The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies

Properties of compatible solutes in aqueous solution

We have performed Molecular Dynamics simulations of ectoine, hydroxyectoine and urea in explicit solvent. Special attention has been spent on the local surrounding structure of water molecules. Our results indicate that ectoine and hydroxyectoine are able to accumulate more water molecules than urea by a pronounced ordering due to hydrogen bonds. We have validated that the charging of the molecules is of main importance resulting in a well defined hydration sphere. The influence of a varying salt concentration is also investigated. Finally we present experimental results of a DPPC monolayer phase transition that validate our numerical findings.

The dynamical mechanism of auto-inhibition of AMP-activated protein kinase

We use a novel normal mode analysis of an elastic network model drawn from configurations generated during microsecond all-atom molecular dynamics simulations to analyze the mechanism of auto-inhibition of AMP-activated protein kinase (AMPK). A recent X-ray and mutagenesis experiment (Chen, et al Nature2009, 459, 1146) of the AMPK homolog S. Pombe sucrose non-fermenting 1 (SNF1) has proposed a new conformational switch model involving the movement of the kinase domain (KD) between an inactive unphosphorylated open state and an active or semi-active phosphorylated closed state, mediated by the autoinhibitory domain (AID), and a similar mutagenesis study showed that rat AMPK has the same auto-inhibition mechanism. However, there is no direct dynamical evidence to support this model and it is not clear whether other functionally important local structural components are equally inhibited. By using the same SNF1 KD-AID fragment as that used in experiment, we show that AID inhibits the catalytic function by restraining the KD into an unproductive open conformation, thereby limiting local structural rearrangements, while mutations that disrupt the interactions between the KD and AID allow for both the local structural rearrangement and global interlobe conformational transition. Our calculations further show that the AID also greatly impacts the structuring and mobility of the activation loop.

AMP-activated protein kinase (AMPK) maintains the balance between ATP production and energy consumption in eukaryotic cells by responding to the rise of intracellular AMP. We report on a novel method that uses normal mode analysis of an elastic network model drawn from microsecond all-atom molecular dynamics simulations to analyze the activation mechanism of the AMPK homolog SNF1, which is believed to have the same mechanism as mammalian AMPK. There has been important new X-ray crystallographic and mutagenesis information on the self-regulation of AMPK based on its auto-inhibitory domain, although that view is primarily static. We provide a dynamical analysis to show that AID inhibits catalytic function by restraining KD into an unproductive open conformation and limiting functional local structural rearrangement, and that mutations that disrupt the interactions between the KD and AID free the KD to undergo both the global interlobe conformational transition and functional local structural rearrangement. This suggests new ways in which drugs might be used to regulate this important molecular machine.

Subunit interface dynamics in hexadecameric rubisco

Ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco) plays an important role in the global carbon cycle as a hub for biomass. Rubisco catalyzes not only the carboxylation of RuBP with carbon dioxide but also a competing oxygenation reaction of RuBP with a negative impact on photosynthetic yield. The functional active site is built from two large (L) subunits that form a dimer. The octameric core of four L(2) dimers is held at each end by a cluster of four small (S) subunits, forming a hexadecamer. Each large subunit contacts more than one S subunit. These interactions exploit the dynamic flexibility of Rubisco, which we address in this study. Here, we describe seven different types of interfaces of hexadecameric Rubisco. We have analyzed these interfaces with respect to the size of the interface area and the number of polar interactions, including salt bridges and hydrogen bonds in a variety of Rubisco enzymes from different organisms and different kingdoms of life, including the Rubisco-like proteins. We have also performed molecular dynamics simulations of Rubisco from Chlamydomonas reinhardtii and mutants thereof. From our computational analyses, we propose structural checkpoints of the S subunit to ensure the functionality and/or assembly of the Rubisco holoenzyme. These checkpoints appear to fine-tune the dynamics of the enzyme in a way that could influence enzyme performance.

