Electrostatic contributions to T4 lysozyme stability: solvent-exposed charges versus semi-buried salt bridges

Atomistic simulations reveal impacts of missense mutations on the structure and function of SynGAP1

De novo mutations in the synaptic GTPase activating protein (SynGAP) are associated with neurological disorders like intellectual disability, epilepsy, and autism. SynGAP is also implicated in Alzheimer's disease and cancer. Although pathogenic variants are highly penetrant in neurodevelopmental conditions, a substantial number of them are caused by missense mutations that are difficult to diagnose. Hence, in silico mutagenesis was performed for probing the missense effects within the N-terminal region of SynGAP structure. Through extensive molecular dynamics simulations, encompassing three 150-ns replicates for 211 variants, the impact of missense mutations on the protein fold was assessed. The effect of the mutations on the folding stability was also quantitatively assessed using free energy calculations. The mutations were categorized as potentially pathogenic or benign based on their structural impacts. Finally, the study introduces wild-type-SynGAP in complex with RasGTPase at the inner membrane, while considering the potential effects of mutations on these key interactions. This study provides structural perspective to the clinical assessment of SynGAP missense variants and lays the foundation for future structure-based drug discovery.

Multi-Level High-Throughput Screening for Discovery of Ligands That Inhibit Insulin Aggregation

We have developed a multi-level virtual screening protocol to identify lead molecules from the FDA inactives database that can inhibit insulin aggregation. The method is based on the presence of structural and interaction specificity in non-native aggregation pathway protein-protein interactions. Some key challenges specific to the present problem, when compared with native protein association, include structural heterogeneity of the protein species involved, multiple association pathways, and relatively higher probability of conformational rearrangement of the association complex. In this multi-step method, the inactives database was first screened using the dominant pharmacophore features of previously identified molecules shown to significantly inhibit insulin aggregation nucleation by binding to its aggregation-prone conformers. We then performed ensemble docking of several low-energy ligand conformations on these aggregation-prone conformers followed by molecular dynamics simulations and binding affinity calculations on a subset of docked complexes to identify a final set of five potential lead molecules to inhibit insulin aggregation nucleation. Their effect on aggregation inhibition was extensively investigated by incubating insulin under aggregation-prone aqueous buffer conditions (low pH, high temperature). Aggregation kinetics were characterized using size exclusion chromatography and Thioflavin T fluorescence assay, and the secondary structure was determined using circular dichroism spectroscopy. Riboflavin provided the best aggregation inhibition, with 85% native monomer retention after 48 h incubation under aggregation-prone conditions, whereas the no-ligand formulation showed complete monomer loss after 36 h. Further, insulin incubated with two of the screened inactives (aspartame, riboflavin) had the characteristic α-helical dip in CD spectra, while the no-ligand formulation showed a change to β-sheet rich conformations.

Using thermodynamic parameters to calibrate a mechanistic dose-response for infection of a host by a virus

Assessing the risk of infection from emerging viruses or of existing viruses jumping the species barrier into novel hosts is limited by the lack of dose response data. The initial stages of the infection of a host by a virus involve a series of specific contact interactions between molecules in the host and on the virus surface. The strength of the interaction is quantified in the literature by the dissociation constant (K_d) which is determined experimentally and is specific for a given virus molecule/host molecule combination. Here, two stages of the initial infection process of host intestinal cells are modelled, namely escape of the virus in the oral challenge dose from the innate host defenses (e.g. mucin proteins in mucus) and the subsequent binding of any surviving virus to receptor molecules on the surface of the host epithelial cells. The strength of virus binding to host cells and to mucins may be quantified by the association constants, K_a and K_mucin, respectively. Here, a mechanistic dose-response model for the probability of infection of a host by a given virus dose is constructed using K_a and K_mucin which may be derived from published K_d values taking into account the number of specific molecular interactions. It is shown that the effectiveness of the mucus barrier is determined not only by the amount of mucin but also by the magnitude of K_mucin. At very high K_mucin values, slight excesses of mucin over virus are sufficient to remove all the virus according to the model. At lower K_mucin values, high numbers of virus may escape even with large excesses of mucin. The output from the mechanistic model is the probability (p₁) of infection by a single virion which is the parameter used in conventional dose-response models to predict the risk of infection of the host from the ingested dose. It is shown here how differences in K_a (due to molecular differences in an emerging virus strain or new host) affect p₁, and how these differences in K_a may be quantified in terms of two thermodynamic parameters, namely enthalpy and entropy. This provides the theoretical link between sequencing data and risk of infection. Lack of data on entropy is a limitation at present and may also affect our interpretation of K_d in terms of infectivity. It is concluded that thermodynamic approaches have a major contribution to make in developing dose-response models for emerging viruses.

Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation

Charged and polar groups, through forming ion pairs, hydrogen bonds, and other less specific electrostatic interactions, impart important properties to proteins. Modulation of the charges on the amino acids, e.g., by pH and by phosphorylation and dephosphorylation, have significant effects such as protein denaturation and switch-like response of signal transduction networks. This review aims to present a unifying theme among the various effects of protein charges and polar groups. Simple models will be used to illustrate basic ideas about electrostatic interactions in proteins, and these ideas in turn will be used to elucidate the roles of electrostatic interactions in protein structure, folding, binding, condensation, and related biological functions. In particular, we will examine how charged side chains are spatially distributed in various types of proteins and how electrostatic interactions affect thermodynamic and kinetic properties of proteins. Our hope is to capture both important historical developments and recent experimental and theoretical advances in quantifying electrostatic contributions of proteins.

Screening for clusters of charge in human virus proteomes

Background

The identification of charge clusters (runs of charged residues) in proteins and their mapping within the protein structure sequence is an important step toward a comprehensive analysis of how these particular motifs mediate, via electrostatic interactions, various molecular processes such as protein sorting, translocation, docking, orientation and binding to DNA and to other proteins. Few algorithms that specifically identify these charge clusters have been designed and described in the literature. In this study, 197 distinctive human viral proteomes were screened for the occurrence of charge clusters (CC) using a new computational approach.

