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The polyproline II (PPII) conformation of protein backbone is an important secondary structure type. It is unusual in that, due to steric constraints, its main-chain hydrogen-bond donors and acceptors cannot easily be satisfied. It is unable to make local hydrogen bonds, in a manner similar to that of alpha-helices, and it cannot easily satisfy the hydrogen-bonding potential of neighboring residues in polyproline conformation in a manner analogous to beta-strands. Here we describe an analysis of polyproline conformations using the HOMSTRAD database of structurally aligned proteins. This allows us not only to determine amino acid propensities from a much larger database than previously but also to investigate conservation of amino acids in polyproline conformations, and the conservation of the conformation itself. Although proline is common in polyproline helices, helices without proline represent 46% of the total. No other amino acid appears to be greatly preferred; glycine and aromatic amino acids have low propensities for PPII. Accordingly, the hydrogen-bonding potential of PPII main-chain is mainly satisfied by water molecules and by other parts of the main-chain. Side-chain to main-chain interactions are mostly nonlocal. Interestingly, the increased number of nonsatisfied H-bond donors and acceptors (as compared with alpha-helices and beta-strands) makes PPII conformers well suited to take part in protein-protein interactions. 相似文献
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In this article, a technique for accurate direct measurement of protein‐to‐protein interactions before and after the introduction of a drug candidate is developed using atomic force microscopy (AFM). The method is applied to known immunosuppressant drug candidate Echinacea purpurea derived cynarin. T‐cell/CD28 is on‐chip immobilized and B‐cell/CD80 is immobilized on an AFM tip. The difference in unbinding force between these two proteins before and after the introduction of cynarin is measured. The method is described in detail including determination of the loading rates, maximum probability of bindings, and average unbinding forces. At an AFM loading rate of 1.44 × 104 pN/s, binding events were largely reduced from 61 ± 5% to 47 ± 6% after cynarin introduction. Similarly, maximum probability of bindings reduced from 70% to 35% with a blocking effect of about 35% for a fixed contact time of 0.5 s or greater. Furthermore, average unbinding forces were reduced from 61.4 to 38.9 pN with a blocking effect of ～37% as compared with ～9% by SPR. AFM, which can provide accurate quantitative measures, is shown to be a good method for drug screening. The method could be applied to a wider variety of drug candidates with advances in bio‐chip technology and a more comprehensive AFM database of protein‐to‐protein interactions. Biotechnol. Bioeng. 2012; 109: 2460–2467. © 2012 Wiley Periodicals, Inc. 相似文献
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Golubovic M van Hateren SH Ottens M Witkamp GJ van der Wielen LA 《Biotechnology and bioengineering》2007,98(6):1209-1218
This article presents a novel method for immobilization of active ingredients. The method is based on CO(2) aided active ingredient co-precipitation with glycinin, a biodegradable protein matrix from edible soybean protein. Glycinin precipitates abundantly under isoelectric conditions and serves as the matrix within which the active substance is trapped during the precipitation process. The enzyme lipase from Candida rugosa was successfully co-precipitated into the protein pellet to prove the principle. It was shown that the lipase within the co-precipitate retained lipase and esterase activity under different pH conditions. In some cases the activity was even higher than the activity of crude lipase, possibly due to the protective role of the matrix protein. Due to the retained lipase activity and food-grade quality of the binary precipitate, it has potential of being used in the food or pharmaceutical industry. Additional quality of the binary precipitate is the potentially significantly reduced downstream processing due to the fact that no organic solvents or precipitants were used in the precipitation process. 相似文献
6.
