorporate information outside the cutoff region, via dielectric medium and isotropic boundary condition, respectively. In contrast, the ZMM is a "subtraction" method that tries to remove the artificial effects, generated near the boundary, from the cutoff sphere. Nonetheless, we find physical and/or mathematical similarities between these methods. In particular, the modified RF method can be derived by the principle of neutralization utilized in the ZMM, and we also found a direct relationship between IPS and ZMM.

Nanoarchitectonics beyond perfect order - not quite perfect but quite useful

Nanoarchitectonics, like architectonics, allows the design and building of structures, but at the nanoscale. Unlike those in architectonics, and even macro-, micro-, and atomic-scale architectonics, the assembled structures at the nanoscale do not always follow the projected design. In fact, they do follow the projected design but only for self-assembly processes producing structures with perfect order. Here, we look at nanoarchitectonics allowing the building of nanostructures without a perfect arrangement of building blocks. Here, fabrication of structures from molecules, polymers, nanoparticles, and nanosheets to polymer brushes, layer-by-layer assembly structures, and hydrogels through self-assembly processes is discussed, where perfect order is not necessarily the aim to be achieved. Both planar substrate and spherical template-based assemblies are discussed, showing the challenging nature of research in this field and the usefulness of such structures for numerous applications, which are also discussed here.

Mapping the per-residue surface electrostatic potential of CAPRIN1 along its phase-separation trajectory

Electrostatic interactions and charge balance are important for the formation of biomolecular condensates involving proteins and nucleic acids. However, a detailed, atomistic picture of the charge distribution around proteins during the phase-separation process is lacking. Here, we use solution NMR spectroscopy to measure residue-specific near-surface electrostatic potentials (ϕ_ENS) of the positively charged carboxyl-terminal intrinsically disordered 103 residues of CAPRIN1, an RNA-binding protein localized to membraneless organelles playing an important role in messenger RNA (mRNA) storage and translation. Measured ϕ_ENS values have been mapped along the adenosine triphosphate (ATP)-induced phase-separation trajectory. In the absence of ATP, ϕ_ENS values for the mixed state of CAPRIN1 are positive and large and progressively decrease as ATP is added. This is coupled to increasing interchain interactions, particularly between aromatic-rich and arginine-rich regions of the protein. Upon phase separation, CAPRIN1 molecules in the condensed phase are neutral (ϕ_ENS [Formula: see text] 0 mV), with ∼five molecules of ATP associated with each CAPRIN1 chain. Increasing the ATP concentration further inverts the CAPRIN1 electrostatic potential, so that molecules become negatively charged, especially in aromatic-rich regions, leading to re-entrance into a mixed phase. Our results collectively show that a subtle balance between electrostatic repulsion and interchain attractive interactions regulates CAPRIN1 phase separation and provides insight into how nucleotides, such as ATP, can induce formation of and subsequently dissolve protein condensates.

Detection of electrostatic molecular binding using the water proton signal

PURPOSE

Saturation transfer MRI has previously been used to probe molecular binding interactions with signal enhancement via the water signal. Here, we detail the relayed nuclear overhauser effect (rNOE) based mechanisms of this signal enhancement, develop a strategy of quantifying molecular binding affinity, i.e., the dissociation constant ( K D $$ {K}_D $$ ), and apply the method to detect electrostatic binding of several charged small biomolecules. Another goal was to estimate the detection limit for transient receptor-substrate binding.

THEORY AND METHODS

The signal enhancement mechanism was quantitatively described by a three-step magnetization transfer model, and numerical simulations were performed to verify this theory. The binding equilibria of arginine, choline, and acetyl-choline to anionic resin were studied as a function of ligand concentration, pH, and salt content. Equilibrium dissociation constants ( K D $$ {K}_D $$ ) were determined by fitting the multiple concentration data.