Results

Three hundred and seventy three CC have been identified within the 2549 viral protein sequences screened. The number of protein sequences that are CC-free is 2176 (85.3 %) while 150 and 180 proteins contained positive charge (PCC) and negative charge clusters (NCC), respectively. The NCCs (211 detected) were more prevalent than PCC (162). PCC-containing proteins are significantly longer than those having NCCs (p = 2.10^-16). The most prevalent virus families having PCC and NCC were Herpesviridae followed by Papillomaviridae. However, the single-strand RNA group has in average three times more NCC than PCC. According to the functional domain classification, a significant difference in distribution was observed between PCC and NCC (p = 2. 10⁻⁸) with the occurrence of NCCs being more frequent in C-terminal region while PCC more often fall within functional domains. Only 29 proteins sequences contained both NCC and PCC. Moreover, 101 NCC were conserved in 84 proteins while only 62 PCC were conserved in 60 protein sequences. To understand the mechanism by which the membrane translocation functionalities are embedded in viral proteins, we screened our PCC for sequences corresponding to cell-penetrating peptides (CPPs) using two online databases: CellPPd and CPPpred. We found that all our PCCs, having length varying from 7 to 30 amino-acids were predicted as CPPs. Experimental validation is required to improve our understanding of the role of these PCCs in viral infection process.

Conclusions

Screening distinctive cluster charges in viral proteomes suggested a functional role of these protein regions and might provide potential clues to improve the current understanding of viral diseases in order to tailor better preventive and therapeutic approaches.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3086-3) contains supplementary material, which is available to authorized users.

Electrostatic effects on the folding stability of FKBP12

The roles of electrostatic interactions in protein folding stability have been a matter of debate, largely due to the complexity in the theoretical treatment of these interactions. We have developed computational methods for calculating electrostatic effects on protein folding stability. To rigorously test and further refine these methods, here we carried out experimental studies into electrostatic effects on the folding stability of the human 12-kD FK506 binding protein (FKBP12). This protein has a close homologue, FKBP12.6, with amino acid substitutions in only 18 of their 107 residues. Of the 18 substitutions, 8 involve charged residues. Upon mutating FKBP12 residues at these 8 positions individually into the counterparts in FKBP12.6, the unfolding free energy (ΔGu) of FKBP12 changed by -0.3 to 0.7 kcal/mol. Accumulating stabilizing substitutions resulted in a mutant with a 0.9 kcal/mol increase in stability. Additional charge mutations were grafted from a thermophilic homologue, MtFKBP17, which aligns to FKBP12 with 31% sequence identity over 89 positions. Eleven such charge mutations were studied, with ΔΔGu varying from -2.9 to 0.1 kcal/mol. The predicted electrostatic effects by our computational methods with refinements herein had a root-mean-square deviation of 0.9 kcal/mol from the experimental ΔΔGu values on 16 single mutations of FKBP12. The difference in ΔΔGu between mutations grafted from FKBP12.6 and those from MtFKBP17 suggests that more distant homologues are less able to provide guidance for enhancing folding stability.

Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins

Proteins change their charge state through protonation and redox reactions as well as through binding charged ligands. The free energy of these reactions is dominated by solvation and electrostatic energies and modulated by protein conformational relaxation in response to the ionization state changes. Although computational methods for calculating these interactions can provide very powerful tools for predicting protein charge states, they include several critical approximations of which users should be aware. This chapter discusses the strengths, weaknesses, and approximations of popular computational methods for predicting charge states and understanding the underlying electrostatic interactions. The goal of this chapter is to inform users about applications and potential caveats of these methods as well as outline directions for future theoretical and computational research.

Exploiting Protein Conformational Change to Optimize Adenosine-Derived Inhibitors of HSP70

HSP70 is a molecular chaperone and a key component of the heat-shock response. Because of its proposed importance in oncology, this protein has become a popular target for drug discovery, efforts which have as yet brought little success. This study demonstrates that adenosine-derived HSP70 inhibitors potentially bind to the protein with a novel mechanism of action, the stabilization by desolvation of an intramolecular salt-bridge which induces a conformational change in the protein, leading to high affinity ligands. We also demonstrate that through the application of this mechanism, adenosine-derived HSP70 inhibitors can be optimized in a rational manner.

Exploring proteome-wide occurrence of clusters of charged residues in eukaryotes

Clusters of charged residues are one of the key features of protein primary structure since they have been associated to important functions of proteins. Here, we present a proteome wide scan for the occurrence of Charge Clusters in Protein sequences using a new search tool (FCCP) based on a score-based methodology. The FCCP was run to search charge clusters in seven eukaryotic proteomes: Arabidopsis thaliana, Caenorhabditis elegans, Danio rerio, Drosophila melanogaster, Homo sapiens, Mus musculus, and Saccharomyces cerevisiae. We found that negative charge clusters (NCCs) are three to four times more frequent than positive charge clusters (PCCs). The Drosophila proteome is on average the most charged, whereas the human proteome is the least charged. Only 3 to 8% of the studied protein sequences have negative charge clusters, while 1.6 to 3% having PCCs and only 0.07 to 0.6% have both types of clusters. NCCs are localized predominantly in the N-terminal and C-terminal domains, while PCCs tend to be localized within the functional domains of the protein sequences. Furthermore, the gene ontology classification revealed that the protein sequences with negative and PCCs are mainly binding proteins.

Oligomers, protofibrils and amyloid fibrils from recombinant human lysozyme (rHL): fibrillation process and cytotoxicity evaluation for ARPE-19 cell line

Amyloid-associated diseases, such Alzheimer's, Huntington's, Parkinson's, and type II diabetes, are related to protein misfolding and aggregation. Herein, the time evolution of scattered light intensity, hydrophobic properties, and conformational changes during fibrillation processes of rHL solutions at 55 °C and pH 2.0 were used to monitor the aggregation process of recombinant human lysozyme (rHL). Dynamic light scattering (DLS), thioflavin T (ThT) fluorescence, and surface tension (ST) at the air-water interface were used to analyze the hydrophobic properties of pre-amyloid aggregates involved in the fibrillation process of rHL to find a correlation between the hydrophobic character of oligomers, protofibrils and amyloid aggregates with the gain in cross-β-sheet structure, depending on the increase in the incubation periods. The ability of the different aggregates of rHL isolated during the fibrillation process to be adsorbed at the air-water interface can provide important information about the hydrophobic properties of the protein, which can be related to changes in the secondary structure of rHL, resulting in cytotoxic or non-cytotoxic species. Thus, we evaluated the cytotoxic effect of oligomers, protofibrils and amyloid fibrils on the cell line ARPE-19 using the MTT reduction test. The more cytotoxic protein species arose after a 600-min incubation time, suggesting that the hydrophobic character of pre-amyloid fibrils, in addition to the high prevalence of the cross-β-sheet conformation, can become toxic for the cell line ARPE-19.

