DFT study of the chemistry of sulfur in graphite,including interactions with defects,edges and folds

Sulfur has several roles, desirable and undesirable, in graphitization. We perform density functional theory calculations within the local density approximation to define the structures and energetics of sulphur in graphite, including its interactions with point defects and edges, in order to understand its role in the later stages of graphitization. We find sulphur does not cross-link layers, except where there are defects. It reacts very strongly with vacancies in neighbouring layers to form a six coordinate split vacancy structure, analogous to that found in diamond. It is also highly stable at basal edge sites, where, as might be expected, the size and valency of sulfur can be easily accommodated. This suggests a role for sulphur in stabilizing graphene edges, and following from this, we show that sulfur dimers can open, i.e. unzip, folds in graphite rapidly and exothermically.     

Determination of the structures of small gold clusters on stepped magnesia by density functional calculations

The structural modifications of small supported gold clusters caused by realistic surface defects (steps) in the MgO(001) support are investigated by computational methods. The most stable gold cluster structures on a stepped MgO(001) surface are searched for in the size range up to 24 Au atoms, and locally optimized by density-functional calculations. Several structural motifs are found within energy differences of 1 eV: inclined leaflets, arched leaflets, pyramidal hollow cages and compact structures. We show that the interaction with the step clearly modifies the structures with respect to adsorption on the flat defect-free surface. We find that leaflet structures clearly dominate for smaller sizes. These leaflets are either inclined and quasi-horizontal, or arched, at variance with the case of the flat surface in which vertical leaflets prevail. With increasing cluster size pyramidal hollow cages begin to compete against leaflet structures. Cage structures become more and more favourable as size increases. The only exception is size 20, at which the tetrahedron is found as the most stable isomer. This tetrahedron is however quite distorted. The comparison of two different exchange-correlation functionals (Perdew-Burke-Ernzerhof and local density approximation) show the same qualitative trends.     

Representation of the Protein Universe using Classifications,Maps, and Networks

A meaningful and coherent global picture of the protein universe is needed to better understand protein evolution and the underlying biophysics. We survey the studies that tackled this fundamental challenge, providing a glimpse of the protein space. A global picture represents all known local relationships among proteins, and needs to do so in a comprehensive and accurate manner. Three types of global representations can be used: classifications, maps, and networks. In these, the local relationships are derived, based on the similarity of the proteins′ sequences, structures, or functions (or a combination of these). Alternatively, the local relationships can be co-occurrences of elements in the protein universe. The representations can be based on different objects: full polypeptide chains, fragments, such as structural domains, or even smaller motifs. Different protein qualities were revealed in each study; many point out the uniqueness of domains of the alpha/beta SCOP (structural classification of proteins) class.     

Optimizing the Kinetics and Thermodynamics of DNA i‐Motif Folding

Under slightly acidic conditions, single cytidine‐rich DNA strands can form four‐stranded structures called i‐motifs. The stability of the i‐motif structure is based on the intercalation of hemiprotonated C–C⁺ base pairs. In addition, the stability of these structures is influenced by pH, temperature, salt concentration, number of cytidines per C‐rich stretch, and length of sequence; it also depends on the nucleotides in the connecting loop regions. Here, we investigated the influence of the loop nucleotides on i‐motif stability, structure, and kinetics of folding, in five structures with the same loop‐size but different adenosine and thymidine residues within the loop. The stabilities of the i‐motif structures were determined by CD melting, and structure and kinetics of folding were studied by static and time‐resolved NMR experiments.     

A consensus residue analysis of loop and helix-capping residues in four- alpha-helical-bundle proteins

A statistical study was performed on a set of proteins which adopt the four-alpha-helical-bundle tertiary motif in order to determine amino acid occurrences at helix-capping and loop positions. Eight X-ray crystal structures from the Brookhaven Protein Data Bank (PDB) were examined and N", N', Ncap, Ccap, C' and C" residues were assigned. In addition, a set of 55 protein sequences for the analogous proteins from different strains and species was taken from the Protein Information Resource and Swiss-Prot databanks. The residues at the capping and loop positions in this expanded data set were deduced by aligning these sequences with those from the PDB files. Similar trends were observed in the two data sets. In general, polar residues were predominant in the loops, although aromatic residues were also fairly common. Glycine, a highly flexible residue with an excellent 'helix-breaking' ability, was very common at the Ccap, C' and C" residues. Proline, which can force sharp turns in the direction of a peptide backbone, was only common at the N" residue. Residues which can participate in the N- capping box motif were found with high frequency. Capping motifs at the helix C-termini (Schellman and alphaL motifs) were also somewhat common, while another helix N-terminal stabilizing motif, the hydrophobic stable, was not common. The data presented in this study should prove useful for applying the 'consensus residue' approach to the de novo design of loop regions in helical bundle proteins.      