RESULTS

The numerical simulations indicate that the signal enhancement is sufficient to detect the molecular binding of sub-millimolar (∼100 μM) concentration ligands to low micromolar levels of molecular targets. The measured rNOE signals from arginine, choline, and acetyl-choline binding experiments show that several magnetization transfer pathways (intra-ligand rNOEs and intermolecular rNOEs) can contribute. The rNOEs that arise from molecular ionic binding were influenced by pH and salt concentration. The molecular binding strengths in terms of K D $$ {K}_{\mathrm{D}} $$ ranged from 70-160 mM for the three cations studied.

CONCLUSION

The capability to use MRI to detect the transient binding of small substrates paves a pathway towards the detection of micromolar level receptor-substrate binding in vivo.

Screening of OTULIN gene mutation with targeted next generation sequencing in Turkish populations and in silico analysis of these mutations

BACKGROUND

OTULIN-related autoinflammatory syndrome (ORAS) is an autosomal recessive disease characterized by systemic inflammation, recurrent fever. Due to limited knowledge about the OTULIN DNA variants that cause ORAS, the diagnosis and treatment of this disease is difficult. In this study, we aim to identify OTULIN DNA variants responsible for the genetic pathology of ORAS and observe the effects of these variants on the OTULIN protein structure and the function with different bioinformatics approaches.

METHODS

The present study included 3230 individuals with the suspicion of an autoinflammatory disease who were referred to Ege University Children's Hospital Molecular Medicine Laboratory. OTULIN variants were detected using a panel consisting of 37 different autoinflammatory diseases (AID) genes via targeted Next-Generation Sequencing.

RESULTS

As a result of the study, DNA variants associated with various AID were detected in 65% of the individuals to whom the panel was applied. Among these variants, only three different OTULIN variants (p.Val82Ile, p.Gln115His and p.Leu131_Arg132insLeuCysThrGlu) were detected. The pathogenic effects of the variants detected in the OTULIN gene were determined by using Polyphen2 as "Probably Pathogenic" for the p.Val82Ile and "benign" for the p.Gln115His. At the same time, the effects of these variants on the structure and function of the OTULIN protein were investigated by in silico approaches. Both variants reduce protein stability and binding affinity.

CONCLUSION

The results of the current study suggest that the evaluation of OTULIN variants with in silico approaches will contribute to the development of personalized treatments by diagnosing the disease specific to the variant.

Controlling hydrogel properties by tuning non-covalent interactions in a charge complementary multicomponent system

Mixing small molecule gelators is a promising route to prepare useful and exciting materials that cannot be accessed from any of the individual components. Here, we describe pH-triggered hydrogelation by mixing of two non-gelling amphiphiles. The intermolecular interactions among the molecules can be tuned either by controlling the degree of ionization of the components or by a preparative pathway, which enables us to control material properties such as gel strength, gel stiffness, thermal stability, and an unusual shrinking/swelling behaviour.

Protein cages as building blocks for superstructures

Proteins naturally self-assemble to function. Protein cages result from the self-assembly of multiple protein subunits that interact to form hollow symmetrical structures with functions that range from cargo storage to catalysis. Driven by self-assembly, building elegant higher-order superstructures with protein cages as building blocks has been an increasingly attractive field in recent years. It presents an engineering challenge not only at the molecular level but also at the supramolecular level. The higher-order constructs are proposed to provide access to diverse functional materials. Focussing on design strategy as a perspective, current work on protein cage supramolecular self-assembly are reviewed from three principles that are electrostatic, metal-ligand coordination and inherent symmetry. The review also summarises possible applications of the superstructure architecture built using modified protein cages.