Salt-bridge energetics in halophilic proteins

Halophilic proteins have greater abundance of acidic over basic and very low bulky hydrophobic residues. Classical electrostatic stabilization was suggested as the key determinant for halophilic adaptation of protein. However, contribution of specific electrostatic interactions (i.e. salt-bridges) to overall stability of halophilic proteins is yet to be understood. To understand this, we use Adaptive-Poison-Boltzmann-Solver Methods along with our home-built automation to workout net as well as associated component energy terms such as desolvation energy, bridge energy and background energy for 275 salt-bridges from 20 extremely halophilic proteins. We then perform extensive statistical analysis on general and energetic attributes on these salt-bridges. On average, 8 salt-bridges per 150 residues protein were observed which is almost twice than earlier report. Overall contributions of salt-bridges are −3.0 kcal mol⁻¹. Majority (78%) of salt-bridges in our dataset are stable and conserved in nature. Although, average contributions of component energy terms are equal, their individual details vary greatly from one another indicating their sensitivity to local micro-environment. Notably, 35% of salt-bridges in our database are buried and stable. Greater desolvation penalty of these buried salt-bridges are counteracted by stable network salt-bridges apart from favorable equal contributions of bridge and background terms. Recruitment of extensive network salt-bridges (46%) with a net contribution of −5.0 kcal mol⁻¹ per salt-bridge, seems to be a halophilic design wherein favorable average contribution of background term (−10 kcal mol⁻¹) exceeds than that of bridge term (−7 kcal mol⁻¹). Interiors of proteins from halophiles are seen to possess relatively higher abundance of charge and polar side chains than that of mesophiles which seems to be satisfied by cooperative network salt-bridges. Overall, our theoretical analyses provide insight into halophilic signature in its specific electrostatic interactions which we hope would help in protein engineering and bioinformatics studies.

Using the concept of transient complex for affinity predictions in CAPRI rounds 20-27 and beyond

Predictions of protein-protein binders and binding affinities have traditionally focused on features pertaining to the native complexes. In developing a computational method for predicting protein-protein association rate constants, we introduced the concept of transient complex after mapping the interaction energy surface. The transient complex is located at the outer boundary of the bound-state energy well, having near-native separation and relative orientation between the subunits but not yet formed most of the short-range native interactions. We found that the width of the binding funnel and the electrostatic interaction energy of the transient complex are among the features predictive of binders and binding affinities. These ideas were very promising for the five affinity-related targets (T43-45, 55, and 56) of CAPRI rounds 20-27. For T43, we ranked the single crystallographic complex as number 1 and were one of only two groups that clearly identified that complex as a true binder; for T44, we ranked the only design with measurable binding affinity as number 4. For the nine docking targets, continuing on our success in previous CAPRI rounds, we produced 10 medium-quality models for T47 and acceptable models for T48 and T49. We conclude that the interaction energy landscape and the transient complex in particular will complement existing features in leading to better prediction of binding affinities.

Side chain dynamics of carboxyl and carbonyl groups in the catalytic function of Escherichia coli ribonuclease H

Many proteins use Asx and Glx (x = n, p, or u) side chains as key functional groups in enzymatic catalysis and molecular recognition. In this study, NMR spin relaxation experiments and molecular dynamics simulations are used to measure the dynamics of the side chain amide and carboxyl groups, (13)C(γ/δ), in Escherichia coli ribonuclease HI (RNase H). Model-free analysis shows that the catalytic residues in RNase H are preorganized on ps-ns time scales via a network of electrostatic interactions. However, chemical exchange line broadening shows that these residues display significant conformational dynamics on μs-ms time scales upon binding of Mg(2+) ions. Two groups of catalytic residues exhibit differential line broadening, implicating distinct reorganizational processes upon binding of metal ions. These results support the "mobile metal ion" hypothesis, which was inferred from structural studies of RNase H.

Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects

The calculation of a protein-ligand binding free energy based on molecular dynamics (MD) simulations generally relies on a thermodynamic cycle in which the ligand is alchemically inserted into the system, both in the solvated protein and free in solution. The corresponding ligand-insertion free energies are typically calculated in nanoscale computational boxes simulated under periodic boundary conditions and considering electrostatic interactions defined by a periodic lattice-sum. This is distinct from the ideal bulk situation of a system of macroscopic size simulated under non-periodic boundary conditions with Coulombic electrostatic interactions. This discrepancy results in finite-size effects, which affect primarily the charging component of the insertion free energy, are dependent on the box size, and can be large when the ligand bears a net charge, especially if the protein is charged as well. This article investigates finite-size effects on calculated charging free energies using as a test case the binding of the ligand 2-amino-5-methylthiazole (net charge +1 e) to a mutant form of yeast cytochrome c peroxidase in water. Considering different charge isoforms of the protein (net charges -5, 0, +3, or +9 e), either in the absence or the presence of neutralizing counter-ions, and sizes of the cubic computational box (edges ranging from 7.42 to 11.02 nm), the potentially large magnitude of finite-size effects on the raw charging free energies (up to 17.1 kJ mol(-1)) is demonstrated. Two correction schemes are then proposed to eliminate these effects, a numerical and an analytical one. Both schemes are based on a continuum-electrostatics analysis and require performing Poisson-Boltzmann (PB) calculations on the protein-ligand system. While the numerical scheme requires PB calculations under both non-periodic and periodic boundary conditions, the latter at the box size considered in the MD simulations, the analytical scheme only requires three non-periodic PB calculations for a given system, its dependence on the box size being analytical. The latter scheme also provides insight into the physical origin of the finite-size effects. These two schemes also encompass a correction for discrete solvent effects that persists even in the limit of infinite box sizes. Application of either scheme essentially eliminates the size dependence of the corrected charging free energies (maximal deviation of 1.5 kJ mol(-1)). Because it is simple to apply, the analytical correction scheme offers a general solution to the problem of finite-size effects in free-energy calculations involving charged solutes, as encountered in calculations concerning, e.g., protein-ligand binding, biomolecular association, residue mutation, pKa and redox potential estimation, substrate transformation, solvation, and solvent-solvent partitioning.

Progress in developing Poisson-Boltzmann equation solvers

This review outlines the recent progress made in developing more accurate and efficient solutions to model electrostatics in systems comprised of bio-macromolecules and nano-objects, the last one referring to objects that do not have biological function themselves but nowadays are frequently used in biophysical and medical approaches in conjunction with bio-macromolecules. The problem of modeling macromolecular electrostatics is reviewed from two different angles: as a mathematical task provided the specific definition of the system to be modeled and as a physical problem aiming to better capture the phenomena occurring in the real experiments. In addition, specific attention is paid to methods to extend the capabilities of the existing solvers to model large systems toward applications of calculations of the electrostatic potential and energies in molecular motors, mitochondria complex, photosynthetic machinery and systems involving large nano-objects.

