Local Protein Structure Research Articles

Discovery of Recurrent Structural Motifs for Approximating Three‐Dimensional Protein Structures

AbstractThe scope of conformation space that protein molecules can adopt is a problem of significant interest. Previous studies by other groups have shown that there are stereochemical constraints that confine local protein structures to a limited range of conformations. Furthermore, the results of many groups have demonstrated that the sequence‐to‐structure relationship remains detectable to some extent on a local level. By studying the conformational space of local protein structures, we may obtain more information concerning the constraints on local structural space and the sequence‐to‐structure mapping, hence facilitate ab initio structure prediction. In this study, we propose a novel algorithm that automatically discovers recurrent pentamer structures in proteins.The algorithm starts by applying Expectation‐Maximization (EM) clustering to the distances between non‐adjacent backbone Cα atoms in a large set of pentamer fragments. A rough partition of the conformation space can thus be derived. In the second stage, by applying a split‐and‐merge algorithm, we can obtain a finite number of clusters and guarantee the homogeneity and distinctiveness of each one. Each cluster of protein structures is represented by a centroid structure. The results show that, with 40 major representative structures, we can approximate most of the protein fragments with an error of 0.378 Å. With only 20 types of structures, the fragment structures can still be modeled at 0.44 Å, which is comparable to or better than the performance of previous methods. We term the representatives “building blocks.” On the global level, we demonstrate that by concatenating different combinations of building blocks, we can model whole protein structures at high resolution: a resolution of 2.54 Å can be achieved simply by using 10 types of building blocks. This finding suggests that the study of molecular structures can be hugely simplified using this reduced representation.

Complex formation between dodecylpyridinium chloride and multicharged anionic planar substances.

The complex formation between dodecylpyridinium chloride (DPC) and multicharged anionic planar substances, 14 azo dyes and 3 benzene- or naphthalenesulfonates, has been studied by the potentiometric titration using a surfactant selective electrode. The agreement between the observed maximum binding number and the number of anionic charges (n) on dye molecules showed n:1 complex formation. The binding isotherms were found to be composed of two types of binding; one is the noncooperative binding observed at low surfactant concentrations and the other is the cooperative binding at the higher concentrations. The microscopic binding constant for the noncooperative binding was found to take the values in the range of 50-200 mol(-)(1) dm(3) for many of the substances, but, takes more large values up to 2500 mol(-)(1) dm(3) for the substances which have a large hydrophobic part or the structure of separate hydrophobic and hydrophilic regions. A multiple regression analysis showed that the data of the corresponding standard free energy change of binding were well interpreted by the equation (in unit of kJ mol(-)(1)) DeltaG degrees = - 5.85 log P(S) - 1.68 log P(D) - 2.12z + 28.4, where P(S) and P(D) are the partition coefficients of the surfactants and planar substances in the 1-octanol/water system and z is the number of anionic charges on the planar molecules. At the beginning of the cooperative binding, precipitate formation was observed for almost all of the present systems. Among these, some of the dyes having the structure of separate hydrophobic and hydrophilic regions formed a needlelike crystal, which was accompanied by a hysteresis phenomenon in the binding isotherm. The stable complex formation by both the hydrophobic and electrostatic interactions between the surfactant and the planar substances was found to be important for the crystal formation. Depending on the manner of arrangement of the charged groups on the planar substances, the origin of the binding cooperativity was ascribed to the interactions between surfactants bound to one planar-substance molecule or to the association of the complexes. It was also found that the present small binding systems are useful as the model of ligand binding to protein local structures.