A new view of the bacterial cytosol environment

The cytosol is the major environment in all bacterial cells. The true physical and dynamical nature of the cytosol solution is not fully understood and here a modeling approach is applied. Using recent and detailed data on metabolite concentrations, we have created a molecular mechanical model of the prokaryotic cytosol environment of Escherichia coli, containing proteins, metabolites and monatomic ions. We use 200 ns molecular dynamics simulations to compute diffusion rates, the extent of contact between molecules and dielectric constants. Large metabolites spend ∼80% of their time in contact with other molecules while small metabolites vary with some only spending 20% of time in contact. Large non-covalently interacting metabolite structures mediated by hydrogen-bonds, ionic and π stacking interactions are common and often associate with proteins. Mg²⁺ ions were prominent in NIMS and almost absent free in solution. Κ⁺ is generally not involved in NIMSs and populates the solvent fairly uniformly, hence its important role as an osmolyte. In simulations containing ubiquitin, to represent a protein component, metabolite diffusion was reduced owing to long lasting protein-metabolite interactions. Hence, it is likely that with larger proteins metabolites would diffuse even more slowly. The dielectric constant of these simulations was found to differ from that of pure water only through a large contribution from ubiquitin as metabolite and monatomic ion effects cancel. These findings suggest regions of influence specific to particular proteins affecting metabolite diffusion and electrostatics. Also some proteins may have a higher propensity for associations with metabolites owing to their larger electrostatic fields. We hope that future studies may be able to accurately predict how binding interactions differ in the cytosol relative to dilute aqueous solution.

The cytosol is the major cellular environment housing the majority of cellular activity. Although the cytosol is an aqueous environment, it contains high concentrations of ions, metabolites, and proteins, making it very different from dilute aqueous solution, which is frequently used for in vitro biochemistry. Recent advances in metabolomics have provided detailed concentration data for metabolites in E.coli. We used this information to construct accurate atomistic models of the cytosol solution. We find that, unlike the situation in dilute solutions, most metabolites spend the majority of their time in contact with other metabolites, or in contact with proteins. Furthermore, we find large non-covalently interacting metabolite structures are common and often associated with proteins. The presence of proteins reduced metabolite diffusion owing to long lasting correlations of motion. The dielectric constant of these simulations was found to differ from that of pure water only through a large contribution from proteins as metabolite and monatomic ion effects largely cancel. These findings suggest specific protein spheres of influence affecting metabolite diffusion and the electrostatic environment.

SDOCK: a global protein-protein docking program using stepwise force-field potentials

Fast Fourier transform (FFT) method limits the forms of scoring functions in global protein-protein docking. On the other hand, force field potentials can effectively describe the energy hyper surface of biological macromolecules. In this study, we developed a new protein-protein docking program, SDOCK, that incorporates van der Waals attractive potential, geometric collision, screened electrostatic potential, and Lazaridis-Karplus desolvation energy into the scoring function in the global searching process. Stepwise potentials were generated from the corresponding continuous forms to treat the structure flexibility. After optimization of the atom solvation parameters and the weights of different potential terms based on a new docking test set that contains 142 cases with small or moderate conformational changes upon binding, SDOCK slightly outperformed the well-known FFT based global docking program ZDOCK3.0. Among the 142 cases tested, 52.8% gave at least one near-native solutions in the top 100 solutions. SDOCK was also tested on six blind testing cases in Critical Assessment of Predicted Interactions rounds 13 to 18. In all six cases, the near-native solutions could be found within the top 350 solutions. Because the SDOCK approach performs global docking based on force-field potentials, one of its advantages is that it provides global binding free energy surface profiles for further analysis. The efficiency of the program is also comparable with that of other FFT based protein-protein docking programs. SDOCK is available for noncommercial applications at http://mdl.ipc.pku.edu.cn/cgi-bin/down.cgi.

Self-association of models of transmembrane domains of ErbB receptors in a lipid bilayer

Association of transmembrane (TM) helices is facilitated by the close packing of small residues present along the amino-acid sequence. Extensive studies have established the role of such small residue motifs (GxxxG) in the dimerization of Glycophorin A (GpA) and helped to elucidate the association of TM domains in the epidermal growth factor family of receptors (ErbBs). Although membrane-mediated interactions are known to contribute under certain conditions to the dimerization of proteins, their effect is often considered nonspecific, and any potential dependence on protein sequence has not been thoroughly investigated. We recently reported that the association of GpA is significantly assisted by membrane-induced contributions as quantified in different lipid bilayers. Herein we extend our studies to explore the origin of these effects and quantify their magnitude using different amino-acid sequences in the same lipid environment. Using a coarse-grained model that accounts for amino-acid specificity, we perform extensive parallel Monte Carlo simulations of ErbB homodimerization in dipalmitoyl-phosphatidylcholine lipid bilayers. A detailed characterization of dimer formation and estimates of the free energy of association reveal that the TM domains show a significant affinity to self-associate in lipid bilayers, in qualitative agreement with experimental findings. The presence of GxxxG motifs enhances favorable protein-protein interactions at short separations. However, the lipid-induced attraction presents a more complex character than anticipated. Depending on the interfacial residues, lipid-entropic contributions support a decrease of separation or a parallel orientation to the membrane normal, with important implications for protein function.