The activity of the protein phosphatase calcineurin (CN) is regulated by an autoinhibition mechanism wherein several domains from its catalytic A subunit, including the calmodulin binding domain (CaMBD), block access to its active site. Upon binding of Ca2+ and calmodulin (Ca2+/CaM) to CaMBD, the autoinhibitory domains dissociate from the catalytic groove, thus activating the enzyme. To date, the structure of the CN/CaM/Ca2+ complex has not been determined in its entirety. Previously, we determined the structure of a fusion protein consisting of CaM and a 25-residue peptide taken from the CaMBD, joined by a 5-glycine linker. This structure revealed a novel CaM binding motif. However, the presence of the extraneous glycine linker cast doubt on the authenticity of this structure as an accurate representation of CN/CaM binding in vivo. Thus, here, we have determined the crystal structure of CaM complexed with the 25-residue CaMBD peptide without the glycine linker at a resolution of 2.1 A. The structure is essentially identical to the fusion construction which displays CaM bound to the CaMBD peptide as a dimer with an open, elongated conformation. The N-lobe from one molecule and C-lobe from another encompass and bind the CaMBD peptide. Thus, it validates the existence of this novel CaM binding motif. Our experiments suggest that the dimeric CaM/CaMBD complex exists in solution, which is unambiguously validated using a carefully-designed CaM-sepharose pull-down experiment. We discuss structural features that produce this novel binding motif, including the role of the CaMBD peptide residues Arg-408, Val-409, and Phe-410, which work to provide rigidity to the otherwise flexible central CaM helix joining the N- and C-lobes, ultimately keeping these lobes apart and forcing \"head-to-tail\" dimerization to attain the requisite N- and C-lobe pairing for CaMBD binding. 相似文献
7.
Bert A. Van Der Reijden Claudia A.J. Erpelinck-Verschueren BOB L
WENBERG Joop H. Jansen 《Protein science : a publication of the Protein Society》1999,8(7):1557-1561
Triad1 was recently identified as a nuclear RING finger protein, which is up-regulated during retinoic acid induced granulocytic differentiation of acute leukemia cells. Here we show that a cysteine-rich domain (C6HC), present in Triad1, is conserved in at least 24 proteins encoded by various eukaryotes. The C6HC consensus pattern C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C defines this structure as the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in 22 of 24 proteins the C6HC domain is flanked by two RING finger structures. We have termed the novel C6HC motif DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (two RING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins. 相似文献
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Deciphering the interaction links between proteins has become one of the main tasks of experimental and bioinformatic methodologies. Reconstruction of complex networks of interactions in simple cellular systems by integrating predicted interaction networks with available experimental data is becoming one of the most demanding needs in the postgenomic era. On the basis of the study of correlated mutations in multiple sequence alignments, we propose a new method (in silico two-hybrid, i2h) that directly addresses the detection of physically interacting protein pairs and identifies the most likely sequence regions involved in the interactions. We have applied the system to several test sets, showing that it can discriminate between true and false interactions in a significant number of cases. We have also analyzed a large collection of E. coli protein pairs as a first step toward the virtual reconstruction of its complete interaction network. 相似文献
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Calculating protein-protein interaction energies is crucial for understanding protein-protein associations. On the basis of the methodology of mean-field potential, we have developed an empirical approach to estimate binding free energy for protein-protein interactions. This knowledge-based approach has been used to derive distance-dependent free energies of protein complexes from a nonredundant training set in the Protein Data Bank (PDB), with a careful treatment of homology. We calculate atom pair potentials for 16 pair interactions, which can reflect the importance of hydrophobic interactions and specific hydrogen-bonding interactions. The derived potentials for hydrogen-bonding interactions show a valley of favorable interactions at a distance of approximately 3 A, corresponding to that of an established hydrogen bond. For the test set of 28 protein complexes, the calculated energies have a correlation coefficient of 0.75 compared with experimental binding free energies. The performance of the method in ranking the binding energies of different protein-protein complexes shows that the energy estimation can be applied to value binding free energies for protein-protein associations. 相似文献
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An equimolar mixture of avian pancreatic polypeptide (aPP) fragments aPP(1-11)-NH2 and Ac-aPP(12-36) had an electronic circular dichroism (ECD) spectrum that was similar to that of whole aPP in H2O and even more so in 30% (v/v) trifluoroethanol (TFE) in 15 mM Na2HPO4, but was different from the sum of the spectra of the individual fragments. The vibrational circular dichroism (VCD) spectrum of the combined fragments in 30% (v/v) TFE in 15 mM Na2HPO4 in D2O was also similar to that of the intact aPP and unlike the sum of the VCD spectra of the fragments. The interaction of these fragments is thus sufficient to support the conformation of whole aPP. This study demonstrates that VCD, in combination with ECD, is useful for the study of protein-protein interactions. 相似文献