Combining evolutionary and structural information for local protein structure prediction

We study the effects of various factors in representing and combining evolutionary and structural information for local protein structural prediction based on fragment selection. We prepare databases of fragments from a set of non-redundant protein domains. For each fragment, evolutionary information is derived from homologous sequences and represented as estimated effective counts and frequencies of amino acids (evolutionary frequencies) at each position. Position-specific amino acid preferences called structural frequencies are derived from statistical analysis of discrete local structural environments in database structures. Our method for local structure prediction is based on ranking and selecting database fragments that are most similar to a target fragment. Using secondary structure type as a local structural property, we test our method in a number of settings. The major findings are: (1) the COMPASS-type scoring function for fragment similarity comparison gives better prediction accuracy than three other tested scoring functions for profile-profile comparison. We show that the COMPASS-type scoring function can be derived both in the probabilistic framework and in the framework of statistical potentials. (2) Using the evolutionary frequencies of database fragments gives better prediction accuracy than using structural frequencies. (3) Finer definition of local environments, such as including more side-chain solvent accessibility classes and considering the backbone conformations of neighboring residues, gives increasingly better prediction accuracy using structural frequencies. (4) Combining evolutionary and structural frequencies of database fragments, either in a linear fashion or using a pseudocount mixture formula, results in improvement of prediction accuracy. Combination at the log-odds score level is not as effective as combination at the frequency level. This suggests that there might be better ways of combining sequence and structural information than the commonly used linear combination of log-odds scores. Our method of fragment selection and frequency combination gives reasonable results of secondary structure prediction tested on 56 CASP5 targets (average SOV score 0.77), suggesting that it is a valid method for local protein structure prediction. Mixture of predicted structural frequencies and evolutionary frequencies improve the quality of local profile-to-profile alignment by COMPASS.

A Hidden Markov Model Derived Structural Alphabet for Proteins

Understanding and predicting protein structures depends on the complexity and the accuracy of the models used to represent them. We have set up a hidden Markov model that discretizes protein backbone conformation as series of overlapping fragments (states) of four residues length. This approach learns simultaneously the geometry of the states and their connections. We obtain, using a statistical criterion, an optimal systematic decomposition of the conformational variability of the protein peptidic chain in 27 states with strong connection logic. This result is stable over different protein sets. Our model fits well the previous knowledge related to protein architecture organisation and seems able to grab some subtle details of protein organisation, such as helix sub-level organisation schemes. Taking into account the dependence between the states results in a description of local protein structure of low complexity. On an average, the model makes use of only 8.3 states among 27 to describe each position of a protein structure. Although we use short fragments, the learning process on entire protein conformations captures the logic of the assembly on a larger scale. Using such a model, the structure of proteins can be reconstructed with an average accuracy close to 1.1 Å root-mean-square deviation and for a complexity of only 3. Finally, we also observe that sequence specificity increases with the number of states of the structural alphabet. Such models can constitute a very relevant approach to the analysis of protein architecture in particular for protein structure prediction.

A Hidden Markov Model Derived Structural Alphabet for Proteins

Understanding and predicting protein structures depends on the complexity and the accuracy of the models used to represent them. We have set up a hidden Markov model that discretizes protein backbone conformation as series of overlapping fragments (states) of four residues length. This approach learns simultaneously the geometry of the states and their connections. We obtain, using a statistical criterion, an optimal systematic decomposition of the conformational variability of the protein peptidic chain in 27 states with strong connection logic. This result is stable over different protein sets. Our model fits well the previous knowledge related to protein architecture organisation and seems able to grab some subtle details of protein organisation, such as helix sub-level organisation schemes. Taking into account the dependence between the states results in a description of local protein structure of low complexity. On an average, the model makes use of only 8.3 states among 27 to describe each position of a protein structure. Although we use short fragments, the learning process on entire protein conformations captures the logic of the assembly on a larger scale. Using such a model, the structure of proteins can be reconstructed with an average accuracy close to 1.1 Å root-mean-square deviation and for a complexity of only 3. Finally, we also observe that sequence specificity increases with the number of states of the structural alphabet. Such models can constitute a very relevant approach to the analysis of protein architecture in particular for protein structure prediction.

The molecular basis for the high photosensitivity of rhodopsin.