Significant enhancement of docking sensitivity using implicit ligand sampling

The efficient and accurate quantification of protein-ligand interactions using computational methods is still a challenging task. Two factors strongly contribute to the failure of docking methods to predict free energies of binding accurately: the insufficient incorporation of protein flexibility coupled to ligand binding and the neglected dynamics of the protein-ligand complex in current scoring schemes. We have developed a new methodology, named the 'ligand-model' concept, to sample protein conformations that are relevant for binding structurally diverse sets of ligands. In the ligand-model concept, molecular-dynamics (MD) simulations are performed with a virtual ligand, represented by a collection of functional groups that binds to the protein and dynamically changes its shape and properties during the simulation. The ligand model essentially represents a large ensemble of different chemical species binding to the same target protein. Representative protein structures were obtained from the MD simulation, and docking was performed into this ensemble of protein conformation. Similar binding poses were clustered, and the averaged score was utilized to rerank the poses. We demonstrate that the ligand-model approach yields significant improvements in predicting native-like binding poses and quantifying binding affinities compared to static docking and ensemble docking simulations into protein structures generated from an apo MD simulation.

ASPDock: protein-protein docking algorithm using atomic solvation parameters model

Background

Atomic Solvation Parameters (ASP) model has been proven to be a very successful method of calculating the binding free energy of protein complexes. This suggests that incorporating it into docking algorithms should improve the accuracy of prediction. In this paper we propose an FFT-based algorithm to calculate ASP scores of protein complexes and develop an ASP-based protein-protein docking method (ASPDock).

Results

The ASPDock is first tested on the 21 complexes whose binding free energies have been determined experimentally. The results show that the calculated ASP scores have stronger correlation (r ≈ 0.69) with the binding free energies than the pure shape complementarity scores (r ≈ 0.48). The ASPDock is further tested on a large dataset, the benchmark 3.0, which contain 124 complexes and also shows better performance than pure shape complementarity method in docking prediction. Comparisons with other state-of-the-art docking algorithms showed that ASP score indeed gives higher success rate than the pure shape complementarity score of FTDock but lower success rate than Zdock3.0. We also developed a softly restricting method to add the information of predicted binding sites into our docking algorithm. The ASP-based docking method performed well in CAPRI rounds 18 and 19.

Conclusions

ASP may be more accurate and physical than the pure shape complementarity in describing the feature of protein docking.

Regulation of cAMP-dependent protein kinases: the human protein kinase X (PrKX) reveals the role of the catalytic subunit alphaH-alphaI loop

cAMP-dependent protein kinases are reversibly complexed with any of the four isoforms of regulatory (R) subunits, which contain either a substrate or a pseudosubstrate autoinhibitory domain. The human protein kinase X (PrKX) is an exemption as it is inhibited only by pseudosubstrate inhibitors, i.e. RIα or RIβ but not by substrate inhibitors RIIα or RIIβ. Detailed examination of the capacity of five PrKX-like kinases ranging from human to protozoa (Trypanosoma brucei) to form holoenzymes with human R subunits in living cells shows that this preference for pseudosubstrate inhibitors is evolutionarily conserved. To elucidate the molecular basis of this inhibitory pattern, we applied bioluminescence resonance energy transfer and surface plasmon resonance in combination with site-directed mutagenesis. We observed that the conserved αH-αI loop residue Arg-283 in PrKX is crucial for its RI over RII preference, as a R283L mutant was able to form a holoenzyme complex with wild type RII subunits. Changing the corresponding αH-αI loop residue in PKA Cα (L277R), significantly destabilized holoenzyme complexes in vitro, as cAMP-mediated holoenzyme activation was facilitated by a factor of 2-4, and lead to a decreased affinity of the mutant C subunit for R subunits, significantly affecting RII containing holoenzymes.