Poisson-Boltzmann Calculations: van der Waals or Molecular Surface?

The Poisson-Boltzmann equation is widely used for modeling the electrostatics of biomolecules, but the calculation results are sensitive to the choice of the boundary between the low solute dielectric and the high solvent dielectric. The default choice for the dielectric boundary has been the molecular surface, but the use of the van der Waals surface has also been advocated. Here we review recent studies in which the two choices are tested against experimental results and explicit-solvent calculations. The assignment of the solvent high dielectric constant to interstitial voids in the solute is often used as a criticism against the van der Waals surface. However, this assignment may not be as unrealistic as previously thought, since hydrogen exchange and other NMR experiments have firmly established that all interior parts of proteins are transiently accessible to the solvent.

Using DelPhi capabilities to mimic protein's conformational reorganization with amino acid specific dielectric constants

Many molecular events are associated with small or large conformational changes occurring in the corresponding proteins. Modeling such changes is a challenge and requires significant amount of computing time. From point of view of electrostatics, these changes can be viewed as a reorganization of local charges and dipoles in response to the changes of the electrostatic field, if the cause is insertion or deletion of a charged amino acid. Here we report a large scale investigation of modeling the changes of the folding energy due to single mutations involving charged group. This allows the changes of the folding energy to be considered mostly electrostatics in origin and to be calculated with DelPhi assigning residue-specific value of the internal dielectric constant of protein. The predicted energy changes are benchmarked against experimentally measured changes of the folding energy on a set of 257 single mutations. The best fit between experimental values and predicted changes is used to find out the effective value of the internal dielectric constant for each type of amino acid. The predicted folding free energy changes with the optimal, amino acid specific, dielectric constants are within RMSD=0.86 kcal/mol from experimentally measured changes.

Electrostatic potential of human immunodeficiency virus type 2 and rhesus macaque simian immunodeficiency virus capsid proteins

Human immunodeficiency virus type 2 (HIV-2) and simian immunodeficiency virus isolated from a macaque monkey (SIVmac) are assumed to have originated from simian immunodeficiency virus isolated from sooty mangabey (SIVsm). Despite their close similarity in genome structure, HIV-2 and SIVmac show different sensitivities to TRIM5α, a host restriction factor against retroviruses. The replication of HIV-2 strains is potently restricted by rhesus (Rh) monkey TRIM5α, while that of SIVmac strain 239 (SIVmac239) is not. Viral capsid protein is the determinant of this differential sensitivity to TRIM5α, as the HIV-2 mutant carrying SIVmac239 capsid protein evaded Rh TRIM5α-mediated restriction. However, the molecular determinants of this restriction mechanism are unknown. Electrostatic potential on the protein-binding site is one of the properties regulating protein-protein interactions. In this study, we investigated the electrostatic potential on the interaction surface of capsid protein of HIV-2 strain GH123 and SIVmac239. Although HIV-2 GH123 and SIVmac239 capsid proteins share more than 87% amino acid identity, we observed a large difference between the two molecules with the HIV-2 GH123 molecule having predominantly positive and SIVmac239 predominantly negative electrostatic potential on the surface of the loop between α-helices 4 and 5 (L4/5). As L4/5 is one of the major determinants of Rh TRIM5α sensitivity of these viruses, the present results suggest that the binding site of the Rh TRIM5α may show complementarity to the HIV-2 GH123 capsid surface charge distribution.

Studying salt effects on protein stability using ribonuclease t1 as a model system

Salt ions affect protein stability in a variety of ways. In general, these effects have either been interpreted from a charge solvation/charge screening standpoint or they have been considered to be the result of ion-specific interactions with a particular protein. Recent theoretical work suggests that a major contribution to salt effects on proteins is through the interaction of salt ions that are located near the protein surface and their induced point image charges that are located in the low-dielectric protein cavity. These interactions form the basis of "salting-out" interactions. Salt ions induce an image charge of the same sign in the low dielectric protein medium. The interaction between the induced charge and its mirror charge is repulsive and consequently thermodynamically destabilizing. However, a folded protein that has a much smaller surface area will be less destabilized than the unfolded state. Consequently, the folded state will be stabilized relative to the unfolded state. This work analyzes salt effects in the model enzyme ribonuclease t1, and demonstrates that interactions between salt ions and their induced point charges provide a major contribution to the observed salt-induced increase in protein stability. This work also demonstrates that in the case of weakly-binding ions (ions with binding constants that are in the order of 50 M(-1) and less), salting-out effects should still be considered in order to provide a more realistic interpretation of ion binding. These results should therefore be considered when salt effects are used to analyze electrostatic contributions to protein structure or are used to study the thermodynamics of proteins associated with halophillic organisms.

A molecular dynamics study of the interprotein interactions in collagen fibrils

Molecular dynamics simulations of collagen are used to investigate at the atomistic level the nature of the interprotein interactions that are present within a collagen fibril, and which are responsible for the fibril's thermodynamic stability. Simulations both of a collagen fibril and of a fully solvated tropcollagen are compared in order to study the interactions that arise between the proteins upon the process of fibrillogenesis. The interactions studied include direct interprotein hydrogen bonds, water-mediated interprotein hydrogen bonds, and hydrophobic interactions. The simulations are used to quantify the number of interprotein interactions that form; to study which functional groups contribute most towards the interactions; and to study the spatial distribution of interprotein interactions throughout the fibril's D period. The processes of collagen fibrillogenesis and protein folding are then compared with each other, because these two physical processes share many similarities in concept, and the latter has been more widely studied. Molecular dynamics simulations of a bacteriophage T4 lysozyme protein, both in its native state and in and unfolded state, are used as an illustrative example of a typical protein folding process, for direct comparison with the collagen simulations.

Ab initio calculations of deuterium isotope effects on chemical shifts of salt-bridged lysines

Deuterium isotope effects measure the change in chemical shift on substitution of a proton by deuterium. They have been calculated by direct treatment of the H/D nuclear quantum effect using a multicomponent ab initio molecular orbital method based on a non-Born-Oppenheimer approximation. This method enables the determination of both the electronic and the protonic (deuteronic) wave functions simultaneously and can directly calculate the geometrical difference induced by H/D isotope effects. The calculations show that the one-bond deuterium isotope effects on (15)N nuclear shielding, (1)Δ(15)N(D), in ammonium and amines decrease as a counterion or water molecule moves closer to the nitrogen. (1)Δ(15)N(D) and (2)Δ(1)H(D) of the NH(3)(+) groups of lysine residues in the B1 domain of protein G have been calculated using truncated side chains and also determined experimentally by NMR. Comparisons show that the structures in solution are different from those in the crystal and that solvation plays an important role in weakening the hydrogen bonds.