Based on structural information derived from the F NMR data of labeled rhodopsins, rhodopsin crystal structure, and excited-state properties of model polyenes, we propose a molecular mechanism that accounts specifically for the causes of the well-known enhanced photoreactivity of rhodopsin (increased rates and quantum yield of isomerization). It involves the key features of close proximity of C-187 to H-12 and chromophore bond lengthening upon light absorption. The resultant "sudden punch" to H-12 triggers dual processes of decay of the Franck-Condon-excited rhodopsin, a productive directed photoisomerization and a nonproductive decay returning to the ground state as two separate molecular pathways [based on real-time fluorescence results of Chosrowjan, H., Mataga, N., Shibata, Y., Tachibanaki, S., Kandori, H., Shichida, Y., Okada, T. & Kouyama, T. (1998) J. Am. Chem. Soc. 120, 9706-9707]. The two processes are controlled by the local protein structure: an empty space provided by the intradiscal loop connecting transmembrane helices 4 and 5 and a protein wall composed of amino acid units in transmembrane 3. Suggestions, involving retinal analogs and rhodopsin mutants, to improve the unusually high photosensitivity of rhodopsin are proposed.

The proline-rich region of mouse p53 influences transactivation and apoptosis but is largely dispensable for these functions.

The N-terminal proline-rich domain of human p53 has been shown to be important for the induction of apoptosis. However, the corresponding region in mouse and other species is not highly conserved and has been less well studied. In this paper, we have characterized mutants with deletions in this region of mouse p53. Our results demonstrate that deletions in the proline-rich domain have varying effects on function ranging from no effect to severe impairment of cell death activity, depending on precisely which residues are deleted. We also show that the mutants differ in their ability to transactivate different p53 target promoters. Although we have been able to obtain mutants selectively impaired for apoptosis, our data are not generally consistent with this region being a functional domain. The data are more consistent with the interpretation that the region influences function by altering local protein structure which may affect promoter discrimination.

Probing Local Dynamics of the Photosynthetic Bacterial Reaction Center with a Cysteine Specific Spin Label

A multifrequency electron paramagnetic resonance (EPR) approach was used to probe the dynamic structure of the bacterial photosynthetic reaction center (RC) protein. We have demonstrated that the cysteine specific nitroxide spin label MTSL can be covalently bound to a surface cysteine residue of Rhodobacter sphaeroides RC protein. We suggest that the MTSL nitroxide is bound to an accessible cysteine residue, H156, which is located on the surface of the protein on the H-subunit. Analysis of the multifrequency EPR spectra of the spin-labeled RC proteins suggests the restricted character of the protein dynamics. These dynamics can be described as fast libration in a cone with a correlation time faster than 10-9 s. Several dynamically nonequivalent sites were observed in the EPR spectra, which may reflect distinct conformational substates of local protein structure. This work provides a foundation for future studies with the goal of correlating protein motions with photosynthetic charge-transfer reactions.

Incorporation of selenomethionine into proteins through selenohomocysteine-mediated ligation.

Site-selective incorporation of selenomethionine into proteins in place of methionine provides a unique spectroscopic probe of local protein structure and dynamics. This was demonstrated with seleno-bPP 1, a synthetic variant of a peptide hormone prepared by ligation of a C-terminal peptide thioester with a peptide fragment containing an N-terminal selenohomocysteine, followed by methylation of the resulting selenol (see scheme; bPP=bovine pancreatic peptide).