Hydrophilic linkers and polar contacts affect aggregation of FG repeat peptides

Transport of large proteins into the nucleus involves two events, binding of the cargo protein to a transport receptor in the cytoplasm and passage of the cargo-transporter complex through the selective permeability barrier of the nuclear pore complex. The permeability barrier is formed by largely disordered polypeptides, each containing a number of conserved hydrophobic phenylalanine-glycine (FG) sequence motifs, connected by hydrophilic linkers of varying sequence (FG nups). How the motifs interact to form the permeability barrier, however, is not yet known. We have, therefore, carried out molecular dynamics simulations on various model FG repeat peptides to study the aggregation propensity of FG nups and the specific roles of the hydrophobic FG motifs and the hydrophilic linkers. Our simulations show spontaneous aggregation of the model nups into hydrated aggregates, which exhibit structural features assumed to be part of the permeability barrier. Our simulations suggest that short beta-sheets are an important structural feature of the aggregates and that Phe residues are sufficiently exposed to allow rapid binding of transport receptors. A surprisingly large influence of the amino acid composition of the hydrophilic linkers on aggregation is seen, as well as a major contribution of hydrogen-bonding patterns.

Insights into the molecular mechanism of an ABC transporter: conformational changes in the NBD dimer of MJ0796

Despite the rapid advances in the study of ABC transporters, many fundamental questions linked to ATP binding/hydrolysis and its relation to the transport cycle remain unanswered. In particular, it is still neither clear nor consensual how the ATP energy is used by the nucleotide binding domains (NBDs) to produce mechanical work and drive the substrate translocation. The major conformational changes in the NBDs following ATP hydrolysis during the transport cycle and the role played by the conserved family motifs in harnessing the energy associated with nucleotide hydrolysis are yet unknown. Additionally, the way energy is transmitted from the catalytic to the membrane domains, in order to drive substrate translocation, is also a fundamental question that remains unanswered. Due to the high structure similarities of the NBD architecture throughout the whole ABC family, it is likely that the mechanism of ATP binding, hydrolysis, and communication with the transmembrane domains is similar in all family members, independently of the nature of the transported substrate. In this work, we focused our attention on the consequences of ATP hydrolysis in the NBDs, especially on the structural changes that occur during this process. For that, we use molecular dynamics simulation techniques taking as a starting point the X-ray structure of the MJ0796 dimer from Methanococcus jannaschii. Several potential intermediate states of the ATP hydrolytic cycle are investigated, each consisting of different combinations of nucleotide-bound forms. The results obtained allowed us to identify the conformational rearrangements induced by hydrolysis on the catalytic subunits, as well as the residues involved in this reorganization. The major changes are localized at specific regions of the protein, namely, involving segments 11-19 and 93-124. Additionally, our results together with the knowledge of complete ABC transporter X-ray structures suggest a possible NBD:TMD signal transmission interface.

The behavior of the hydrophobic effect under pressure and protein denaturation

It is well known that proteins denature under high pressure. The mechanism that underlies such a process is still not clearly understood, however, giving way to controversial interpretations. Using molecular dynamics simulation on systems that may be regarded experimentally as limiting examples of the effect of high pressure on globular proteins, such as lysozyme and apomyoglobin, we have effectively reproduced such similarities and differences in behavior as are interpreted from experiment. From the analysis of such data, we explain the experimental evidence at hand through the effect of pressure on the change of water structure, and hence the weakening of the hydrophobic effect that is known to be the main driving force in protein folding.