Interaction energy based protein structure networks

The three-dimensional structure of a protein is formed and maintained by the noncovalent interactions among the amino-acid residues of the polypeptide chain. These interactions can be represented collectively in the form of a network. So far, such networks have been investigated by considering the connections based on distances between the amino-acid residues. Here we present a method of constructing the structure network based on interaction energies among the amino-acid residues in the protein. We have investigated the properties of such protein energy-based networks (PENs) and have shown correlations to protein structural features such as the clusters of residues involved in stability, formation of secondary and super-secondary structural units. Further we demonstrate that the analysis of PENs in terms of parameters such as hubs and shortest paths can provide a variety of biologically important information, such as the residues crucial for stabilizing the folded units and the paths of communication between distal residues in the protein. Finally, the energy regimes for different levels of stabilization in the protein structure have clearly emerged from the PEN analysis.

Optimal salt bridge for Trp-cage stabilization

Gai and co-workers [Bunagan, M. R., et al. (2006) J. Phys. Chem. B 110, 3759-3763] reported computational design studies suggesting that a D9E mutation would stabilize the Trp-cage. Experimental studies for this mutation were reported in 2008 [Hudaky, P., et al. (2008) Biochemistry 47, 1007-1016]; the authors suggested that [D9E]-TC5b presented a more compact and melting resistant structure because of the "optimal distance between the two sides of the molecule". Nonetheless, the authors reported essentially the same circular dichroism (CD) melting temperature, 38 ± 0.3 °C, for TC5b and its [D9E] mutant. In this study, a more stable Trp-cage, DAYAQ WLKDG GPSSG RPPPS, was examined by nuclear magnetic resonance and CD with the following mutations: [D9E], [D9R,R16E], [R16O], [D9E,R16O], [R16K], and [D9E,R16K]. Of these, the [D9E] mutant displayed the smallest acidification-induced change in the apparent T(m). In analogy to the prior study, the CD melts of TC10b and its [D9E] mutant were, however, very similar; all of the other mutations were significantly fold destabilizing by all measures. A detailed analysis indicates that the original D9-R16 salt bridge is optimal with regard to fold cooperativity and fold stabilization. Evidence of salt bridge formation is also provided for a swapped pair, the [D9R,R16E] mutant. Model systems reveal that an ionized aspartate at the C-terminus of a helix significantly decreases intrinsic helicity, a requirement for Trp-cage fold stability. The CD evidence that was cited as supporting increased fold stability for [D9E]-TC5b at higher temperatures appears to be a reflection of increased helix stability in both the folded and unfolded states rather than a more favorable salt bridge. Our study also provides evidence of other Trp-cage stabilizing roles of the R16 side chain.

Inverse tuning of metal binding affinity and protein stability by altering charged coordination residues in designed calcium binding proteins

Ca(2+ )binding proteins are essential for regulating the role of Ca(2+ )in cell signaling and maintaining Ca(2+ )homeostasis. Negatively charged residues such as Asp and Glu are often found in Ca(2+ )binding proteins and are known to influence Ca(2+ )binding affinity and protein stability. In this paper, we report a systematic investigation of the role of local charge number and type of coordination residues in Ca(2+ )binding and protein stability using de novo designed Ca(2+ )binding proteins. The approach of de novo design was chosen to avoid the complications of cooperative binding and Ca(2+)-induced conformational change associated with natural proteins. We show that when the number of negatively charged coordination residues increased from 2 to 5 in a relatively restricted Ca(2+)-binding site, Ca(2+ )binding affinities increased by more than 3 orders of magnitude and metal selectivity for trivalent Ln(3+ )over divalent Ca(2+ )increased by more than 100-fold. Additionally, the thermal transition temperatures of the apo forms of the designed proteins decreased due to charge repulsion at the Ca(2+ )binding pocket. The thermal stability of the proteins was regained upon Ca(2+ )and Ln(3+ )binding to the designed Ca(2+ )binding pocket. We therefore observe a striking tradeoff between Ca(2+)/Ln(3+ )affinity and protein stability when the net charge of the coordination residues is varied. Our study has strong implications for understanding and predicting Ca(2+)-conferred thermal stabilization of natural Ca(2+ )binding proteins as well as for designing novel metalloproteins with tunable Ca(2+ )and Ln(3+ )binding affinity and selectivity.PACS codes: 05.10.-a.

Exploring the molecular design of protein interaction sites with molecular dynamics simulations and free energy calculations

The significant work that has been invested toward understanding protein-protein interaction has not translated into significant advances in structure-based predictions. In particular redesigning protein surfaces to bind to unrelated receptors remains a challenge, partly due to receptor flexibility, which is often neglected in these efforts. In this work, we computationally graft the binding epitope of various small proteins obtained from the RCSB database to bind to barnase, lysozyme, and trypsin using a previously derived and validated algorithm. In an effort to probe the protein complexes in a realistic environment, all native and designer complexes were subjected to a total of nearly 400 ns of explicit-solvent molecular dynamics (MD) simulation. The MD data led to an unexpected observation: some of the designer complexes were highly unstable and decomposed during the trajectories. In contrast, the native and a number of designer complexes remained consistently stable. The unstable conformers provided us with a unique opportunity to define the structural and energetic factors that lead to unproductive protein-protein complexes. To that end we used free energy calculations following the MM-PBSA approach to determine the role of nonpolar effects, electrostatics and entropy in binding. Remarkably, we found that a majority of unstable complexes exhibited more favorable electrostatics than native or stable designer complexes, suggesting that favorable electrostatic interactions are not prerequisite for complex formation between proteins. However, nonpolar effects remained consistently more favorable in native and stable designer complexes reinforcing the importance of hydrophobic effects in protein-protein binding. While entropy systematically opposed binding in all cases, there was no observed trend in the entropy difference between native and designer complexes. A series of alanine scanning mutations of hot-spot residues at the interface of native and designer complexes showed less than optimal contacts of hot-spot residues with their surroundings in the unstable conformers, resulting in more favorable entropy for these complexes. Finally, disorder predictions revealed that secondary structures at the interface of unstable complexes exhibited greater disorder than the stable complexes.

Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pKa, redox reactions and solvation free energies

Hybrid quantum mechanical/molecular mechanical (QM/MM) approaches have been used to provide a general scheme for chemical reactions in proteins. However, such approaches still present a major challenge to computational chemists, not only because of the need for very large computer time in order to evaluate the QM energy but also because of the need for proper computational sampling. This review focuses on the sampling issue in QM/MM evaluations of electrostatic energies in proteins. We chose this example since electrostatic energies play a major role in controlling the function of proteins and are key to the structure-function correlation of biological molecules. Thus, the correct treatment of electrostatics is essential for the accurate simulation of biological systems. Although we will be presenting different types of QM/MM calculations of electrostatic energies (and related properties) here, our focus will be on pKa calculations. This reflects the fact that pKa's of ionizable groups in proteins provide one of the most direct benchmarks for the accuracy of electrostatic models of macromolecules. While pKa calculations by semimacroscopic models have given reasonable results in many cases, existing attempts to perform pKa calculations using QM/MM-FEP have led to discrepancies between calculated and experimental values. In this work, we accelerate our QM/MM calculations using an updated mean charge distribution and a classical reference potential. We examine both a surface residue (Asp3) of the bovine pancreatic trypsin inhibitor and a residue buried in a hydrophobic pocket (Lys102) of the T4-lysozyme mutant. We demonstrate that, by using this approach, we are able to reproduce the relevant side chain pKa's with an accuracy of 3 kcal/mol. This is well within the 7 kcal/mol energy difference observed in studies of enzymatic catalysis, and is thus sufficient accuracy to determine the main contributions to the catalytic energies of enzymes. We also provide an overall perspective of the potential of QM/MM calculations in general evaluations of electrostatic free energies, pointing out that our approach should provide a very powerful and accurate tool to predict the electrostatics of not only solution but also enzymatic reactions, as well as the solvation free energies of even larger systems, such as nucleic acid bases incorporated into DNA.

Development and validation of an empirical free energy function for calculating protein-protein binding free energy surfaces

In a previous paper, we described a novel empirical free energy function that was used to accurately predict experimental binding free energies for a diverse test set of 31 protein-protein complexes to within approximately 1.0 kcal. Here, we extend that work and show that an updated version of the function can be used to (1) accurately predict native binding free energies and (2) rank crystallographic, native-like and non-native binding modes in a physically realistic manner. The modified function includes terms designed to capture some of the unfavorable interactions that characterize non-native interfaces. The function was used to calculate one-dimensional binding free energy surfaces for 21 protein complexes. In roughly 90% of the cases tested, the function was used to place native-like and crystallographic binding modes in global free energy minima. Our analysis further suggests that buried hydrogen bonds might provide the key to distinguishing native from non-native interactions. To the best of our knowledge our function is the only one of its kind, a single expression that can be used to accurately calculate native and non-native binding free energies for a large number of proteins. Given the encouraging results presented in this paper, future work will focus on improving the function and applying it to the protein-protein docking problem.

Rational design of a conformation-switchable Ca2+- and Tb3+-binding protein without the use of multiple coupled metal-binding sites

Ca2+, as a messenger of signal transduction, regulates numerous target molecules via Ca2+-induced conformational changes. Investigation into the determinants for Ca2+-induced conformational change is often impeded by cooperativity between multiple metal-binding sites or protein oligomerization in naturally occurring proteins. To dissect the relative contributions of key determinants for Ca2+-dependent conformational changes, we report the design of a single-site Ca2+-binding protein (CD2.trigger) created by altering charged residues at an electrostatically sensitive location on the surface of the host protein rat Cluster of Differentiation 2 (CD2).CD2.trigger binds to Tb3+ and Ca2+ with dissociation constants of 0.3 +/- 0.1 and 90 +/- 25 microM, respectively. This protein is largely unfolded in the absence of metal ions at physiological pH, but Tb3+ or Ca2+ binding results in folding of the native-like conformation. Neutralization of the charged coordination residues, either by mutation or protonation, similarly induces folding of the protein. The control of a major conformational change by a single Ca2+ ion, achieved on a protein designed without reliance on sequence similarity to known Ca2+-dependent proteins and coupled metal-binding sites, represents an important step in the design of trigger proteins.

Accurate Calculations of Binding, Folding, and Transfer Free Energies by a Scaled Generalized Born Method

The Poisson-Boltzmann (PB) equation is widely used for modeling solvation effects. The computational cost of PB has restricted its applications largely to single-conformation calculations. The generalized Born (GB) model provides an approximation at substantially reduced cost. Currently the best GB methods reproduce PB results for electrostatic solvation energies with errors at ~5 kcal/mol. When two proteins form a complex, the net electrostatic contributions to the binding free energy are typically of the order of 5 to 10 kcal/mol. Similarly, the net contributions of individual residues to protein folding free energy are < 5 kcal/mol. Clearly in these applications the accuracy of current GB methods is insufficient. Here we present a simple scaling scheme that allows our GB method, GBr⁶, to reproduce PB results for binding, folding, and transfer free energies with high accuracy. From an ensemble of conformations sampled from molecular dynamics simulations, five were judiciously selected for PB calculations. These PB results were used for scaling GBr⁶. Tests on the binding free energies of the barnase-barstar, GTPase-WASp, and U1A-U1hpII complexes and on the folding free energy of FKBP show that the effects of point mutations calculated by scaled GBr⁶ are accurate to within 0.3 kcal/mol of PB results. Similar accuracy was also achieved for the free energies of transfer for ribonuclease Sa and insulin from the crystalline phase to the solution phase at various pH's. This method makes it possible to thoroughly sample the transient-complex ensemble in predicting protein binding rate constants and to incorporate conformational sampling in electrostatic modeling (such as done in the MM-GBSA approach) without loss of accuracy.

Electrostatic rate enhancement and transient complex of protein-protein association

The association of two proteins is bounded by the rate at which they, via diffusion, find each other while in appropriate relative orientations. Orientational constraints restrict this rate to approximately 10(5)-10(6) M(-1) s(-1). Proteins with higher association rates generally have complementary electrostatic surfaces; proteins with lower association rates generally are slowed down by conformational changes upon complex formation. Previous studies (Zhou, Biophys J 1997;73:2441-2445) have shown that electrostatic enhancement of the diffusion-limited association rate can be accurately modeled by $k_{\bf D}$ = $k_{D}0\ {exp} ( - \langle U_{el} \rangle;{\star}/k_{B} T),$ where k(D) and k(D0) are the rates in the presence and absence of electrostatic interactions, respectively, U(el) is the average electrostatic interaction energy in a "transient-complex" ensemble, and k(B)T is the thermal energy. The transient-complex ensemble separates the bound state from the unbound state. Predictions of the transient-complex theory on four protein complexes were found to agree well with the experiment when the electrostatic interaction energy was calculated with the linearized Poisson-Boltzmann (PB) equation (Alsallaq and Zhou, Structure 2007;15:215-224). Here we show that the agreement is further improved when the nonlinear PB equation is used. These predictions are obtained with the dielectric boundary defined as the protein van der Waals surface. When the dielectric boundary is instead specified as the molecular surface, electrostatic interactions in the transient complex become repulsive and are thus predicted to retard association. Together these results demonstrate that the transient-complex theory is predictive of electrostatic rate enhancement and can help parameterize PB calculations.

