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Protein contact prediction

Ognjen Perišić
Physical interactions between proteins are often difficult to decipher. The aim of this paper is to present an algorithm that is designed to recognize binding patches and supporting structural scaffolds of interacting heterodimer proteins using the Gaussian Network Model (GNM). The recognition is based on the (self) adjustable identification of kinetically hot residues and their connection to possible binding scaffolds. The kinetically hot residues are residues with the lowest entropy, i.e., the highest contribution to the weighted sum of the fastest modes per chain extracted via GNM...
March 16, 2018: Pharmaceuticals
Kazuhiro Takemura, Nobuyuki Matubayasi, Akio Kitao
To aid the evaluation of protein-protein complex model structures generated by protein docking prediction (decoys), we previously developed a method to calculate the binding free energies for complexes. The method combines a short (2 ns) all-atom molecular dynamics simulation with explicit solvent and solution theory in the energy representation (ER). We showed that this method successfully selected structures similar to the native complex structure (near-native decoys) as the lowest binding free energy structures...
March 14, 2018: Journal of Chemical Physics
Karolis Uziela, David Menéndez Hurtado, Nanjiang Shu, Björn Wallner, Arne Elofsson
Protein modeling quality is an important part of protein structure prediction. We have for more than a decade developed a set of methods for this problem. We have used various types of description of the protein and different machine learning methodologies. However, common to all these methods has been the target function used for training. The target function in ProQ describes the local quality of a residue in a protein model. In all versions of ProQ the target function has been the S-score. However, other quality estimation functions also exist, which can be divided into superposition- and contact-based methods...
March 9, 2018: Proteins
Suvobrata Chakravarty, Adron Robert Ung, Brian G Moore, Jay S Shore, Mona Alshamrani
The edgewise interactions of anions with phenylalanine (Phe) aromatic rings in proteins, known as anion-π interactions, have been well studied. However, the anion-π interactions of the tyrosine (Tyr) and tryptophan (Trp) rings have been less well studied, probably because these have been considered weaker interactions than anions hydrogen bonded to Trp/Tyr sidechains. Distinguishing from such hydrogen bonding interactions, we comprehensively surveyed the edgewise interactions of certain anions (aspartate, glutamate, and phosphate) with Trp, Tyr, and Phe rings in high-resolution, non-redundant protein single chains and interfaces (protein-protein, DNA/RNA-protein, and membrane-protein)...
February 26, 2018: Biochemistry
Amber R Krauchunas, Ernesto Mendez, Julie Zhouli Ni, Marina Druzhinina, Amanda Mulia, Jean Parry, Sam Guoping Gu, Gillian M Stanfield, Andrew Singson
Successful fertilization requires that sperm are activated prior to contacting an oocyte. In C. elegans, this activation process, called spermiogenesis, transforms round immobile spermatids into motile, fertilization-competent spermatozoa. We describe the phenotypic and genetic characterization of spe-43, a new component of the spe-8 pathway, which is required for spermiogenesis in hermaphrodites; spe-43 hermaphrodites are self-sterile, while spe-43 males show wild-type fertility. When exposed to Pronase to activate sperm in vitro, spe-43 spermatids form long rigid spikes radiating outward from the cell periphery instead of forming a motile pseudopod, indicating that spermiogenesis initiates but is not completed...
February 22, 2018: Developmental Biology
Derek T Bernstein, Lee S Haruno, Shiva Daram, John R Dawson, Wei Zhang, Scott B Rosenfeld
Staphylococcus aureus is the most common causative organism in pediatric septic arthritis, with methicillin-resistant Staphylococcus aureus (MRSA) being responsible for a significant portion of these infections. Early identification and initiation of proper treatment may improve outcomes by minimizing potential morbidity. The purpose of this study was to identify variables obtained on initial patient presentation associated with MRSA septic arthritis. Sixteen factors were retrospectively evaluated in 109 consecutive pediatric patients diagnosed with culture-confirmed septic arthritis...