Stepwise hydration and evaporation of adenosine monophosphate nucleotide anions: a multiscale theoretical study

The structure and finite-temperature properties of hydrated nucleotide anion adenosine 5'-monophosphate (AMP) have been theoretically investigated with a variety of methods. Using a polarizable version of the Amber force field and replica-exchange molecular dynamics simulations, putative lowest-energy structures have been located for the AMP(-)(H(2)O)(n) cluster anions with n = 0-20. The hydration energies obtained with the molecular mechanics potential slightly overestimate experimental measurements. However, closer values are found after reoptimizing the structures locally at more sophisticated levels, namely semi-empirical (PM6) and density-functional theory (B3LYP/6-31+G*). Upon heating the complexes, various indicators such as the heat capacity, number of hydrogen bonds or surface area provide evidence that the water cluster melts below 200 K but remains bonded to the AMP anion. The sequential loss of water molecules after sudden heating has been studied using a statistical approach in which unimolecular evaporation is described using the orbiting transition state version of phase space theory, together with anharmonic densities of vibrational states. The evaporation rates are calibrated based on the results of molecular dynamics trajectories at high internal energy. Our results indicate that between 4 and 10 water molecules are lost from AMP(-)(H(2)O)(20) after one second depending on the initial heating in the 250-350 K range, with a concomitant cooling of the remaining cluster by 75-150 K.

Insulin dimer dissociation and unfolding revealed by amide I two-dimensional infrared spectroscopy

A structurally sensitive probe of the monomer/dimer equilibrium of insulin was developed using 2DIR spectroscopy and interpreted using calculated spectra.

Improvement and analysis of computational methods for prediction of residual dipolar couplings

We describe a new, computationally efficient method for computing the molecular alignment tensor based on the molecular shape. The increase in speed is achieved by re-expressing the problem as one of numerical integration, rather than a simple uniform sampling (as in the PALES method), and by using a convex hull rather than a detailed representation of the surface of a molecule. This method is applicable to bicelles, PEG/hexanol, and other alignment media that can be modeled by steric restrictions introduced by a planar barrier. This method is used to further explore and compare various representations of protein shape by an equivalent ellipsoid. We also examine the accuracy of the alignment tensor and residual dipolar couplings (RDC) prediction using various ab initio methods. We separately quantify the inaccuracy in RDC prediction caused by the inaccuracy in the orientation and in the magnitude of the alignment tensor, concluding that orientation accuracy is much more important in accurate prediction of RDCs.

McVol - a program for calculating protein volumes and identifying cavities by a Monte Carlo algorithm

In this paper, we describe a Monte Carlo method for determining the volume of a molecule. A molecule is considered to consist of hard, overlapping spheres. The surface of the molecule is defined by rolling a probe sphere over the surface of the spheres. To determine the volume of the molecule, random points are placed in a three-dimensional box, which encloses the whole molecule. The volume of the molecule in relation to the volume of the box is estimated by calculating the ratio of the random points placed inside the molecule and the total number of random points that were placed. For computational efficiency, we use a grid-cell based neighbor list to determine whether a random point is placed inside the molecule or not. This method in combination with a graph-theoretical algorithm is used to detect internal cavities and surface clefts of molecules. Since cavities and clefts are potential water binding sites, we place water molecules in the cavities. The potential water positions can be used in molecular dynamics calculations as well as in other molecular calculations. We apply this method to several proteins and demonstrate the usefulness of the program. The described methods are all implemented in the program McVol, which is available free of charge from our website at http://www.bisb.uni-bayreuth.de/software.html .

Urea impedes the hydrophobic collapse of partially unfolded proteins

Proteins are denatured in aqueous urea solution. The nature of the molecular driving forces has received substantial attention in the past, whereas the question how urea acts at different phases of unfolding is not yet well understood at the atomic level. In particular, it is unclear whether urea actively attacks folded proteins or instead stabilizes unfolded conformations. Here we investigated the effect of urea at different phases of unfolding by molecular dynamics simulations, and the behavior of partially unfolded states in both aqueous urea solution and in pure water was compared. Whereas the partially unfolded protein in water exhibited hydrophobic collapses as primary refolding events, it remained stable or even underwent further unfolding steps in aqueous urea solution. Further, initial unfolding steps of the folded protein were found not to be triggered by urea, but instead, stabilized. The underlying mechanism of this stabilization is a favorable interaction of urea with transiently exposed, less-polar residues and the protein backbone, thereby impeding back-reactions. Taken together, these results suggest that, quite generally, urea-induced protein unfolding proceeds primarily not by active attack. Rather, thermal fluctuations toward the unfolded state are stabilized and the hydrophobic collapse of partially unfolded proteins toward the native state is impeded. As a result, the equilibrium is shifted toward the unfolded state.