Main-chain complementarity in protein-protein recognition

We present a statistical analysis of protein structures basedon interatomic C_a distances. The overall distance distributionsreflect in detail the contents of sequence-specific substructuresmaintained by local interactions (such as -helixes) and longerrange interactions (such as disulfide bridges and ß-sheets).We also show that a volume scaling of the distances makes distancedistributions for protein chains of different length superimposable.Distance distributions were also calculated specifically foramino acids separated by a given number of residues. Specificfeatures in these distributions are visible for sequence separationsof up to 20 amino acid residues. A simple representation, whichpreserves most of the information in the distance distributions,was obtained using six parameters only. The parameters giverise to canonical distance intervals and when predicting coarse-graineddistance constraints by methods such as data-driven artificialneural networks, these should preferably be selected from theseintervals. We discuss the use of the six parameters for determiningor reconstructing 3-D protein structures.     

Distance distributions in proteins: a six-parameter representation

We present a statistical analysis of protein structures basedon interatomic C_a distances. The overall distance distributionsreflect in detail the contents of sequence-specific substructuresmaintained by local interactions (such as -helixes) and longerrange interactions (such as disulfide bridges and ß-sheets).We also show that a volume scaling of the distances makes distancedistributions for protein chains of different length superimposable.Distance distributions were also calculated specifically foramino acids separated by a given number of residues. Specificfeatures in these distributions are visible for sequence separationsof up to 20 amino acid residues. A simple representation, whichpreserves most of the information in the distance distributions,was obtained using six parameters only. The parameters giverise to canonical distance intervals and when predicting coarse-graineddistance constraints by methods such as data-driven artificialneural networks, these should preferably be selected from theseintervals. We discuss the use of the six parameters for determiningor reconstructing 3-D protein structures.     

Deterministic features of side-chain main-chain hydrogen bonds in globular protein structures

A total of 19 835 polar residues from a data set of 250 non-homologousand highly resolved protein crystal structures were used toidentify side-chain main-chain (SC-MC) hydrogen bonds. The ratioof the number of SC-MC hydrogen bonds to the total number ofpolar residues is close to 1:2, indicating the ubiquitous natureof such hydrogen bonds. Close to 56% of the SC-MC hydrogen bondsare local involving side-chain acceptor/donor (`i') and a main-chaindonor/acceptor within the window i–5 to i+5. These short-rangehydrogen bonds form well defined conformational motifs characterizedby specific combinations of backbone and side-chain torsionangles. (a) The Ser/Thr residues show the greatest preferencein forming intra-helical hydrogen bonds between the atoms O_iand O_i–4. More than half the examples of such hydrogenbonds are found at the middle of -helices rather than at theirends. The most favoured motif of these examples is _RRRR(g^–).(b) These residues also show great preference to form hydrogenbonds between O_i and O_i–3, which are closely related tothe previous type and though intra-helical, these hydrogen bondsare more often found at the C-termini of helices than at themiddle. The motif represented by _RRRR(g⁺) is most preferredin these cases. (c) The Ser, Thr and Glu are the most frequentlyfound residues participating in intra-residue hydrogen bonds(between the side-chain and main-chain of the same residue)which are characterized by specific motifs of the form ß(g⁺)for Ser/Thr residues and _R(g^–g⁺t) for Glu/Gln. (d) Theside-chain acceptor atoms of Asn/Asp and Ser/Thr residues showhigh preference to form hydrogen bonds with acceptors two residuesahead in the chain, which are characterized by the motifs ß (tt')Rand ß(t)_R, respectively. These hydrogen bonded segments,referred to as Asx turns, are known to provide stability totype I and type I' ß-turns. (e) Ser/Thr residues oftenform a combination of SC-MC hydrogen bonds, with the side-chaindonor hydrogen bonded to the carbonyl oxygen of its own peptidebackbone and the side-chain acceptor hydrogen bonded to an amidehydrogen three residues ahead in the sequence. Such motifs arequite often seen at the beginning of -helices, which are characterizedby the ß(g⁺)_RR motif. A remarkable majority of all thesehydrogen bonds are buried from the protein surface, away fromthe surrounding solvent. This strongly indicates the possibilityof side-chains playing the role of the backbone, in the proteininteriors, to satisfy the potential hydrogen bonding sites andmaintaining the network of hydrogen bonds which is crucial tothe structure of the protein.     