Local protein structure and dynamics at kinked transmembrane α-helices of [1- 13C]Pro-labeled bacteriorhodopsin as revealed by site-directed solid-state 13C NMR

We have recorded 13C NMR spectra of [1- 13C]Pro-labeled bacteriorhodopsin (bR) and P50G, P91G, and P186A mutants under fully hydrated condition, by high-resolution solid-state NMR utilizing cross polarization-magic angle spinning (CP-MAS) and dipolar decoupled-magic angle spinning (DD-MAS) techniques. Seven well-resolved 13C NMR signals including a shoulder peak were distinguished by CP-MAS NMR, although only two signals were resolved by DD-MAS NMR. We assigned these 13C NMR signals among them to Pro50, 91 and 186 residues at the kinks in the inner part of the transmembrane α-helices, on the basis of compared peak-intensities between wild type bR and the above-mentioned site-directed mutants, together with aid of Mn 2+-induced suppression of peaks from residues located near at the surfaces due to accelerated spin–spin relaxation times. It turned out that these Pro 13C NMR signals of wild type were appreciably broadened at temperature below −40 °C as in [3- 13C]Ala-bR, as a result of superposition of a variety of frozen conformers of the transmembrane α-helices exhibiting dispersion of chemical shifts. This means that the dynamic behavior of bR as viewed from Pro residue is very similar to that of ordinary amino acid residues such as Ala, Val, Phe, etc. Further, it was found that no appreciable conformational change was noted for wild type bR within a temperature range between −20 and 35 °C at these kinked portions, although such change was noted at 35 °C for Y185F mutant which lacks interchain hydrogen bonding interaction as observed for wild type bR between the side-chains of Asp212 and Tyr185.

Energy transduction optical sensor in skeletal myosin.

The skeletal myosin cross-bridge in dynamic association with actin is the unitary energy transducer in muscle, converting free energy from ATP hydrolysis into contractile force. Myosin's conserved ATP-sensitive tryptophan (AST) is an energy transduction optical sensor signaling transduction-related transient conformation change by modulating its fluorescence intensity amplitude and relaxation rate. Recently introduced techniques have provided the means of observing the time-resolved intensity decay from this single residue in the native protein to elucidate the mechanism of its ATP sensitivity. AST signal characteristics could be derived from local protein structure by a scenario involving interactions with excited-state tryptophan. This investigation suggests the very different possibility that hypochromism induced in the tryptophan absorption band, a ground-state effect, is a significant structural effector of optical transduction sensing. This possibility makes feasible the interpretation of the transient AST optical signal in terms of dynamical protein structure, thereby raising the empirical signal to the level of a structural determinant. Using the crystallographically based geometry from several myosin structures, the maximum calculated AST hypochromism is <10% to be compared with the value of approximately 30% observed here experimentally. Rationalizing the discrepancy invites further investigation of S1 dynamical structure local to the AST during transduction.

Protein decoy assembly using short fragments under geometric constraints.

A small set of protein fragments can represent adequately all known local protein structure. This set of fragments, along with a construction scheme that assembles these fragments into structures, defines a discrete (relatively small) conformation space, which approximates protein structures accurately. We generate protein decoys by sampling geometrically valid structures from this conformation space, biased by the secondary structure prediction for the protein. Unlike other methods, secondary structure prediction is the only protein-specific information used for generating the decoys. Nevertheless, these decoys are qualitatively similar to those found by others. The method works well for all-alpha proteins, and shows promising results for alpha and beta proteins.

Protein local structure prediction from sequence

A basis set of protein canonical fragments, or centroids, represents the range of local structure found in globular proteins. We develop a methodology to predict centroids from the amino acid sequence. The predictor gives the probability of each centroid in the basis set, at each loci along the backbone. The predictor selects the best-fit centroid at about 40% of the loci. The predicted probabilities are accurate and can be used to judge the confidence of each centroid prediction. For example, when filtering out centroids with <0.50 probability, the predictor is 65% accurate, although such high-probability centroids occur at only 28% of the loci. Centroids with high probability can be interpreted as segments that are highly influenced by the amino acid sequence, whereas centroids with low probability can be interpreted as segments that are more likely influenced by tertiary contacts. Low-resolution, starting point structures, can be generated by fitting the predicted centroids together.