Conformational behaviour determines the low-relaxivity state of a conditional MRI contrast agent

The conformational behaviour in aqueous solution of the EgadMe complex, a conditional gadolinium-based contrast agent sensitive to beta-galactosidase enzymatic activity, is investigated by means of ab initio calculations and classical molecular dynamics simulations. Furthermore, force field parameterization of gadolinium-ligand interactions is performed, and its reliability is tested on the bench mark [Gd(DOTA)](-) system by MD simulations. Both computational methods highlight the presence in EgadMe of two main conformational isomers. The lowest energy conformation is a "close" form, corresponding to a state of low-relaxivity (MRI "inactive"), in which the ninth coordination site of the gadolinium ion is occupied by one oxygen atom of the galactopyranose residue. The second isomer, which is 2.9 (at ab initio level) and 4.2 (at MD level) kcal mol(-1) above the global minimum, presents an "open" form, corresponding to a state of high-relaxivity (MRI "active") in which one water molecule coordinates the ion. These results are consistent with experimental findings reported for EgadMe, and show that competition at the ninth coordination site of gadolinium ion, between the intra (the galactopyranose residue) and inter (water molecules) molecular interactions, affects the relaxivity of this system.

Surface activity of amphiphilic helical beta-peptides from molecular dynamics simulation

The surface activity of beta-peptides is investigated using molecular simulations. The type and display of hydrophobic and hydrophilic groups on helical beta-peptides is varied systematically. Peptides with 2/3 hydrophobic groups are found to be surface active, and to adopt an orientation parallel to the air-water interface. For select beta-peptides, we also determine the potential of mean force required to bring a peptide to the air-water interface. Facially amphiphilic helices with 2/3 hydrophobic groups are found to exhibit the lowest free energy of adsorption. The adsorption process is driven by a favorable energetic term and opposed by negative entropic changes. The temperature dependence of adsorption is also investigated; facially amphiphilic helices are found to adopt orientations that are largely independent of temperature, while nonfacially amphiphilic helices sample a broader range of interfacial orientations at elevated temperatures. The thermodynamics of adsorption of beta-peptides is compared to that of 1-octanol, a well-known surfactant, and ovispirin, a naturally occurring antimicrobial peptide. It is found that the essential difference lies in the sign of the entropy of adsorption, which is negative for beta- and alpha-peptides and positive for traditional surfactants such as octanol.

Surface features of a Mononegavirales matrix protein indicate sites of membrane interaction

The matrix protein (M) of respiratory syncytial virus (RSV), the prototype viral member of the Pneumovirinae (family Paramyxoviridae, order Mononegavirales), has been crystallized and the structure determined to a resolution of 1.6 A. The structure comprises 2 compact beta-rich domains connected by a relatively unstructured linker region. Due to the high degree of side-chain order in the structure, an extensive contiguous area of positive surface charge covering approximately 600 A(2) can be resolved. This unusually large patch of positive surface potential spans both domains and the linker, and provides a mechanism for driving the interaction of the protein with a negatively-charged membrane surface or other virion components such as the nucleocapsid. This patch is complemented by regions of high hydrophobicity and a striking planar arrangement of tyrosine residues encircling the C-terminal domain. Comparison of the RSV M sequence with other members of the Pneumovirinae shows that regions of divergence correspond to surface exposed loops in the M structure, with the majority of viral species-specific differences occurring in the N-terminal domain.

Solvent exposure imparts similar selective pressures across a range of yeast proteins

We study how an amino acid residue's solvent exposure influences its propensity for substitution by analyzing multiple alignments of 61 yeast genes for which the crystal structure is known. We find that the selective constraint on the interior residues is on average 10 times that of residues on the surface. Surprisingly, there is no correlation between the overall selective constraint observed for a protein alignment and the ratio of constraints on interior and surface residues. By modeling the selective constraint on several amino acid properties, we show that although residue volume and hydropathy are strongly conserved across most alignments, there is little variation in interior versus surface conservation for these two properties. By contrast, residue charge (isoelectric point) is less generally conserved when considering the protein as a whole but shows a strong constraint against the introduction of charged residues into the protein interior.