Relative Stabilities of Conserved and Non-Conserved Structures in the OB-Fold Superfamily

The OB-fold is a diverse structure superfamily based on a β-barrel motif that is often supplemented with additional non-conserved secondary structures. Previous deletion mutagenesis and NMR hydrogen exchange studies of three OB-fold proteins showed that the structural stabilities of sites within the conserved β-barrels were larger than sites in non-conserved segments. In this work we examined a database of 80 representative domain structures currently classified as OB-folds, to establish the basis of this effect. Residue-specific values were obtained for the number of Cα-Cα distance contacts, sequence hydrophobicities, crystallographic B-factors, and theoretical B-factors calculated from a Gaussian Network Model. All four parameters point to a larger average flexibility for the non-conserved structures compared to the conserved β-barrels. The theoretical B-factors and contact densities show the highest sensitivity. Our results suggest a model of protein structure evolution in which novel structural features develop at the periphery of conserved motifs. Core residues are more resistant to structural changes during evolution since their substitution would disrupt a larger number of interactions. Similar factors are likely to account for the differences in stability to unfolding between conserved and non-conserved structures.     

Molecular shape comparisons in searches for active sites and functional similarity

Here we examine the reliability of surface comparisons in searches for active sites in proteins. Detection of a patch of surface on one protein which is similar to an active site in another, may suggest similarities in enzymatic mechanisms, in enzyme functions and implicate a potential target for ligand/inhibitor design. Specifically, we compare the efficacy of molecular surface comparisons with comparisons of surface atoms and of C(alpha) backbone atoms. We further investigate comparisons of specific atoms, belonging to a predefined pattern of catalytic residues versus comparisons of molecular surfaces and, separately, of surface atoms. This aspect is particularly relevant, as catalytic residues may be (partially) buried. We also explore active site comparisons versus comparisons in which the entire molecular surfaces are scanned. While here we focus on the geometrical aspect of the problem, we also investigate the effect of adding residue labels in these comparisons. Our extensive studies cover the serine proteases, containing the highly conserved triad motif, and the chorismate mutases. Since such active site comparisons entail comparisons between unconnected points in 3D space, an order-independent comparison technique is necessary. The geometric hashing algorithm is ideally suited to handling such a task. It can perform both global shape matching for the whole surfaces of large protein molecules and searching for local shape similarities for small surface motifs. Our results show that molecular surface comparisons work best when the similarity is high. As the similarity deteriorates, the number of potential solutions increases rapidly, making their ranking difficult, particularly when scanning entire molecular surfaces. Utilizing atomic coordinates directly appears more adequate under such circumstances.      

Transport properties of porous media from the microgeometry of a three-dimensional voronoi network

In this work a way of calculating effective transport coefficients from the microgeometry of a porous medium is presented. The model material consists of a random packing of uniform spheres, and by applying the Voronoi—Delaunay tessellation technique the void between the spheres is simulated as a network of cylindrical pores. The tessellation yields all the necessary information for the structural characterization, such as the pore diameter, pore angle and pore length distribution functions and the topological interconnection. The effective transport coefficients of ordinary diffusion, Knudsen flow and viscous flow are calculated numerically by mass balancing at each network node and over all nodes of the system. The results obtained agree very well with the experimental ones, especially for ordinary diffusion. For Knudsen and viscous flow, inaccuracies in the estimation of the pore overlapping volume cause a relative error between the numerical and experimental results of the order of 16%–33%.     