Charge Transfer on the Surface-Enhanced Raman Scattering of Ag/4-MBA/PEDOT:PSS System: Intermolecular Hydrogen Bonding

A sandwich-structured noble metal-probe molecule-organic semiconductor consisting of Ag nanoparticles (NPs), 4-mercaptobenzoic acid (4-MBA) and different concentrations of poly(styrenesulfonate:poly(3,4-ethylenedioxythiophene) (PEDOT:PSS) was prepared by layer-by-layer assembly. Intermolecular hydrogen bonding was observed to have a significant effect on the surface-enhanced Raman scattering (SERS) of Ag/4-MBA/PEDOT:PSS. Upon increasing the PEDOT:PSS concentration, the characteristic Raman band intensity of 4-MBA was enhanced. In addition, the selected b2 vibration mode was significantly enhanced due to the influence of the charge transfer (CT) mechanism. The CT degree (ρCT) of the composite system was calculated before and after doping with PEDOT:PSS; when the concentration of PEDOT:PSS was 0.8%, the SERS intensity tended to be stable, and ρCT reached a maximum. Compared with that of the undoped PEDOT:PSS system, ρCT was significantly enhanced after doping, which can be explained by the CT effect induced by hydrogen bonds. These results indicate that hydrogen bonding transfers a charge from the Fermi energy level of Ag to the lowest unoccupied molecular orbital (LUMO) of 4-MBA, and due to the resulting potential difference, the charge will continue to transfer to the LUMO of PEDOT:PSS. Therefore, the introduction of organic semiconductors into the field of SERS not only expands the SERS substrate scope, but also provides a new idea for exploring the SERS mechanism. In addition, the introduction of hydrogen bonds has become an important guide for the study of CT and the structure of composite systems.

Accessing Highly Tunable Nanostructured Hydrogels in a Short Ionic Complementary Peptide Sequence via pH Trigger

Creating diverse nanostructures from a single gelator through modulating the self-assembly pathway has been gaining much attention in recent years. To this direction, we are exploring the effect of modulation of pH as a potential self-assembly pathway in governing the physicochemical properties of the final gel phase material. In this context, we used a classical nongelator with the ionic complementary sequence FEFK, which was rationally conjugated to an aromatic group naphthoxyacetic acid (Nap) at the N-terminal end to tune its gelation behavior. Interestingly, the presence of oppositely charged amino acids in the peptide amphiphile resulted in pH-responsive behavior, leading to the formation of hydrogels over a wide pH range (2.0-12.0); however, their structures differ significantly at the nanoscale. Thus, by simply manipulating the overall charge over the exposed surface of the peptide amphiphiles as a function of pH, we were able to access diverse self-assembled nanostructures within a single gelator domain. The charged state of the gelator at the extreme pH (2.0, 12.0) led to a thinner fiber formation, in contrast to the thicker fibers observed near the physiological pH owing to charge neutralization, thus promoting the lateral association. Such variation in molecular packing was found to be further reflected in the variable mechanical strengths of the peptide hydrogels obtained at different pH values. Moreover, the gelation of the peptide at physiological pH offers an additional advantage to explore this hydrogel as a cell culture scaffold. We anticipate that our study on controlling the self-assembly pathway of the ionic complementary peptide amphiphile can be an elegant approach to access diverse self-assembled materials, which can expand the zone of its applicability as a stimuli-responsive biomaterial.

Electric Field Measurements Reveal the Pivotal Role of Cofactor-Substrate Interaction in Dihydrofolate Reductase Catalysis

The contribution of ligand–ligand electrostatic interaction to transition state formation during enzyme catalysis has remained unexplored, even though electrostatic forces are known to play a major role in protein functions and have been investigated by the vibrational Stark effect (VSE). To monitor electrostatic changes along important steps during catalysis, we used a nitrile probe (T46C-CN) inserted proximal to the reaction center of three dihydrofolate reductases (DHFRs) with different biophysical properties, Escherichia coli DHFR (EcDHFR), its conformationally impaired variant (EcDHFR-S148P), and Geobacillus stearothermophilus DHFR (BsDHFR). Our combined experimental and computational approach revealed that the electric field projected by the substrate toward the probe negates those exerted by the cofactor when both are bound within the enzymes. This indicates that compared to previous models that focus exclusively on subdomain reorganization and protein–ligand contacts, ligand–ligand interactions are the key driving force to generate electrostatic environments conducive for catalysis.