Development of a structure based protein function prediction method: Calcium binding protein

Three-dimensional local structures located near active sites are responsible for protein functions. To predict protein functions, we developed a method to extract three-dimensional structural characteristics of functions. We chose EF-hand calcium binding proteins as the model target. We defined a local structure as the structure within 12A from an arbitrary Asp(Cα). Analysis of the amino acid propensities in the active sites showed that there were clear preferences for certain amino acids to locate at the binding sites. Furthermore, the analysis of the distributions of the distances between Asp(Cα) and any other amino acids(Cα) showed that there were preferred distances for respective amino acids. Using such structural data, we derived a DB (distance based) score and a DPB (distance and propensity based) score for the prediction of functional sites. A search for EF-hand calcium binding sites was performed to test the method. EF-hand calcium binding sites were successfully predicted. Key Words: protein local structures, calcium binding protein, EF-hand calcium binding site, amino acid propensity, distance distribution

Magic angle spinning nuclear magnetic resonance of isotopically labeled rhodopsin

This chapter discusses the design of magic angle spinning (MAS) experiments for targeting selected regions in GPCRs and describes experimental protocols for isotope labeling of rhodopsin by using mammalian HEK293S cells. MAS nuclear magnetic resonance (NMR) spectroscopy is well suited to high-resolution studies of the local structure and dynamics of membrane proteins. Much of the work since the early 1990s has focused on rhodopsin. An advantage of MAS NMR over diffraction and solution NMR methods is that high-resolution structural measurements can be made on proteins in native bilayer environments. In contrast to the lack of structural data, there is a wealth of biochemical and molecular biological data on rhodopsin and other GPCRs. In particular, site-directed mutagenesis has proved extremely valuable for mapping residues that are critical for GPCR structure and function. There are several residues in the transmembrane helices of the GPCR family that are highly conserved and, therefore, are likely to be important in defining the structure of the receptor or to be involved in the activation mechanism.

Compacting local protein folds with a "hybrid protein model"

The “hybrid protein model” is a fuzzy model for compacting local protein structures. It learns a nonredundant database encoded in a previously defined structural alphabet composed of 16 protein blocks (PBs). The hybrid protein is composed of a series of distributions of the probability of observing the PBs. The training is an iterative unsupervised process that for every fold to be learnt consists of looking for the most similar pattern present in the hybrid protein and modifying it slightly. Finally each position of the hybrid protein corresponds to a set of similar local structures. Superimposing those local structures yields an average root mean square of 3.14 A. The significant amino acid characteristics related to the local structures are determined. The use of this model is illustrated by finding the most similar folds between two cytochromes P450.

Significance of aromatic‐backbone amide interactions in protein structure

Weakly polar interactions between aromatic rings of amino acids and hydrogens of backbone amides (Ar-HN) have been shown to support local structures in proteins. Their role in secondary structures, however, has not been elucidated. To investigate the relationship between Ar-HN interaction and the stability of local and secondary structures of polypeptides and to improve the prediction of this interaction based on amino acid sequence, the structures of 560 nonhomologous proteins, from the Protein Data Bank, were searched for Ar-HN interactions between the aromatic ring of each Phe, Tyr, and Trp residue at position i and the backbone amide group of any residue, except Pro, at the positions i, i - 1, i - 2, i - 3, i + 1, i + 2, and i + 3. Ar-HN interactions were identified by calculating the chemical shift of the amide hydrogen caused by the proximal aromatic ring. Ar(i)-HN(i + 1, i + 2 and i + 3) interactions were more common (7.10%, 2.08%, and 0.54%, respectively) than were Ar(i)-HN(i - 1, i - 2, and i - 3) interactions (0.66%, <0.1%, and 0.18%, respectively). The value of the chi(1) torsion angle of the aromatic residue in position i depended on the direction of the Ar-HN interaction. The position of the aromatic ring in Ar(i)-HN(i + 1, i + 2, and i + 3) interactions was mostly trans, in Ar(i)-HN(i - 1, i - 2, and i - 3) interactions mainly gauche(-), and in Ar(i)-HN(i) interactions mostly gauche(+). The analyses of the secondary structures of the protein fragments containing Ar-HN interactions showed that Ar-HN interactions were in all types of secondary structures. Search results suggest that Ar-HN interactions have a stabilizing effect on all types of secondary structures.