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Approaches for the determination of interacting partners from different protein families (such as ligands and their receptors) have made use of the property that interacting proteins follow similar patterns and relative rates of evolution. Interacting protein partners can then be predicted from the similarity of their phylogenetic trees or evolutionary distances matrices. We present a novel method called Codep, for the determination of interacting protein partners by maximizing co-evolutionary signals. The order of sequences in the multiple sequence alignments from two protein families is determined in such a manner as to maximize the similarity of substitution patterns at amino acid sites in the two alignments and, thus, phylogenetic congruency. This is achieved by maximizing the total number of interdependencies of amino acids sites between the alignments. Once ordered, the corresponding sequences in the two alignments indicate the predicted interacting partners. We demonstrate the efficacy of this approach with computer simulations and in analyses of several protein families. A program implementing our method, Codep, is freely available to academic users from our website: http://www.uhnresearch.ca/labs/tillier/. 相似文献
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To evaluate the evolutionary constraints placed on viral proteins by the structure and assembly of the capsid, we calculate Shannon entropies in the aligned sequences of 45 polypeptide chains in 32 icosahedral viruses, and relate these entropies to the residue location in the three-dimensional structure of the capsids. Three categories of residues have entropies lower than the chain average implying that they are better conserved than average: residues that are buried within a subunit (the protein core), residues that contain atoms buried at an interface between subunits (the interface core), and residues that contribute to several such interfaces. The interface core is also conserved in homomeric proteins and in transient protein-protein complexes, which have only one interface whereas capsids have many. In capsids, the subunit interfaces implicate most of the polypeptide chain: on average, 66% of the capsid residues are at an interface, 34% at more than one, and 47% at the interface core. Nevertheless, we observe that the degree of residue conservation can vary widely between interfaces within a capsid and between regions within an interface. The interfaces and regions of interfaces that show a low sequence variability are likely to play major roles in the self-assembly of the capsid, with implications on its mechanism that we discuss taking adeno-associated virus as an example. 相似文献
13.
A genetic algorithm (GA) for protein-protein docking is described, in which the proteins are represented by dot surfaces calculated using the Connolly program. The GA is used to move the surface of one protein relative to the other to locate the area of greatest surface complementarity between the two. Surface dots are deemed complementary if their normals are opposed, their Connolly shape type is complementary, and their hydrogen bonding or hydrophobic potential is fulfilled. Overlap of the protein interiors is penalized. The GA is tested on 34 large protein-protein complexes where one or both proteins has been crystallized separately. Parameters are established for which 30 of the complexes have at least one near-native solution ranked in the top 100. We have also successfully reassembled a 1,400-residue heptamer based on the top-ranking GA solution obtained when docking two bound subunits. 相似文献
14.
Bello M Pérez-Hernández G Fernández-Velasco DA Arreguín-Espinosa R García-Hernández E 《Proteins》2008,70(4):1475-1487
Transient protein-protein interactions are functionally relevant as a control mechanism in a variety of biological processes. Analysis of the 3D structure of protein-protein complexes indicates that water molecules trapped at the interface are very common; however, their role in the stability and specificity of protein homodimer interactions has been not addressed yet. To provide new insights into the energetic bases that govern the formation of highly hydrated interfaces, the dissociation process of bovine beta lg variant A at a neutral pH was characterized here thermodynamically by conducting dilution experiments with an isothermal titration calorimeter. Association was enthalpically driven throughout the temperature range spanned. DeltaH and deltaC(p) were significantly more negative than estimates based on surface area changes, suggesting the occurrence of effects additional to the dehydration of the contact surfaces between subunits. Near-UV CD spectra proved to be independent of protein concentration, indicating a rigid body-like association. Furthermore, the process proved not to be coupled to significant changes in the protonation state of ionizable groups or counterion exchange. In contrast, both osmotic stress experiments and a computational analysis of the dimer's 3D structure indicated that a large number of water molecules are incorporated into the interface upon association. Numerical estimates considering the contributions of interface area desolvation and water immobilization accounted satisfactorily for the experimental deltaC(p). Thus, our study highlights the importance of explicitly considering the effects of water sequestering to perform a proper quantitative analysis of the formation of homodimers with highly hydrated interfaces. 相似文献
15.