Developing an effective polarizable bond method for small molecules with application to optimized molecular docking

Electrostatic interaction plays an essential role in protein-ligand binding. Due to the polarization effect, electrostatic interactions are largely impacted by their local environments. However, traditional force fields use fixed point charge-charge interactions to describe electrostatic interactions but is unable to include the polarization effect. The lack of the polarization effect in the force field representation can result in substantial error in biomolecular studies, such as molecular dynamics and molecular docking. Docking programs usually employ traditional force fields to estimate the binding energy between a ligand and a protein for pose selection or scoring. The intermolecular interaction energy mainly consists of van der Waals and electrostatic interaction in the force field representation. In the current study, we developed an Effective Polarizable Bond (EPB) method for small organic molecules and applied this EPB method to optimize protein-ligand docking in computational tests for a variety of protein-ligand systems. We tested the method on a set of 38 cocrystallized structures taken from the Protein Data Bank (PDB) and found that the maximum error was reduced from 7.98 Å to 2.03 Å when using EPB Dock, providing strong evidence that the use of EPB charges is important. We found that our optimized docking approach with EPB charges could improve the docking performance, sometimes dramatically, and the maximum error was reduced from 12.88 Å to 1.57 Å in Optimized Docking (in the case of 1fqx). The average RMSD decreased from 2.83 Å to 1.85 Å. Further investigations showed that the use of the EBP method could enhance intermolecular hydrogen bonding, which is a major contributing factor to improved docking performance. Developed tools for the calculation of the polarized ligand charge from a protein-ligand complex structure with the EPB method are freely available on GitHub (https://github.com/Xundrug/EPB).

The urokinase plasminogen activator binding to its receptor: a quantum biochemistry description within an in/homogeneous dielectric function framework with application to uPA–uPAR peptide inhibitors

DFT calculations using the MFCC fragment-based model considering a spatial-dependent dielectric function based on the Poisson–Boltzmann approximation were performed to describe the uPA–uPAR interactions.

Spontaneous Rupture and Entanglement of Human Neuronal Tau Protein Induced by Piconewton Compressive Force

Mechanical force vector fluctuations in living cells can have a significant impact on protein behavior and functions. Here we report that a human tau protein tertiary structure can abruptly and spontaneously rupture, like a balloon, under biologically available piconewton compressive force, using a home-modified atomic force microscopy single-molecule manipulation. The rupture behavior is dependent on the physiological level of presence of ions, such as K⁺ and Mg²⁺. We observed rupture events in the presence of K⁺ but not in the presence of Mg²⁺ ions. We have also explored the entangled protein state formed following the events of the multiple and simultaneous protein ruptures under crowding. Crowded proteins simultaneously rupture and then spontaneously refold to an entangled folding state, different from either folded and unfolded states of the tau protein, which can be a plausible pathway for the tau protein aggregation that is related to a number of neurodegenerative diseases.

Assessment of human leukocyte antigen immunogenicity: current methods, challenges and opportunities

Purpose of review

Donor–recipient human leukocyte antigen (HLA) matching improves outcomes after solid-organ transplantation, but current assessment of HLA incompatibility is inadequate as it does not consider the relative immunogenicity of individual HLA mismatches. In this article, we review existing strategies for assessing HLA immunogenicity and discuss current challenges and future opportunities in this field.

Recent findings

Current HLA immunogenicity algorithms focus primarily on the humoral component of the alloimmune response and aim to determine a measure of ‘dissimilarity’ between donor and recipient HLA. This can be achieved by deriving information from comparison of donor and recipient HLA at the amino acid sequence, structural and/or the physicochemical level, accounting for both B-cell and T-cell pathways of alloreactivity. Substantial evidence now supports the superiority of this molecular definition of HLA incompatibility, over conventional enumeration of HLA antigenic differences, for assessing the risk of humoral alloimmunity and for predicting graft outcomes after transplantation.

