A Search for Energy Minimized Sequences of Proteins

In this paper, we present numerical evidence that supports the notion of minimization in the sequence space of proteins for a target conformation. We use the conformations of the real proteins in the Protein Data Bank (PDB) and present computationally efficient methods to identify the sequences with minimum energy. We use edge-weighted connectivity graph for ranking the residue sites with reduced amino acid alphabet and then use continuous optimization to obtain the energy-minimizing sequences. Our methods enable the computation of a lower bound as well as a tight upper bound for the energy of a given conformation. We validate our results by using three different inter-residue energy matrices for five proteins from protein data bank (PDB), and by comparing our energy-minimizing sequences with 80 million diverse sequences that are generated based on different considerations in each case. When we submitted some of our chosen energy-minimizing sequences to Basic Local Alignment Search Tool (BLAST), we obtained some sequences from non-redundant protein sequence database that are similar to ours with an E-value of the order of 10^-7. In summary, we conclude that proteins show a trend towards minimizing energy in the sequence space but do not seem to adopt the global energy-minimizing sequence. The reason for this could be either that the existing energy matrices are not able to accurately represent the inter-residue interactions in the context of the protein environment or that Nature does not push the optimization in the sequence space, once it is able to perform the function.     

A Free-Energy Approach for All-Atom Protein Simulation

All-atom free-energy methods offer a promising alternative to kinetic molecular mechanics simulations of protein folding and association. Here we report an accurate, transferable all-atom biophysical force field (PFF02) that stabilizes the native conformation of a wide range of proteins as the global optimum of the free-energy landscape. For 32 proteins of the ROSETTA decoy set and six proteins that we have previously folded with PFF01, we find near-native conformations with an average backbone RMSD of 2.14 Å to the native conformation and an average Z-score of −3.46 to the corresponding decoy set. We used nonequilibrium sampling techniques starting from completely extended conformations to exhaustively sample the energy surface of three nonhomologous hairpin-peptides, a three-stranded β-sheet, the all-helical 40 amino-acid HIV accessory protein, and a zinc-finger ββα motif, and find near-native conformations for the minimal energy for each protein. Using a massively parallel evolutionary algorithm, we also obtain a near-native low-energy conformation for the 54 amino-acid engrailed homeodomain. Our force field thus stabilized near-native conformations for a total of 20 proteins of all structure classes with an average RMSD of only 3.06 Å to their respective experimental conformations.     

Medline (PubMed)遗传学杂志文献搜索引擎开发研究

为了方便遗传学工作者快捷、准确地查阅遗传学杂志文献,开发和利用NCBI 的 Medline数据库的遗传学杂志文献资源。从Medline (PubMed)中检索并列出173种有关遗传学的杂志名录,制作了每种杂志及部分杂志年份相应的超级链接,组成一个有关遗传学杂志文献的搜索引擎。此搜索引擎能快捷、准确、动态地检索173种遗传学杂志全部文献题录及部分杂志各年的文献题录,并可在PubMed中进一步检索出文献的摘要和部分全文。 Abstract：To help geneticists look up genetics journals more quickly and exactly,this paper developed this search engine of genetics journals. The paper exploited the search engine with genetics journals sources of Medline database in NCBI, indexed and listed 173 names of genetics journals from Medline. Then obtained one search engine concerning genetics journals after making every journal´s super linkage. The search engine can search out not only all articles´ titles of 173 genetics journals but also some articles’ titles of the journals each year quickly,exactly and variablely. We can further obtain all articles´ abstracts and some full texts in PubMed.     

All-Atom Ensemble Modeling to Analyze Small-Angle X-Ray Scattering of Glycosylated Proteins

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Highlights? MW determined from zero angle scattering is accurate for glycoproteins ? All-atom modeling with SAXS data can identify structural features of glycans ? SAXS ab initio reconstructions provide little structural information for glycans     