Current Understanding of the Structure,Stability and Dynamic Properties of Amyloid Fibrils

Amyloid fibrils are supramolecular protein assemblies represented by a cross-β structure and fibrous morphology, whose structural architecture has been previously investigated. While amyloid fibrils are basically a main-chain-dominated structure consisting of a backbone of hydrogen bonds, side-chain interactions also play an important role in determining their detailed structures and physicochemical properties. In amyloid fibrils comprising short peptide segments, a steric zipper where a pair of β-sheets with side chains interdigitate tightly is found as a fundamental motif. In amyloid fibrils comprising longer polypeptides, each polypeptide chain folds into a planar structure composed of several β-strands linked by turns or loops, and the steric zippers are formed locally to stabilize the structure. Multiple segments capable of forming steric zippers are contained within a single protein molecule in many cases, and polymorphism appears as a result of the diverse regions and counterparts of the steric zippers. Furthermore, the β-solenoid structure, where the polypeptide chain folds in a solenoid shape with side chains packed inside, is recognized as another important amyloid motif. While side-chain interactions are primarily achieved by non-polar residues in disease-related amyloid fibrils, the participation of hydrophilic and charged residues is prominent in functional amyloids, which often leads to spatiotemporally controlled fibrillation, high reversibility, and the formation of labile amyloids with kinked backbone topology. Achieving precise control of the side-chain interactions within amyloid structures will open up a new horizon for designing useful amyloid-based nanomaterials.     

Folding core predictions from network models of proteins

Two different computational methods are employed to predict protein folding nuclei from native state structures, one based on an elastic network (EN) model and the other on a constraint network model of freely rotating rods. Three sets of folding cores are predicted with these models, and their correlation against the slow exchange folding cores identified by native state hydrogen-deuterium exchange (HX) experiments is used to test each method. These three folding core predictions rely on differences in the underlying models and relative importance of global or local motions for protein unfolding/folding reactions. For non-specific residue interactions, we use the Gaussian Network Model (GNM) to identify folding cores in the limits of two classes of motions, shortly referred to as global and local. The global mode minima from GNM represent the residues with the greatest potential for coordinating collective motions and are explored as potential folding nuclei. Additionally, the fast mode peaks that have previously been labeled as the kinetically hot residues are identified as a second folding core set dependent on local interactions. Finally, a third folding core set is defined by the most stable residues in a simulated thermal denaturation procedure of the FIRST software. This method uses an all-atomic analysis of the rigidity and flexibility of protein structures, which includes specific hydrophobic, polar and charged interactions. Comparison of the three folding core sets to HX data indicate that the fast mode peak residues determined by the GNM and the rigid folding cores of FIRST provide statistically significant enhancements over random correlation. The role of specific interactions in protein folding is also investigated by contrasting the differences between these two network-based computational methods.     

PPII Helical Peptidomimetics Templated by Cation–π Interactions

Poly‐proline type II (PPII) helical PXXP motifs are the recognition elements for a variety of protein–protein interactions that are critical for cellular signaling. Despite development of protocols for locking peptides into α‐helical and β‐strand conformations, there remains a lack of analogous methods for generating mimics of PPII helical structures. We describe herein a strategy to enforce PPII helical secondary structure in the 19‐residue TrpPlexus miniature protein. Through sequence variation, we showed that a network of cation–π interactions could drive the formation of PPII helical conformations for both peptide and N‐substituted glycine peptoid residues. The achievement of chemically diverse PPII helical scaffolds provides a new route towards discovering peptidomimetic inhibitors of protein–protein interactions mediated by PXXP motifs.     

Increasing the hydrophobic interaction between terminal W-motifs enhances the stability of Salmonella typhimurium sialidase. A general strategy for the stabilization of {beta}-propeller protein fold

Protein engineering of the ß-propeller protein aimedat enhancing the structural stability of the protein was carriedout using a monomeric single domain ß-propeller protein,Salmonella typhimurium sialidase, as a model. Ala53 and Ala69each located at strands B and C of the W1 motif were mutatedto Leu and Val, respectively, to increase the hydrophobic interactionbetween W1 and W6 motifs. The mutants showed enhanced stabilitytowards guanidine hydrochloride and thermal unfolding. Ala53Leushowed higher stability, probably owing to the capability ofthe mutated Leu to interact extensively with more residues involvedin the hydrophobic interactions between the terminal W-motifs.The mutations, which are located far from the active site, haveno significant effect on the enzymatic properties. The strategyto enhance the stability proposed here might be applied to theother ß-propeller proteins.