Summary

Significant progress has been made in developing computational HLA immunogenicity algorithms that offer exciting opportunities for a more rational approach to determining the degree of donor–recipient HLA incompatibility and to defining HLA-related immunological risk. A number of challenges now need to be overcome to enable their implementation into clinical practice.

Novel Immune Microlens Imaging for Detection of Antigen and Antibody

Detection and analysis of antigen-antibody reaction is one of the most critical detection techniques in the fields of medicine, biology, environmental science, and food safety. Traditional and classical methods for detecting antigen and antibody encounter many problems, such as time-consuming, high cost, and low accuracy. A novel immune microsphere imaging technique by the microlens is used to test the changes of refractive index before and after antigen-antibody reaction. It can quickly perform qualitative and quantitative determination for antigen-antibody reaction without any labeling, premodification, postwashing, and expensive enzymes. Here, we feature and discuss its principle and advantages, structure of a microlens immunoassay instrument, and potential in measuring clinical samples. It is promising to be developed for application to diagnosis of clinical diseases.

Computational Investigation on Electrostatic Loop Mutants Instigating Destabilization and Aggregation on Human SOD1 Protein Causing Amyotrophic Lateral Sclerosis

Mutations in the gene encoding Cu/Zn Superoxide Dismutase 1 (SOD1) protein are contemplated to be a protruding reason for Amyotrophic lateral sclerosis (ALS), which leads towards protein aggregation, misfolding and destabilization. Thus, we investigated the systematic action of entire mutations reported on electrostatic loop of SOD1 protein through thermodynamical and discrete molecular dynamics (DMD) studies. Accordingly, we analyzed the outcomes distinctly for screening the mutant structures having both, deleterious and destabilizing effect. Progressively, the impacts of those mutations on SOD1 were studied using DMD program. Surprisingly, our results predicted that the mutants viz., L126S, N139H and G141A to be the most destabilizing, misfolded and disease-causing compared to other mutants. Besides, the outcomes from secondary structural propensities and free energy landscapes, together assertively suggested that L126S, N139H and G141A tend to increase the formation of aggregates in SOD1 relative to other mutants. Hence, this study could provide an insight into the sprouting neurodegenerative disorder distressing the humans.

Structural Perspective on Revealing and Altering Molecular Functions of Genetic Variants Linked with Diseases

Structural information of biological macromolecules is crucial and necessary to deliver predictions about the effects of mutations-whether polymorphic or deleterious (i.e., disease causing), wherein, thermodynamic parameters, namely, folding and binding free energies potentially serve as effective biomarkers. It may be emphasized that the effect of a mutation depends on various factors, including the type of protein (globular, membrane or intrinsically disordered protein) and the structural context in which it occurs. Such information may positively aid drug-design. Furthermore, due to the intrinsic plasticity of proteins, even mutations involving radical change of the structural and physico⁻chemical properties of the amino acids (native vs. mutant) can still have minimal effects on protein thermodynamics. However, if a mutation causes significant perturbation by either folding or binding free energies, it is quite likely to be deleterious. Mitigating such effects is a promising alternative to the traditional approaches of designing inhibitors. This can be done by structure-based in silico screening of small molecules for which binding to the dysfunctional protein restores its wild type thermodynamics. In this review we emphasize the effects of mutations on two important biophysical properties, stability and binding affinity, and how structures can be used for structure-based drug design to mitigate the effects of disease-causing variants on the above biophysical properties.