A Rapid Screening Assay to Search for Phosphorylated Proteins in Tissue Extracts

Reversible protein phosphorylation is an essential mechanism in the regulation of diverse biological processes, nonetheless is frequently altered in disease. As most phosphoproteome studies are based on optimized in-vitro cell culture studies new methods are in need to improve de novo identification and characterization of phosphoproteins in extracts from tissues. Here, we describe a rapid and reliable method for the detection of phosphoproteins in tissue extract based on an experimental strategy that employs 1D and 2D SDS PAGE, Western immunoblotting of phosphoproteins, in-gel protease digestion and enrichment of phosphorpeptides using metal oxide affinity chromatography (MOAC). Subsequently, phosphoproteins are identified by MALDI-TOF-MS/MS with the CHCA-TL or DHB ML sample matrix preparation method and further characterized by various bioinformatic software tools to search for candidate kinases and phosphorylation-dependent binding motifs. The method was applied to mouse lung tissue extracts and resulted in an identification of 160 unique phosphoproteins. Notably, TiO₂ enrichment of pulmonary protein extracts resulted in an identification of additional 17 phosphoproteins and 20 phosphorylation sites. By use of MOAC, new phosphorylation sites were identified as evidenced for the advanced glycosylation end product-specific receptor. So far this protein was unknown to be phosphorylated in lung tissue of mice. Overall the developed methodology allowed efficient and rapid screening of phosphorylated proteins and can be employed as a general experimental strategy for an identification of phosphoproteins in tissue extracts.     

Dynamic Strategies for Target-Site Search by DNA-Binding Proteins

Gene regulatory proteins find their target sites on DNA remarkably quickly; the experimental binding rate for lac repressor is orders-of-magnitude higher than predicted by free diffusion alone. It has been proposed that nonspecific binding aids the search by allowing proteins to slide and hop along DNA. We develop a reaction-diffusion theory of protein translocation that accounts for transport both on and off the strand and incorporates the physical conformation of DNA. For linear DNA modeled as a wormlike chain, the distribution of hops available to a protein exhibits long, power-law tails that make the long-time displacement along the strand superdiffusive. Our analysis predicts effective superdiffusion coefficients for given nonspecific binding and unbinding rate parameters. Translocation rate exhibits a maximum at intermediate values of the binding rate constant, while search efficiency is optimized at larger binding rate constant values. Thus, our theory predicts a region of values of the nonspecific binding and unbinding rate parameters that balance the protein translocation rate and the efficiency of the search. Published data for several proteins falls within this predicted region of parameter values.     

A Structural Overview of the Vertebrate Prion Proteins

Among the large family of diseases caused by protein aggregation and misfolding is that associated to the Prion Protein (PrP). This is a small extracellular membrane-anchored molecule of yet unknown function. Understanding how PrP folds both into its cellular and pathological forms is thought to be crucial for explaining protein misfolding in general and the specific role of PrP in disease. Since the first structure determination, an increasing number of structural studies of PrP have become available, showing that the protein is formed by a flexible N-terminal region and a highly conserved globular C-terminal domain. We review here the current knowledge on PrP structure. We focus on vertebrate PrPs and analyse in detail the similarities and the differences among the coordinates of the C-terminal domain of PrP from different species, in search for understanding the mechanism of disease-causing mutations and the molecular bases of species barrier.     

A Structural Overview of the Vertebrate Prion Proteins

Among the diseases caused by protein misfolding is the family associated with the prion protein (PrP). This is a small extracellular membrane-anchored molecule of yet unknown function. Understanding how PrP folds both into its cellular and pathological forms is thought to be crucial for explaining protein misfolding in general and the specific role of PrP in disease. Since the first structure determination, an increasing number of structural studies of PrP have become available, showing that the protein is formed by a flexible N-terminal region and a highly conserved globular C-terminal domain. We review here the current knowledge on PrP structure. We focus on vertebrate PrPs and analyse in detail the similarities and the differences among the coordinates of the C-terminal domain of PrP from different species, in search for understanding the mechanism of disease-causing mutations and the molecular bases of species barrier.Key Words: amyloid, NMR, prion, scrapie, structure, X-ray     

Structural Proteins of Reoviruses

Polyacrylamide gel electrophoresis of the solubilized proteins from the three serotypes of reovirus revealed that each contained three major and four minor components. Subviral particles were prepared by brief treatment of complete virions with urea. Electron microscopy, density-gradient centrifugation, and chemical analyses of these particles indicated that their outer capsid structure had been selectively removed. They contained only two proteins, but their ribonucleic acid composition was similar to that of complete virions. The subviral particles were not infectious.     

蛋白质的结构转换

许多不相关的蛋白质含有相同的短肽序列却形成不同的空间构象. 结构转换广泛存在于蛋白质折叠和功能过程中, 具有重要的生物学意义. 综述了Serpin和EF-Tu的失活、血细胞凝集素的激活、蛋白酶成熟、亚基装配和蛋白质淀粉样化等过程中肽链同源肽段的结构转换模式, 并讨论了它在理解蛋白质折叠机理和“构象病”病因中的应用.     