Crystal structures of spin labeled T4 lysozyme mutants: implications for the interpretation of EPR spectra in terms of structure.

High resolution (1.43-1.8 A) crystal structures and the corresponding electron paramagnetic resonance (EPR) spectra were determined for T4 lysozyme derivatives with a disulfide-linked nitroxide side chain [-CH(2)-S-S-CH(2)-(3-[2,2,5,5-tetramethyl pyrroline-1-oxyl]) identical with R1] substituted at solvent-exposed helix surface sites (Lys65, Arg80, Arg119) or a tertiary contact site (Val75). In each case, electron density is clearly resolved for the disulfide group, revealing distinct rotamers of the side chain, defined by the dihedral angles X(1) and X(2). The electron density associated with the nitroxide ring in the different mutants is inversely correlated with its mobility determined from the EPR spectrum. Residue 80R1 assumes a single g(+)()g(+)() conformation (Chi(1) = 286, X(2) = 294). Residue 119R1 has two EPR spectral components, apparently corresponding to two rotamers, one similar to that for 80R1 and the other in a tg(-)() conformation (Chi(1) = 175, X(2) = 54). The latter state is apparently stabilized by interaction of the disulfide with a Gln at i + 4, a situation also observed at 65R1. R1 residues at helix surface site 65 and tertiary contact site 75 make intra- as well as intermolecular contacts in the crystal and serve to identify the kind of molecular interactions possible for the R1 side chain. A single conformation of the entire 75R1 side chain is stabilized by a variety of interactions with the nitroxide ring, including hydrophobic contacts and two unconventional C-H.O hydrogen bonds, one in which the nitroxide acts as a donor (with tyrosine) and the other in which it acts as an acceptor (with phenylalanine). The interactions revealed in these structures provide an important link between the dynamics of the R1 side chain, reflected in the EPR spectrum, and local protein structure. A library of such interactions will provide a basis for the quantitative interpretation of EPR spectra in terms of protein structure and dynamics.

Magnetization Transfer via Residual Dipolar Couplings: Application to Proton–Proton Correlations in Partially Aligned Proteins

A novel three-dimensional NMR experiment is reported that allows the observation of correlations between amide and other protons via residual dipolar couplings in partially oriented proteins. The experiment is designed to permit quantitative measurement of the magnitude of proton-proton residual dipolar couplings in larger molecules and at higher degree of alignments. The observed couplings contain data valuable for protein resonance assignment, local protein structure refinement, and determination of low-resolution protein folds.

Chemical properties of alcohols and their protein binding sites.

Alcohols affect a wide array of biological processes including protein folding, neurotransmission and immune responses. It is becoming clear that many of these effects are mediated by direct binding to proteins such as neurotransmitter receptors and signaling molecules. This review summarizes the unique chemical properties of alcohols which contribute to their biological effects. It is concluded that alcohols act mainly as hydrogen bond donors whose binding to the polypeptide chain is stabilized by hydrophobic interactions. The electronegativity of the O atom may also play a role in stabilizing contacts with the protein. Properties of alcohol binding sites have been derived from X-ray crystal structures of alcohol-protein complexes and from mutagenesis studies of ion channels and enzymes that bind alcohols. Common amino acid sequences and structural features are shared among the protein segments that are involved in alcohol binding. The alcohol binding site is thought to consist of a hydrogen bond acceptor in a turn or loop region that is often situated at the N-terminal end of an alpha-helix. The methylene chain of the alcohol molecule appears to be accommodated by a hydrophobic groove formed by two or more structural elements, frequently a turn and an alpha-helix. Binding at these sites may alter the local protein structure or displace bound solvent molecules and perturb the function of key proteins.