Predicting Humoral Alloimmunity from Differences in Donor and Recipient HLA Surface Electrostatic Potential

In transplantation, development of humoral alloimmunity against donor HLA is a major cause of organ transplant failure, but our ability to assess the immunological risk associated with a potential donor–recipient HLA combination is limited. We hypothesized that the capacity of donor HLA to induce a specific alloantibody response depends on their structural and physicochemical dissimilarity compared with recipient HLA. To test this hypothesis, we first developed a novel computational scoring system that enables quantitative assessment of surface electrostatic potential differences between donor and recipient HLA molecules at the tertiary structure level [three-dimensional electrostatic mismatch score (EMS-3D)]. We then examined humoral alloimmune responses in healthy females subjected to a standardized injection of donor lymphocytes from their male partner. This analysis showed a strong association between the EMS-3D of donor HLA and donor-specific alloantibody development; this relationship was strongest for HLA-DQ alloantigens. In the clinical transplantation setting, the immunogenic potential of HLA-DRB1 and -DQ mismatches expressed on donor kidneys, as assessed by their EMS-3D, was an independent predictor of development of donor-specific alloantibody after graft failure. Collectively, these findings demonstrate the translational potential of our approach to improve immunological risk assessment and to decrease the burden of humoral alloimmunity in organ transplantation.

Influential Mutations in the SMAD4 Trimer Complex Can Be Detected from Disruptions of Electrostatic Complementarity

This article examines three techniques for rapidly assessing the electrostatic contribution of individual amino acids to the stability of protein-protein complexes. Whereas the energetic minimization of modeled oligomers may yield more accurate complexes, we examined the possibility that simple modeling may be sufficient to identify amino acids that add to or detract from electrostatic complementarity. The three methods evaluated were (a) the elimination of entire side chains (e.g., glycine scanning), (b) the elimination of the electrostatic contribution from the atoms of a side chain, called nullification, and (c) side chain structure prediction using SCWRL4. These techniques generate models in seconds, enabling large-scale mutational scanning. We evaluated these techniques on the SMAD2/SMAD4 heterotrimer, whose formation plays a crucial role in antitumor pathways. Many studies have documented the clinical and structural effect of specific mutations on trimer formation. Our results describe how glycine scanning yields more specific predictions, although nullification may be more sensitive, and how side chain structure prediction enables the identification of uncharged-to-charge mutations.

Hidden electrostatic basis of dynamic allostery in a PDZ domain

Allosteric effect implies ligand binding at one site leading to structural and/or dynamical changes at a distant site. PDZ domains are classic examples of dynamic allostery without conformational changes, where distal side-chain dynamics is modulated on ligand binding and the origin has been attributed to entropic effects. In this work, we unearth the energetic basis of the observed dynamic allostery in a PDZ3 domain protein using molecular dynamics simulations. We demonstrate that electrostatic interaction provides a highly sensitive yardstick to probe the allosteric modulation in contrast to the traditionally used structure-based parameters. There is a significant population shift in the hydrogen-bonded network and salt bridges involving side chains on ligand binding. The ligand creates a local energetic perturbation that propagates in the form of dominolike changes in interresidue interaction pattern. There are significant changes in the nature of specific interactions (nonpolar/polar) between interresidue contacts and accompanied side-chain reorientations that drive the major redistribution of energy. Interestingly, this internal redistribution and rewiring of side-chain interactions led to large cancellations resulting in small change in the overall enthalpy of the protein, thus making it difficult to detect experimentally. In contrast to the prevailing focus on the entropic or dynamic effects, we show that the internal redistribution and population shift in specific electrostatic interactions drive the allosteric modulation in the PDZ3 domain protein.

Over-Destabilization of Protein-Protein Interaction in Generalized Born Model and Utility of Energy Density Integration Cutoff

The generalize Born (GB) model is frequently used in MD simulations of biomolecular systems in aqueous solution. The GB model is usually based on the so-called Coulomb field approximation (CFA) for the energy density integration. In this study, we report that the GB model with CFA overdestabilizes the long-range electrostatic attraction between oppositely charged molecules (ionic bond forming two-helix system and kinesin-tubulin system) when the energy density integration cutoff, r_max, which is used to calculate the Born energy, is set to a large value. We show that employing large r_max, which is usually expected to make simulation results more accurate, worsens the accuracy so that the attraction is changed into repulsion. It is demonstrated that the overdestabilization is caused by the overestimation of the desolvation penalty upon binding that originates from CFA. We point out that the overdestabilization can be corrected by employing a relatively small cutoff (r_max = 10-15 Å), affirming that the GB models, even with CFA, can be used as a powerful tool to theoretically study the protein-protein interaction, particularly on its dynamical aspect, such as binding and unbinding.