February 16, 2018: Orthopedics
Dominic Simm, Martin Kollmar
Stable single-alpha helices (SAH-domains) function as rigid connectors and constant force springs between structural domains, and can provide contact surfaces for protein-protein and protein-RNA interactions. SAH-domains mainly consist of charged amino acids and are monomeric and stable in polar solutions, characteristics which distinguish them from coiled-coil domains and intrinsically disordered regions. Although the number of reported SAH-domains is steadily increasing, genome-wide analyses of SAH-domains in eukaryotic genomes are still missing...
2018: PloS One
Han Li, Jin-Shen Wang, Lin-Jun Mu, Ke-Shu Shan, Le-Ping Li, Yan-Bing Zhou
AIM: To study the role of semaphorin 4D (Sema4D) expression promoted by tumor-associated macrophages (TAMs) in gastric carcinoma cells and its clinical significance in the invasion and metastasis of gastric carcinoma. METHODS: CD68 and Sema4D expression was analyzed in gastric carcinoma and adjacent normal tissues from 290 patients using the immunohistochemical streptavidin-peroxidase method, and their relationships with clinicopathological features were evaluated...
February 7, 2018: World Journal of Gastroenterology: WJG
Robert McCoy Vernon, Paul Andrew Chong, Brian Tsang, Tae Hun Kim, Alaji Bah, Patrick Farber, Hong Lin, Julie Deborah Forman-Kay
Protein phase separation is implicated in formation of membraneless organelles, signaling puncta and the nuclear pore. Multivalent interactions of modular binding domains and their target motifs can drive phase separation. However, forces promoting the more common phase separation of intrinsically disordered regions are less understood, with suggested roles for multivalent cation-pi, pi-pi, and charge interactions and the hydrophobic effect. Known phase-separating proteins are enriched in pi-orbital containing residues and thus we analyzed pi-interactions in folded proteins...
February 9, 2018: ELife
Jiangning Song, Fuyi Li, Kazuhiro Takemoto, Gholamreza Haffari, Tatsuya Akutsu, Kuo-Chen Chou, Geoffrey I Webb
Determining the catalytic residues in an enzyme is critical to our understanding the relationship between protein sequence, structure, function, and enhancing our ability to design novel enzymes and their inhibitors. Although many enzymes have been sequenced, and their primary and tertiary structures determined, experimental methods for enzyme functional characterization lag behind. Because experimental methods used for identifying catalytic residues are resource- and labor-intensive, computational approaches have considerable value and are highly desirable for their ability to complement experimental studies in identifying catalytic residues and helping to bridge the sequence-structure-function gap...
January 30, 2018: Journal of Theoretical Biology
Suman Das, Adam Eisen, Yi-Hsuan Lin, Hue Sun Chan
In view of recent intense experimental and theoretical interests in the biophysics of liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs), heteropolymer models with chain molecules configured as self-avoiding walks on the simple cubic lattice are constructed to study how phase behaviors depend on the sequence of monomers along the chains. To address pertinent general principles, we focus primarily on two fully charged 50-monomer sequences with significantly different charge patterns...
February 3, 2018: Journal of Physical Chemistry. B
Lingci Zhao, H Peter Lu, Jin Wang
HPPK (6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase) is a monomeric protein with 158 residues, which undergoes large scale conformational changes between apo, open, and holo states responding to ligand binding for its function. It has been explored widely as an excellent target for potential antibacterial drug development. However, little is known about how conformational dynamics between the native states influences the substrate recognition and the functionality of enzymatic catalysis. Here, we report a coarse-grained triple-basin structure-based model upon ligand binding to describe such multiple-state system by the molecular dynamics simulation...
January 31, 2018: Journal of Physical Chemistry. B
Sherlyn Jemimah, M Michael Gromiha
Additivity in binding affinity of protein-protein complexes refers to the change in free energy of binding (ΔΔGbind ) for double (or multiple) mutations which is approximately equal to the sum of their corresponding single mutation ΔΔGbind values. In this work, we have explored the additivity effect of double mutants, which shows a linear relationship between the binding affinity of double and sum of single mutants with a correlation of 0.90. However, the comparison of ΔΔGbind values showed a mean absolute deviation of 0...