VASCo: computation and visualization of annotated protein surface contacts

BACKGROUND

Structural data from crystallographic analyses contain a vast amount of information on protein-protein contacts. Knowledge on protein-protein interactions is essential for understanding many processes in living cells. The methods to investigate these interactions range from genetics to biophysics, crystallography, bioinformatics and computer modeling. Also crystal contact information can be useful to understand biologically relevant protein oligomerisation as they rely in principle on the same physico-chemical interaction forces. Visualization of crystal and biological contact data including different surface properties can help to analyse protein-protein interactions.

RESULTS

VASCo is a program package for the calculation of protein surface properties and the visualization of annotated surfaces. Special emphasis is laid on protein-protein interactions, which are calculated based on surface point distances. The same approach is used to compare surfaces of two aligned molecules. Molecular properties such as electrostatic potential or hydrophobicity are mapped onto these surface points. Molecular surfaces and the corresponding properties are calculated using well established programs integrated into the package, as well as using custom developed programs. The modular package can easily be extended to include new properties for annotation. The output of the program is most conveniently displayed in PyMOL using a custom-made plug-in.

CONCLUSION

VASCo supplements other available protein contact visualisation tools and provides additional information on biological interactions as well as on crystal contacts. The tool provides a unique feature to compare surfaces of two aligned molecules based on point distances and thereby facilitates the visualization and analysis of surface differences.

Polar or apolar--the role of polarity for urea-induced protein denaturation

Urea-induced protein denaturation is widely used to study protein folding and stability; however, the molecular mechanism and driving forces of this process are not yet fully understood. In particular, it is unclear whether either hydrophobic or polar interactions between urea molecules and residues at the protein surface drive denaturation. To address this question, here, many molecular dynamics simulations totalling ca. 7 µs of the CI2 protein in aqueous solution served to perform a computational thought experiment, in which we varied the polarity of urea. For apolar driving forces, hypopolar urea should show increased denaturation power; for polar driving forces, hyperpolar urea should be the stronger denaturant. Indeed, protein unfolding was observed in all simulations with decreased urea polarity. Hyperpolar urea, in contrast, turned out to stabilize the native state. Moreover, the differential interaction preferences between urea and the 20 amino acids turned out to be enhanced for hypopolar urea and suppressed (or even inverted) for hyperpolar urea. These results strongly suggest that apolar urea–protein interactions, and not polar interactions, are the dominant driving force for denaturation. Further, the observed interactions provide a detailed picture of the underlying molecular driving forces. Our simulations finally allowed characterization of CI2 unfolding pathways. Unfolding proceeds sequentially with alternating loss of secondary or tertiary structure. After the transition state, unfolding pathways show large structural heterogeneity.

To perform their physiological function, proteins have to fold into their characteristic three-dimensional structure. While the folded state is stable under physiological conditions, changes in the solvent can destabilize the folded state and even induce denaturation. One of the most commonly used denaturants is urea. Despite its widespread use to study protein folding and stability, however, the molecular mechanism and particularly the driving forces of urea-induced protein denaturation are not yet understood. Two mechanisms have been suggested, according to which denaturation is driven either by polar interactions via hydrogen bonds or by hydrophobic interactions with apolar amino acids. By systematically varying urea polarity and quantifying the interactions of the solvent molecules with all amino acids of the protein, the present simulation study reveals that it is mainly the apolar interactions that drive denaturation. Our results suggest a coherent microscopic picture for urea-induced denaturation and bear more general implications for protein stability in other environments, e.g., in chaperone-assisted folding.

NMR: prediction of molecular alignment from structure using the PALES software

Orientational restraints such as residual dipolar couplings promise to overcome many of the problems that traditionally limited liquid-state nuclear magnetic resonance spectroscopy. Recently, we developed methods to predict a molecular alignment tensor and thus residual dipolar couplings for a given molecular structure. This provides many new opportunities for the study of the structure and dynamics of proteins, nucleic acids, oligosaccharides and small molecules. This protocol details the use of the software PALES (Prediction of AlignmEnt from Structure) for prediction of an alignment tensor from a known three-dimensional (3D) coordinate file of a solute. The method is applicable to alignment of molecules in many neutral and charged orienting media and takes into account the molecular shape and 3D charge distribution of the molecule.