Medline(PubMed)生物化学杂志文献搜索引擎开发研究

为了方便生物化学工作快捷、准确地查阅生物化学杂志献,开发和利用NCBI的Medline数据库的生物化学杂志献资源。从Medline(PubMed)中检索并列出175种有关生物化学的杂志名录,制作了每种杂志及部分杂志年份相应的超级链接,组成一个有关生物化学杂志献的搜索引擎。此搜索引擎能快捷、准确、动态地检索175种生物化学杂志全部献题录及部分杂志各年的献题录,并可在PubMed中进一步检索出献的要和部分全。     

All-Atom Structural Models for Complexes of Insulin-Like Growth Factors IGF1 and IGF2 with Their Cognate Receptor

Type 1 insulin-like growth factor receptor (IGF1R) is a membrane-spanning glycoprotein of the insulin receptor family that has been implicated in a variety of cancers. The key questions related to molecular mechanisms governing ligand recognition by IGF1R remain unanswered, partly due to the lack of testable structural models of apo or ligand-bound receptor complexes. Using a homology model of the IGF1R ectodomain IGF1RΔβ, we present the first experimentally consistent all-atom structural models of IGF1/IGF1RΔβ and IGF2/IGF1RΔβ complexes. Our explicit-solvent molecular dynamics (MD) simulation of apo-IGF1RΔβ shows that it displays asymmetric flexibility mechanisms that result in one of two binding pockets accessible to growth factors IGF1 and IGF2, as demonstrated via an MD-assisted Monte Carlo docking procedure. Our MD-generated ensemble of structures of apo and IGF1-bound IGF1RΔβ agrees reasonably well with published small-angle X-ray scattering data. We observe simultaneous contacts of each growth factor with sites 1 and 2 of IGF1R, suggesting cross-linking of receptor subunits. Our models provide direct evidence in favor of suggested electrostatic complementarity between the C-domain (IGF1) and the cysteine-rich domain (IGF1R). Our IGF1/IGF1RΔβ model provides structural bases for the observation that a single IGF1 molecule binds to IGF1RΔβ at low concentrations in small-angle X-ray scattering studies. We also suggest new possible structural bases for differences in the affinities of insulin, IGF1, and IGF2 for their noncognate receptors.     

A Taxonomic Search Engine: Federating taxonomic databases using web services

Background  

The taxonomic name of an organism is a key link between different databases that store information on that organism. However, in the absence of a single, comprehensive database of organism names, individual databases lack an easy means of checking the correctness of a name. Furthermore, the same organism may have more than one name, and the same name may apply to more than one organism.     

Structural Aspects of Hydroxyproline-Containing Proteins

Abstract

The occurrence of hydroxyproline (Hyp) in collagen, Clq and acetylcholinesterase (AChE) raises important questions concerning the role of this unusual imino acid in the structure and function of these proteins. Available data on collagen indicate that Hyp is necessary for the normal secretion of the protein after its synthesis and for the integrity of the triple-helical conformation. Studies from our laboratory have dealt with the structural aspects of the posttranslational conversion of proline to hydroxyproline in collagen mediated by prolyl hydroxylase. We proposed that the β-turn conformation at the Pro-Gly segments in the nascent procollagen molecule are the sites of the enzymatic hydroxylation and that this conformation changes over to the collagen-like helix as a result of the hydroxylation process. Recently, we have provided additional experimental support to our proposal by a) synthesizing specific β-turn oligopeptides containing the Pro-Gly as well as Pro-Ala and Pro-DAla sequences and showing that these act as inhibitors of the enzymatic hydroxylation of a synthetic substrate and b) demonstrating, by circular dichroism spectroscopy, the occurrence of a conformational change leading to the triple-helix as a direct consequence of proline hydroxylation in a non-helical polypeptide substrate. We have also observed that the acquisition of hydroxylation results in a significant enhancement of the rate of folding of the polypeptide chain from the unfolded to the triple-helical conformation. We believe that our observations on proline hydroxylation in collagen should also be applicable to Clq and acetylcholineesterase both of which share the general structural and functional properties of collagen in their “tail” regions. Using the techniques employed in collagen studies, one should be able to assess the role of hydroxyproline in the folding, structural stabilities and functions of Clq and AChE. This would also involve the study of the unhydroxylated and hydroxylated precursors of these proteins which may share common structural features with their collagen counterparts. Finally, a systematic study of hydroxyproline-containing peptides and polypeptides has been initiated by us so as to understand the exact manner in which Hyp participates in the formation and stability of the triple-helical conformation in the proteins in which it occurs.     