January 31, 2018: Proteins
Mitchell G Thompson, Nima Sedaghatian, Jesus F Barajas, Maren Wehrs, Constance B Bailey, Nurgul Kaplan, Nathan J Hillson, Aindrila Mukhopadhyay, Jay D Keasling
pSC101 is a narrow host range, low-copy plasmid commonly used for genetically manipulating Escherichia coli. As a byproduct of a genetic screen for a more sensitive lactam biosensor, we identified multiple novel mutations that increase the copy number of plasmids with the pSC101 origin. All mutations identified in this study occurred on plasmids which also contained at least one mutation localized to the RepA protein encoded within the origin. Homology modelling predicts that many of these mutations occur within the dimerization interface of RepA...
January 25, 2018: Scientific Reports
Badri Adhikari, Jianlin Cheng
BACKGROUND: Contact-guided protein structure prediction methods are becoming more and more successful because of the latest advances in residue-residue contact prediction. To support contact-driven structure prediction, effective tools that can quickly build tertiary structural models of good quality from predicted contacts need to be developed. RESULTS: We develop an improved contact-driven protein modelling method, CONFOLD2, and study how it may be effectively used for ab initio protein structure prediction with predicted contacts as input...
January 25, 2018: BMC Bioinformatics
Dmitry Suplatov, Yana Sharapova, Daria Timonina, Kirill Kopylov, Vytas Švedas
The visualCMAT web-server was designed to assist experimental research in the fields of protein/enzyme biochemistry, protein engineering, and drug discovery by providing an intuitive and easy-to-use interface to the analysis of correlated mutations/co-evolving residues. Sequence and structural information describing homologous proteins are used to predict correlated substitutions by the Mutual information-based CMAT approach, classify them into spatially close co-evolving pairs, which either form a direct physical contact or interact with the same ligand (e...
December 28, 2017: Journal of Bioinformatics and Computational Biology
Matteo Figliuzzi, Pierre Barrat-Charlaix, Martin Weigt
Global coevolutionary models of homologous protein families, as constructed by direct coupling analysis (DCA), have recently gained popularity in particular due to their capacity to accurately predict residueresidue contacts from sequence information alone, and thereby to facilitate tertiary and quaternary protein structure prediction. More recently, they have also been used to predict fitness effects of aminoacid substitutions in proteins, and to predict evolutionary conserved protein-protein interactions...
January 17, 2018: Molecular Biology and Evolution
Michael Schmidt, Kay Hamacher
The prediction of residue contacts in a protein solely from sequence information is a promising approach to computational structure prediction. Recent developments use statistical or information theoretic methods to extract contact information from a multiple sequence alignment. Despite good results, accuracy is limited due to usage of two-body interactions within a Potts model. In this paper we generalize this approach and propose a Hamiltonian with an additional three-body interaction term. We derive a mean-field approximation for inference of three-body couplings within a Potts model which is fast enough on modern computers...
November 2017: Physical Review. E
Patrick N Reardon, Eric D Walter, Carrie L Marean-Reardon, Chad W Lawrence, Markus Kleber, Nancy M Washton
The degradation and turnover of soil organic matter is an important part of global carbon cycling and of particular importance with respect to attempts to predict the response of ecosystems to global climate change. Thus, it is important to mechanistically understand the processes by which organic matter can be degraded in the soil environment, including contact with reactive or catalytic mineral surfaces. We have characterized the outcome of the interaction of two minerals, birnessite and kaolinite, with two disaccharides, cellobiose and trehalose...
January 16, 2018: Scientific Reports
Paula V Monje, David Sant, Gaofeng Wang
This study comprehensively addresses the phenotype, function, and whole transcriptome of primary human and rodent Schwann cells (SCs) and highlights key species-specific features beyond the expected donor variability that account for the differential ability of human SCs to proliferate, differentiate, and interact with axons in vitro. Contrary to rat SCs, human SCs were insensitive to mitogenic factors other than neuregulin and presented phenotypic variants at various stages of differentiation, along with a mixture of proliferating and senescent cells, under optimal growth-promoting conditions...
January 11, 2018: Molecular Neurobiology
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