Scrutiny of electrostatic-driven conformational ordering of polypeptide chains in DMSO: a study with a model oligopeptide

The molecular mechanism of DMSO-induced stabilisation of β-sheets is attributed to the combination of polar electrostatic interactions among side chains, and backbone desolvation through bulky side chains which promotes backbone hydrogen bonding.

Protein Assembly: Versatile Approaches to Construct Highly Ordered Nanostructures

Nature endows life with a wide variety of sophisticated, synergistic, and highly functional protein assemblies. Following Nature's inspiration to assemble protein building blocks into exquisite nanostructures is emerging as a fascinating research field. Dictating protein assembly to obtain highly ordered nanostructures and sophisticated functions not only provides a powerful tool to understand the natural protein assembly process but also offers access to advanced biomaterials. Over the past couple of decades, the field of protein assembly has undergone unexpected and rapid developments, and various innovative strategies have been proposed. This Review outlines recent advances in the field of protein assembly and summarizes several strategies, including biotechnological strategies, chemical strategies, and combinations of these approaches, for manipulating proteins to self-assemble into desired nanostructures. The emergent applications of protein assemblies as versatile platforms to design a wide variety of attractive functional materials with improved performances have also been discussed. The goal of this Review is to highlight the importance of this highly interdisciplinary field and to promote its growth in a diverse variety of research fields ranging from nanoscience and material science to synthetic biology.

Expressing Redundancy among Linear-Epitope Sequence Data Based on Residue-Level Physicochemical Similarity in the Context of Antigenic Cross-Reaction

Epitope-based design of vaccines, immunotherapeutics, and immunodiagnostics is complicated by structural changes that radically alter immunological outcomes. This is obscured by expressing redundancy among linear-epitope data as fractional sequence-alignment identity, which fails to account for potentially drastic loss of binding affinity due to single-residue substitutions even where these might be considered conservative in the context of classical sequence analysis. From the perspective of immune function based on molecular recognition of epitopes, functional redundancy of epitope data (FRED) thus may be defined in a biologically more meaningful way based on residue-level physicochemical similarity in the context of antigenic cross-reaction, with functional similarity between epitopes expressed as the Shannon information entropy for differential epitope binding. Such similarity may be estimated in terms of structural differences between an immunogen epitope and an antigen epitope with reference to an idealized binding site of high complementarity to the immunogen epitope, by analogy between protein folding and ligand-receptor binding; but this underestimates potential for cross-reactivity, suggesting that epitope-binding site complementarity is typically suboptimal as regards immunologic specificity. The apparently suboptimal complementarity may reflect a tradeoff to attain optimal immune function that favors generation of immune-system components each having potential for cross-reactivity with a variety of epitopes.

Protein self-assembly via supramolecular strategies

Proteins, as the elemental basis of living organisms, mostly execute their biological tasks in the form of supramolecular self-assemblies with subtle architectures, dynamic interactions and versatile functionalities. Inspired by the structural harmony and functional beauty of natural protein self-assemblies to fabricate sophisticated yet highly ordered protein superstructures represents an adventure in the pursuit of nature's supreme wisdom. In this review, we focus on building protein self-assembly systems based on supramolecular strategies and classify recent progress by the types of utilized supramolecular driving forces. Especially, the design strategy, structure control and the thermodynamic/kinetic regulation of the self-assemblies, which will in turn provide insights into the natural biological self-assembly mechanism, are highlighted. In addition, recently, this research field is starting to extend its interest beyond constructing complex morphologies towards the potential applications of the self-assembly systems; several attempts to design functional protein complexes are also discussed. As such, we hope that this review will provide a panoramic sketch of the field and draw a roadmap towards the ultimate construction of advanced protein self-assemblies that even can serve as analogues of their natural counterparts.