Mechanical stability of helical beta-peptides and a comparison of explicit and implicit solvent models

Synthetic beta-peptide oligomers have been shown to form stable folded structures analogous to those encountered in naturally occurring proteins. Literature studies have speculated that the conformational stability of beta-peptides is greater than that of alpha-peptides. Direct measurements of that stability, however, are not available. Molecular simulations are used in this work to quantify the mechanical stability of four helical beta-peptides. This is achieved by subjecting the molecules to tension. The potential of mean force associated with the resulting unfolding process is determined using both an implicit and an explicit solvent model. It is found that all four molecules exhibit a highly stable helical structure. It is also found that the energetic contributions to the potential of mean force do not change appreciably when the molecules are stretched in explicit water. In contrast, the entropic contributions decrease significantly. As the peptides unfold, a loss of intramolecular energy is compensated by the formation of additional water-peptide hydrogen bonds. These entropic effects lead in some cases to a loss of stability upon cooling the peptides, a phenomenon akin to the cold denaturing of some proteins. While the location of the free energy minimum and the structural helicity of the peptides are comparable in the implicit-solvent and explicit-water cases, it is found that, in general, the helical structure of the molecules is more stable in the implicit solvent model than in explicit water.

Effects of surface-to-volume ratio of proteins on hydrophilic residues: decrease in occurrence and increase in buried fraction

The size of a protein is an important factor for understanding the sequence-structure relationship, and it affects both the amino acid composition and the residue burial of proteins. However, it is usually measured as the number of amino acids, although these effects would result from the reduction of surface regions relative to the volume of core regions in larger proteins. In addition, although these two effects are dependent on each other, they have been studied separately. In this study, we investigated them by considering the surface-to-volume ratio (SVR), and observed the correlation between them. We found that the reduction of several hydrophilic residues is more strongly correlated with SVR than with protein size (the number of amino acids) and that SVR directly affects the amino acid composition. The difference as a descriptor between SVR and size is also supported by the observation that the secondary structural elements correlate completely differently with SVR and with size. Furthermore, for the four most hydrophilic residues, glutamine, arginine, glutamic acid, and lysine, balances between the decrease in composition and the increase in core burial were observed. We found that the burial of glutamine and arginine became accelerated at SVR = 0.3 A(-1) (approximately 132 residues) as the protein size increased, but that lysine has an upper limit of 0.9% for its occurrence in the core. The uniqueness of lysine was also elucidated by comparison with the burial environments of the four hydrophilic residues.

Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners

Background

Proteins are involved in many interactions with other proteins leading to networks that regulate and control a wide variety of physiological processes. Some of these proteins, called hub proteins or hubs, bind to many different protein partners. Protein intrinsic disorder, via diversity arising from structural plasticity or flexibility, provide a means for hubs to associate with many partners (Dunker AK, Cortese MS, Romero P, Iakoucheva LM, Uversky VN: Flexible Nets: The roles of intrinsic disorder in protein interaction networks. FEBS J 2005, 272:5129-5148).

Results

Here we present a detailed examination of two divergent examples: 1) p53, which uses different disordered regions to bind to different partners and which also has several individual disordered regions that each bind to multiple partners, and 2) 14-3-3, which is a structured protein that associates with many different intrinsically disordered partners. For both examples, three-dimensional structures of multiple complexes reveal that the flexibility and plasticity of intrinsically disordered protein regions as well as induced-fit changes in the structured regions are both important for binding diversity.

Conclusions

These data support the conjecture that hub proteins often utilize intrinsic disorder to bind to multiple partners and provide detailed information about induced fit in structured regions.

Proton pathways in a [NiFe]-hydrogenase: A theoretical study

We present here a theoretical study to investigate possible proton pathways in the [NiFe]-hydrogenase from Desulfovibrio gigas. The approach used in this study consists of a combination of Poisson-Boltzmann and Monte Carlo simulations together with a distance-based network analysis to find possible groups involved in the proton transfer. Results obtained at different pH values show a reasonable number of proton active residues distributed by the protein interior and surface, with a concentration around the metal centres. The electrostatic interactions in this protein are strong, as shown by the unusual shape of the titration curves of several sites. Some residue pairs show strongly correlated protonations, indicating the sharing and probably exchange of a proton between them. The conjugation of the PB and MC simulations with the distance-based analysis allows a detailed characterization of the possible proton pathways. We discuss previous suggestions and propose a new complete pathway for the proton transfer between the active site and the surface. This pathway is mainly composed of histidines and glutamic acid residues.