Structural Proteins of Rabies Virus

Purified rabies virions, unlabeled or labeled with radioactive amino acids or d-glucosamine, were dissociated into their polypeptides by treatment with sodium dodecyl sulfate in a reducing environment and fractionated by electroiphoresis in sodium dodecyl sulfate-containing polyacrylamide gel. The molecular weights of individual polypeptides were estimated by comparison of their rate of migration with that of protein markers of known molecular weight. Purified viral nucleocapsid and a mixture of envelope components, isolated from virions disrupted by sodium deoxycholate, were analyzed by the same procedure. The number of molecules per virion of each polypeptide was estimated from the proportions of the separated components, the known molecular weight of the viral ribonucleic acid, and the chemical composition of the nucleocapsid. The protein moiety of the nucleocapsid particle was estimated to consist of 1,713 molecules of a major polypeptide (molecular weight, 62,000 daltons) and 76 molecules of a minor polypeptide (molecular weight, 55,000 daltons). In addition to 1,783 molecules of a glycoprotein component (molecular weight, 80,000 daltons), the viral envelope contains 789 and 1,661 molecules, respectively, of two other polypeptides (molecular weight, 40,000 and 25,000 daltons).     

Structural Proteins of Pichinde Virus

Pichinde virus, a member of the arenovirus group, was found to have four polypeptides by polyacrylamide gel electrophoresis. Two components, V(I) and V(II), had molecular weights of about 72,000, whereas V(III) had a molecular weight of 34,000. A minor component, V(IV), had a molecular weight of about 12,000. Glucosamine was incorporated into V(II) and V(III), suggesting that these components were glycopeptides whereas V(I) and V(IV) were polypeptides. Treatment of the virus with Nonidet P-40 removed V(III), but V(I) and V(II) remained associated with the virus nucleic acid. This suggests a functional role of a ribonucleoprotein for V(I) and an envelope glycoprotein for V(III). V(II), the major glycopeptide, could function both as a membrane component and as a nucleoprotein.     

Structural Proteins of Adenovirus-Associated Viruses

The structural proteins of adenovirus-associated virus (AAV) types 1, 2, and 3 were analyzed by acrylamide gel electrophoresis. In each case, one major protein (C) and two minor proteins (A and B) were identified. Component C had an estimated molecular weight of 62,000 daltons, and the molecular weights of components A and B were found to be 87,000 and 73,000 daltons, respectively. Coelectrophoresis of adenovirus and AAV proteins revealed an overlap only between the adenovirus fiber-penton component and the AAV C polypeptide. Among AAV serotypes, homologous components were electrophoretically identical, except that the C component of AAV-2 was of slightly lower molecular weight than the C components of AAV-1 and AAV-3. The relative incorporation of (14)C-arginine and (14)C-mixed amino acids into the three polypeptides of AAV-2 was similar, indicating an absence of an arginine-rich component. In addition, AAV-2 was found to have a substantially lower arginine content than helper adenoviruses.     

BioText Search Engine: beyond abstract search

The BioText Search Engine is a freely available Web-based application that provides biologists with new ways to access the scientific literature. One novel feature is the ability to search and browse article figures and their captions. A grid view juxtaposes many different figures associated with the same keywords, providing new insight into the literature. An abstract/title search and list view shows at a glance many of the figures associated with each article. The interface is carefully designed according to usability principles and techniques. The search engine is a work in progress, and more functionality will be added over time. Availability: http://biosearch.berkeley.edu.     

All-Atom Contact Model for Understanding Protein Dynamics from Crystallographic B-Factors

An all-atom local contact model is described that can be used to predict protein motions underlying isotropic crystallographic B-factors. It uses a mean-field approximation to represent the motion of an atom in a harmonic potential generated by the surrounding atoms resting at their equilibrium positions. Based on a 400-ns molecular dynamics simulation of ubiquitin in explicit water, it is found that each surrounding atom stiffens the spring constant by a term that on average scales exponentially with the interatomic distance. This model combines features of the local density model by Halle and the local contact model by Zhang and Brüschweiler. When applied to a nonredundant set of 98 ultra-high resolution protein structures, an average correlation coefficient of 0.75 is obtained for all atoms. The systematic inclusion of crystal contact contributions and fraying effects is found to enhance the performance substantially. Because the computational cost of the local contact model scales linearly with the number of protein atoms, it is applicable to proteins of any size for the prediction of B-factors of both backbone and side-chain atoms. The model performs as well as or better than several other models tested, such as rigid-body motional models, the local density model, and various forms of the elastic network model. It is concluded that at the currently achievable level of accuracy, collective intramolecular motions are not essential for the interpretation of B-factors.