Local electric fields and molecular properties in heterogeneous environments through polarizable embedding

In spectroscopies, the local field experienced by a molecule embedded in an environment will be different from the externally applied electromagnetic field, and this difference may significantly alter the response and transition properties of the molecule. The polarizable embedding (PE) model has previously been developed to model the local field contribution stemming from the direct molecule-environment coupling of the electromagnetic response properties of molecules in solution as well as in heterogeneous environments, such as proteins. Here we present an extension of this approach to address the additional effective external field effect, i.e., the manifestations of the environment polarization induced by the external field, which allows for the calculation of properties defined in terms of the external field. Within a response framework, we report calculations of the one- and two-photon absorption (1PA and 2PA, respectively) properties of PRODAN-methanol clusters as well as the fluorescent protein DsRed. Our results demonstrate the necessity of accounting for both the dynamical reaction field and effective external field contributions to the local field in order to reproduce full quantum chemical reference calculations. For the lowest π→π* transition in DsRed, inclusion of effective external field effects gives rise to a 1.9- and 3.5-fold reduction in the 1PA and 2PA cross-sections, respectively. The effective external field is, however, strongly influenced by the heterogeneity of the protein matrix, and the resulting effect can lead to either screening or enhancement depending on the nature of the transition under consideration.

pH-Regulated Reversible Transition Between Polyion Complexes (PIC) and Hydrogen-Bonding Complexes (HBC) with Tunable Aggregation-Induced Emission

The mimicking of biological supramolecular interactions and their mutual transitions to fabricate intelligent artificial systems has been of increasing interest. Herein, we report the fabrication of supramolecular micellar nanoparticles consisting of quaternized poly(ethylene oxide)-b-poly(2-dimethylaminoethyl methacrylate) (PEO-b-PQDMA) and tetrakis(4-carboxylmethoxyphenyl)ethene (TPE-4COOH), which was capable of reversible transition between polyion complexes (PIC) and hydrogen bonding complexes (HBC) with tunable aggregation-induced emission (AIE) mediated by solution pH. At pH 8, TPE-4COOH chromophores can be directly dissolved in aqueous milieu without evident fluorescence emission. However, upon mixing with PEO-b-PQDMA, polyion complexes were formed by taking advantage of electrostatic interaction between carboxylate anions and quaternary ammonium cations and the most compact PIC micelles were achieved at the isoelectric point (i.e., [QDMA(+)]/[COO(-)] = 1), as confirmed by dynamic light scattering (DLS) measurement. Simultaneously, fluorescence spectroscopy revealed an evident emission turn-on and the maximum fluorescence intensity was observed near the isoelectric point due to the restriction of intramolecular rotation of TPE moieties within the PIC cores. The kinetic study supported a micelle fusion/fission mechanism on the formation of PIC micelles at varying charge ratios, exhibiting a quick time constant (τ1) relating to the formation of quasi-equilibrium micelles and a slow time constant (τ2) corresponding to the formation of final equilibrium micelles. Upon deceasing the pH of PIC micelles from 8 to 2 at the [QDMA(+)]/[COO(-)] molar ratio of 1, TPE-4COOH chromophores became gradually protonated and hydrophobic. The size of micellar nanoparticles underwent a remarkable decrease, whereas the fluorescence intensity exhibited a further increase by approximately 7.35-fold, presumably because of the formation of HBC micelles comprising cationic PQDMA coronas and PEO/TPE-4COOH hydrogen-bonded cores, an inverted micellar structures compared to initial PIC micelles. Moreover, the pH-mediated schizophrenic micellar transition from PIC to HBC with tunable AIE characteristic was reversible.