Experimental processes to collect and process proteomics data are increasingly complex, and the computational methods to assess the quality and significance of these data remain unsophisticated. These challenges have led to many biological oversights and computational misconceptions. We developed an empirical Bayes model to analyze multiprotein complex (MPC) proteomics data derived from peptide mass spectrometry detections of purified protein complex pull-down experiments. Using our model and two yeast proteomics data sets, we estimated that there should be an average of about 20 true associations per MPC, almost 10 times as high as was previously estimated. For data sets generated to mimic a real proteome, our model achieved on average 80% sensitivity in detecting true associations, as compared with the 3% sensitivity in previous work, while maintaining a comparable false discovery rate of 0.3%. Cross-examination of our results with protein complexes confirmed by various experimental techniques demonstrates that many true associations that cannot be identified by previous approach are identified by our method. 相似文献
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Using an efficient iterative method, we have developed a distance-dependent knowledge-based scoring function to predict protein-protein interactions. The function, referred to as ITScore-PP, was derived using the crystal structures of a training set of 851 protein-protein dimeric complexes containing true biological interfaces. The key idea of the iterative method for deriving ITScore-PP is to improve the interatomic pair potentials by iteration, until the pair potentials can distinguish true binding modes from decoy modes for the protein-protein complexes in the training set. The iterative method circumvents the challenging reference state problem in deriving knowledge-based potentials. The derived scoring function was used to evaluate the ligand orientations generated by ZDOCK 2.1 and the native ligand structures on a diverse set of 91 protein-protein complexes. For the bound test cases, ITScore-PP yielded a success rate of 98.9% if the top 10 ranked orientations were considered. For the more realistic unbound test cases, the corresponding success rate was 40.7%. Furthermore, for faster orientational sampling purpose, several residue-level knowledge-based scoring functions were also derived following the similar iterative procedure. Among them, the scoring function that uses the side-chain center of mass (SCM) to represent a residue, referred to as ITScore-PP(SCM), showed the best performance and yielded success rates of 71.4% and 30.8% for the bound and unbound cases, respectively, when the top 10 orientations were considered. ITScore-PP was further tested using two other published protein-protein docking decoy sets, the ZDOCK decoy set and the RosettaDock decoy set. In addition to binding mode prediction, the binding scores predicted by ITScore-PP also correlated well with the experimentally determined binding affinities, yielding a correlation coefficient of R = 0.71 on a test set of 74 protein-protein complexes with known affinities. ITScore-PP is computationally efficient. The average run time for ITScore-PP was about 0.03 second per orientation (including optimization) on a personal computer with 3.2 GHz Pentium IV CPU and 3.0 GB RAM. The computational speed of ITScore-PP(SCM) is about an order of magnitude faster than that of ITScore-PP. ITScore-PP and/or ITScore-PP(SCM) can be combined with efficient protein docking software to study protein-protein recognition. 相似文献
17.
Through bioinformatics and experimental approaches, we have assigned the first biochemical property to a predicted protein product in the human genome as a new 14-3-3 binding protein. 14-3-3 client proteins represent a diverse group of regulatory molecules that often function as signaling integrators in response to various environmental cues and include proteins such as Bad and Foxo. Using 14-3-3 as a probe in a yeast two-hybrid screen, we identified a novel 14-3-3 binding protein with unknown function, initially designated as clone 546. Confocal microscopy revealed that clone 546 localized to the nucleus of mammalian cells. Additional studies show that the gene encoding clone 546 is expressed in many human tissues, including the thymus, as well as a number of cancer cell lines. The interaction of clone 546 with 14-3-3 was confirmed in mammalian cells. Interestingly, this interaction was markedly enhanced by the expression of activated Akt/PKB, suggesting a phosphorylation dependent event. Mutational analysis was carried out to identify Ser479 as the predominant residue that mediates the clone 546/14-3-3 association. Phosphorylation of Ser479 by AKT/PKB further supports a critical role for Akt/PKB in regulation of the clone 546/14-3-3 interaction. On the basis of these findings, we named this undefined protein FAKTS: Fourteen-three-three associated AKT Substrate. 相似文献
18.