On the Dielectric Boundary in Poisson-Boltzmann Calculations

In applying the Poisson-Boltzmann (PB) equation for calculating the electrostatic free energies of solute molecules, an open question is how to specify the boundary between the low-dielectric solute and the high-dielectric solvent. Two common specifications of the dielectric boundary, as the molecular surface (MS) or the van der Waals (vdW) surface of the solute, give very different results for the electrostatic free energy of the solute. With the same atomic radii, the solute is more solvent-exposed in the vdW specification. One way to resolve the difference is to use different sets of atomic radii for the two surfaces. The radii for the vdW surface would be larger in order to compensate for the higher solvent exposure. Here we show that radius re-parameterization required for bringing MS-based and vdW-based PB results to agreement is solute-size dependent. The difference in atomic radii for individual amino acids as solutes is only 2-5% but increases to over 20% for proteins with ~200 residues. Therefore two sets of radii that yield identical MS-based and vdW-based PB results for small solutes will give very different PB results for large solutes. This finding raises issues about two common practices. The first is the use of atomic radii, which are parameterized against either experimental solvation data or data obtained from explicit-solvent simulations on small compounds, for PB calculations on proteins. The second is the parameterization of vdW-based generalized Born models against MS-based PB results.

Computational methods for biomolecular electrostatics

An understanding of intermolecular interactions is essential for insight into how cells develop, operate, communicate, and control their activities. Such interactions include several components: contributions from linear, angular, and torsional forces in covalent bonds, van der waals forces, as well as electrostatics. Among the various components of molecular interactions, electrostatics are of special importance because of their long range and their influence on polar or charged molecules, including water, aqueous ions, and amino or nucleic acids, which are some of the primary components of living systems. Electrostatics, therefore, play important roles in determining the structure, motion, and function of a wide range of biological molecules. This chapter presents a brief overview of electrostatic interactions in cellular systems, with a particular focus on how computational tools can be used to investigate these types of interactions.

Do electrostatic interactions destabilize protein-nucleic acid binding?

The negatively charged phosphates of nucleic acids are often paired with positively charged residues upon binding proteins. It was thus counter-intuitive when previous Poisson-Boltzmann (PB) calculations gave positive energies from electrostatic interactions, meaning that they destabilize protein-nucleic acid binding. Our own PB calculations on protein-protein binding have shown that the sign and the magnitude of the electrostatic component are sensitive to the specification of the dielectric boundary in PB calculations. A popular choice for the boundary between the solute low dielectric and the solvent high dielectric is the molecular surface; an alternative is the van der Waals (vdW) surface. In line with results for protein-protein binding, in this article, we found that PB calculations with the molecular surface gave positive electrostatic interaction energies for two protein-RNA complexes, but the signs are reversed when the vdW surface was used. Therefore, whether destabilizing or stabilizing effects are predicted depends on the choice of the dielectric boundary. The two calculation protocols, however, yielded similar salt effects on the binding affinity. Effects of charge mutations differentiated the two calculation protocols; PB calculations with the vdW surface had smaller deviations overall from experimental data.

PIC: Protein Interactions Calculator

Interactions within a protein structure and interactions between proteins in an assembly are essential considerations in understanding molecular basis of stability and functions of proteins and their complexes. There are several weak and strong interactions that render stability to a protein structure or an assembly. Protein Interactions Calculator (PIC) is a server which, given the coordinate set of 3D structure of a protein or an assembly, computes various interactions such as disulphide bonds, interactions between hydrophobic residues, ionic interactions, hydrogen bonds, aromatic–aromatic interactions, aromatic–sulphur interactions and cation–π interactions within a protein or between proteins in a complex. Interactions are calculated on the basis of standard, published criteria. The identified interactions between residues can be visualized using a RasMol and Jmol interface. The advantage with PIC server is the easy availability of inter-residue interaction calculations in a single site. It also determines the accessible surface area and residue-depth, which is the distance of a residue from the surface of the protein. User can also recognize specific kind of interactions, such as apolar–apolar residue interactions or ionic interactions, that are formed between buried or exposed residues or near the surface or deep inside.

pKa calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols

The accuracy of biological simulations depends, in large part, on the treatment of electrostatics. Due to the availability of accurate experimental values, calculation of pKa provides stringent evaluation of computational methods. The generalized solvent boundary potential (GSBP) and Ewald summation electrostatic treatments were recently implemented for combined quantum mechanical and molecular mechanics (QM/MM) simulations by our group. These approaches were tested by calculating pKa shifts due to differences in electronic structure and electrostatic environment; the shifts were determined for a series of small molecules in solution, using various electrostatic treatments, and two residues (His 31, Lys 102) in the M102K T4-lysozyme mutant with large pKa shifts, using the GSBP approach. The calculations utilized a free energy perturbation scheme with the QM/MM potential function involving the self-consistent charge density functional tight binding (SCC-DFTB) and CHARMM as the QM and MM methods, respectively. The study of small molecules demonstrated that inconsistent electrostatic models produced results that were difficult to correct in a robust manner; by contrast, extended electrostatics, GSBP, and Ewald simulations produced consistent results once a bulk solvation contribution was carefully chosen. In addition to the electrostatic treatment, the pKa shifts were also sensitive to the level of the QM method and the scheme of treating QM/MM Coulombic interactions; however, simple perturbative corrections based on SCC-DFTB/CHARMM trajectories and higher level single point energy calculations were found to give satisfactory results. Combining all factors gave a root-mean-square difference of 0.7 pKa units for the relative pKa values of the small molecules compared to experiment. For the residues in the lysozyme, an accurate pKa shift was obtained for His 31 with multiple nanosecond simulations. For Lys 102, however, the pKa shift was estimated to be too large, even after more than 10 nanosecond simulations for each lambda window; the difficulty was due to the significant, but slow, reorganization of the protein and water structure when Lys 102 was protonated. The simulations support that Lys 102 is deprotonated in the X-ray structure and the protein is highly destabilized when this residue is protonated.