The recognition of protein interaction sites is an important intermediate step toward identification of functionally relevant residues and understanding protein function, facilitating experimental efforts in that regard. Toward that goal, the authors propose a novel representation for the recognition of protein-protein interaction sites that integrates enhanced relative solvent accessibility (RSA) predictions with high resolution structural data. An observation that RSA predictions are biased toward the level of surface exposure consistent with protein complexes led the authors to investigate the difference between the predicted and actual (i.e., observed in an unbound structure) RSA of an amino acid residue as a fingerprint of interaction sites. The authors demonstrate that RSA prediction-based fingerprints of protein interactions significantly improve the discrimination between interacting and noninteracting sites, compared with evolutionary conservation, physicochemical characteristics, structure-derived and other features considered before. On the basis of these observations, the authors developed a new method for the prediction of protein-protein interaction sites, using machine learning approaches to combine the most informative features into the final predictor. For training and validation, the authors used several large sets of protein complexes and derived from them nonredundant representative chains, with interaction sites mapped from multiple complexes. Alternative machine learning techniques are used, including Support Vector Machines and Neural Networks, so as to evaluate the relative effects of the choice of a representation and a specific learning algorithm. The effects of induced fit and uncertainty of the negative (noninteracting) class assignment are also evaluated. Several representative methods from the literature are reimplemented to enable direct comparison of the results. Using rigorous validation protocols, the authors estimated that the new method yields the overall classification accuracy of about 74% and Matthews correlation coefficients of 0.42, as opposed to up to 70% classification accuracy and up to 0.3 Matthews correlation coefficient for methods that do not utilize RSA prediction-based fingerprints. The new method is available at http://sppider.cchmc.org. 相似文献
19.
Systematic protein-protein docking methods need to evaluate a huge number of different probe configurations, thus leading to high computational cost. We present an efficient filter-ray casting filter (RCF)-that enables a notable speed-up of systematic protein-protein docking. The high efficiency of RCF is the outcome of the following factors: (i) extracting of pockets and protrusions on the surfaces of the proteins using visibilities; (ii) a ray casting method that finds aligned receptor pocket/probe protrusion pairs without explicit similarity computations. The RCF method enables the integration of systematic methods and local shape feature matching methods. To verify the efficiency and the accuracy of RCF, we integrated it with a systematic protein-protein docking approach (ATTRACT) based on a reduced protein representation. The test results show that the integrated docking approach is much faster. At the same time, it ranks the lowest ligand root-mean-square deviation (RMSD) (L_rms) solutions higher when docking enzyme-enzyme inhibitor complexes. Consequently, RCF not only enables much faster execution of systematic docking runs but also improves the qualities of docking predictions. 相似文献
20.
Wen Y Makagiansar IT Fukushi J Liu FT Fukuda MN Stallcup WB 《Journal of cellular biochemistry》2006,98(1):115-127
Previous work has demonstrated the ability of the NG2 proteoglycan, a component of microvascular pericytes, to stimulate endothelial cell motility and morphogenesis. This function of NG2 depends on formation of a complex with galectin-3 and alpha3beta1 integrin to stimulate integrin-mediated transmembrane signaling. In addition, the co-expression of galectin-3 and NG2 in A375 melanoma cells suggests that the malignant properties of these cells may be affected by interaction between the two molecules. Here, we extend the theme of co-expression and interaction of NG2 and galectin-3 to human glioma cells. We also establish a molecular basis for the NG2/galectin-3 interaction. The C-terminal carbohydrate recognition domain of galectin-3 is responsible for binding to the NG2 core protein. Within the NG2 extracellular domain, the membrane-proximal D3 segment of the proteoglycan contains the primary binding site for interaction with galectin-3. The interaction between galectin-3 and NG2 is a carbohydrate-dependent one mediated by N-linked rather than O-linked oligosaccharides within the D3 domain of the NG2 core protein. These studies establish a foundation for attempts to reduce the aggressive properties of tumor cells by disrupting the NG2/galectin-3 interaction. 相似文献