GBr6: A Parameterization-Free, Accurate, Analytical Generalized Born Method

The Poisson-Boltzmann (PB) equation is widely used for modeling electrostatic effects and solvation for macromolecules. The generalized Born (GB) model has been developed to mimic PB results at substantial lower computational cost. Here, we report an analytical GB method that reproduces PB results with high accuracy. The analytical approach builds on previous work of Gallicchio and Levy (J. Comput. Chem. 2004, 25, 479), and incorporates an improvement, proposed by Grycuk (J. Chem. Phys. 2003, 119, 4817), of the Coulomb-field approximation used in most GB methods. Tested against PB results, our GB method has an average unsigned relative error of only 0.6% for a representative set of 55 proteins and of 0.4% and 0.3%, respectively, for folded and unfolded conformations of cytochrome b562 sampled in molecular dynamics simulations. The dependencies of the electrostatic solvation free energy on solute and solvent dielectric constants and on salt concentration are fully accounted for in our method.

Electrostatic interactions modulate the conformation of collagen I

The pH- and electrolyte-dependent charging of collagen I fibrils was analyzed by streaming potential/streaming current experiments using the Microslit Electrokinetic Setup. Differential scanning calorimetry and circular dichroism spectroscopy were applied in similar electrolyte solutions to characterize the influence of electrostatic interactions on the conformational stability of the protein. The acid base behavior of collagen I was found to be strongly influenced by the ionic strength in KCl as well as in CaCl(2) solutions. An increase of the ionic strength with KCl from 10(-4) M to 10(-2) M shifts the isoelectric point (IEP) of the protein from pH 7.5 to 5.3. However, a similar increase of the ionic strength in CaCl(2) solutions shifts the IEP from 7.5 to above pH 9. Enhanced thermal stability with increasing ionic strength was observed by differential scanning calorimetry in both electrolyte systems. In line with this, circular dichroism spectroscopy results show an increase of the helicity with increasing ionic strength. Better screening of charged residues and the formation of salt bridges are assumed to cause the stabilization of collagen I with increasing ionic strength in both electrolyte systems. Preferential adsorption of hydroxide ions onto intrinsically uncharged sites in KCl solutions and calcium binding to negatively charged carboxylic acid moieties in CaCl(2) solutions are concluded to shift the IEP and influence the conformational stability of the protein.

Electrostatic contribution to the binding stability of protein-protein complexes

To investigate roles of electrostatic interactions in protein binding stability, electrostatic calculations were carried out on a set of 64 mutations over six protein-protein complexes. These mutations alter polar interactions across the interface and were selected for putative dominance of electrostatic contributions to the binding stability. Three protocols of implementing the Poisson-Boltzmann model were tested. In vdW4 the dielectric boundary between the protein low dielectric and the solvent high dielectric is defined as the protein van der Waals surface and the protein dielectric constant is set to 4. In SE4 and SE20, the dielectric boundary is defined as the surface of the protein interior inaccessible to a 1.4-A solvent probe, and the protein dielectric constant is set to 4 and 20, respectively. In line with earlier studies on the barnase-barstar complex, the vdW4 results on the large set of mutations showed the closest agreement with experimental data. The agreement between vdW4 and experiment supports the contention of dominant electrostatic contributions for the mutations, but their differences also suggest van der Waals and hydrophobic contributions. The results presented here will serve as a guide for future refinement in electrostatic calculation and inclusion of nonelectrostatic effects.

Modeling electrostatic effects in proteins

Electrostatic energies provide what is perhaps the most effective tool for structure-function correlation of biological molecules. This review considers the current state of simulations of electrostatic energies in macromolecules as well as the early developments of this field. We focus on the relationship between microscopic and macroscopic models, considering the convergence problems of the microscopic models and the fact that the dielectric 'constants' in semimacroscopic models depend on the definition and the specific treatment. The advances and the challenges in the field are illustrated considering a wide range of functional properties including pK(a)'s, redox potentials, ion and proton channels, enzyme catalysis, ligand binding and protein stability. We conclude by pointing out that, despite the current problems and the significant misunderstandings in the field, there is an overall progress that should lead eventually to quantitative descriptions of electrostatic effects in proteins and thus to quantitative descriptions of the function of proteins.

Unusual effect of salts on the homodimeric structure of NADH oxidase from Thermus thermophilus in acidic pH

The unusual salt-dependent behavior of the homodimeric flavoenzyme NADH oxidase from Thermus thermophilus in acidic pH has been studied using circular dichroism (CD) and sedimentation velocity. The native-like secondary and quaternary structures in acidic low ionic strength conditions were significantly perturbed by the addition of salts. The peptide region of the CD spectra showed a major salt-induced conformational change in the protein secondary structure. Sedimentation velocity experiments showed dissociation of the homodimeric structure of NADH oxidase in the presence of salt (>1 M). The new acidic conformation of the protein was stabilized by high ionic strength as indicated by a salt-induced increase in the melting temperature of the protein, and by a shift in the apparent pK(a) values of the conformational transition to a less acidic pH. Distortion of the dominant alpha-helical signal was expressed as the disappearance of the parallel polarized Moffitt exciton band at 208 nm without an accompanying loss of amplitude of n-->pi* electronic transitions at 222 nm. The unusual CD spectra correlated qualitatively with the theoretically calculated CD spectra of short alpha-helical structures and/or twisted beta-sheets. Differences between the experimentally obtained CD spectra and theoretical calculations (AGADIR) of the alpha-helical content of NADH oxidase indicate a role for non-local interactions in the protein conformation at high ionic strength and low pH. These findings indicate the importance of the homodimeric interface and electrostatic interactions for maintaining the structural integrity of this thermophilic protein.

An epidemiologically significant epitope of a 1998 human influenza virus neuraminidase forms a highly hydrated interface in the NA-antibody complex

The crystal structure of the complex between neuraminidase (NA) of influenza virus A/Memphis/31/98 (H3N2) and Fab of monoclonal antibody Mem5 has been determined at 2.1A resolution and shows a novel pattern of interactions compared to other NA-Fab structures. The interface buries a large area of 2400 A2 and the surfaces have high complementarity. However, the interface is also highly hydrated. There are 33 water molecules in the interface>or=95% buried from bulk solvent, but only 13 of these are isolated from other water molecules. The rest are involved in an intricate network of water-mediated hydrogen bonds throughout the interface, stabilizing the complex. Glu199 on NA, the most critical side-chain to the interaction as previously determined by escape mutant analysis and site-directed mutation, is located in a non-aqueous island. Glu199 and three other residues that contribute the major part of the antigen buried surface of the complex have mutated in human influenza viruses isolated after 1998, confirming that Mem5 identifies an epidemiologically important antigenic site. We conclude that antibody selection of NA variants is a significant component of recent antigenic drift in human H3N2 influenza viruses, supporting the idea that influenza vaccines should contain NA in addition to hemagglutinin.