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Protein Science: a Publication of the Protein Society

Zheng Dong, Hongyu Zhou, Peng Tao
OBJECTIVES: PAS domains are widespread in archaea, bacteria and eukaryota, and play important roles in various functions. In this study, we aim to explore functional evolutionary relationship among proteins in the PAS domain superfamily in view of the sequence-structure-dynamics-function relationship. METHODS: We collected protein sequences and crystal structures data from RCSB Protein Data Bank of the PAS domain superfamily belonging to three biological functions (nucleotide binding, photoreceptor activity and transferase activity)...
October 20, 2017: Protein Science: a Publication of the Protein Society
Rajesh Gumpena, George T Lountos, Sreejith Raran-Kurussi, Joseph E Tropea, Scott Cherry, David S Waugh
The dual specificity phosphatase DUSP1 was the first mitogen activated protein kinase phosphatase (MKP) to be identified. It dephosphorylates conserved tyrosine and threonine residues in the activation loops of mitogen activated protein kinases ERK2, JNK1 and p38-alpha. Here, we report the crystal structure of the human DUSP1 catalytic domain at 2.49 Å resolution. Uniquely, the protein was crystallized as an MBP fusion protein in complex with a monobody that binds to MBP. Sulfate ions occupy the phosphotyrosine and putative phosphothreonine binding sites in the DUSP1 catalytic domain...
October 20, 2017: Protein Science: a Publication of the Protein Society
Gang Xu, Tianqi Ma, Tianwu Zang, Qinghua Wang, Jianpeng Ma
We report a C-atom-based scoring function, named OPUS-CSF, for ranking protein structural models. Rather than using traditional Boltzmann formula, we built a scoring function (CSF score) based on the native distributions (derived from the entire PDB) of coordinate components of mainchain C (carbonyl) atoms on selected residues of peptide segments of 5, 7, 9, and 11 residues in length. In testing OPUS-CSF on decoy recognition, it maximally recognized 257 native structures out of 278 targets in 11 commonly used decoy sets, significantly more than other popular all-atom empirical potentials...
October 19, 2017: Protein Science: a Publication of the Protein Society
Jimin Wang
Three basic electronic properties of molecules, electron density (ED), charge density (CD), and electrostatic potentials (ESP), are dependent on both atomic mobility and occupancy of components in the molecules. Small protein subunits may bind large macromolecular complexes with a reduced occupancy or an increased atomic mobility or both due to affinity-based functional regulation, and so may substrates, products, cofactors, ions or solvent molecule to the active sites of enzymes. A quantitative theory is presented in this study that describes the dependence of atomic functions on atomic B-factor in Fourier transforms of the corresponding maps...
October 13, 2017: Protein Science: a Publication of the Protein Society
Joyce Liu, James Kaganjo, Wenjun Zhang, Jill Zeilstra-Ryalls
The precursor to all tetrapyrroles is 5-aminolevulinic acid, which is made either via the condensation of glycine and succinyl-CoA catalyzed by an ALA synthase (the C4 or Shemin pathway) or by a pathway that uses glutamyl-tRNA as a precursor and involves other enzymes (the C5 pathway). Certain ALA synthases also catalyze the cyclization of ALA-CoA to form 2-amino-3-hydroxycyclopent-2-en-1-one. Organisms with synthases that possess this second activity nevertheless rely upon the C5 pathway to supply ALA for tetrapyrrole biosynthesis...
October 13, 2017: Protein Science: a Publication of the Protein Society
Vincent Frappier, Madeleine Duran, Amy E Keating
PixelDB, the Peptide Exosite Location Database, compiles 1966 non-redundant, high-resolution structures of protein-peptide complexes filtered to minimize the impact of crystal packing on peptide conformation. The database is organized to facilitate study of structurally conserved vs. non-conserved elements of protein-peptide engagement. PixelDB clusters complexes based on the structural similarity of the peptide-binding protein, and by comparing complexes within a cluster highlights examples of domains that engage peptides using more than one binding mode...
October 12, 2017: Protein Science: a Publication of the Protein Society
Maristella De Cicco, Lech-G Milroy, Sonja A Dames
Increased efforts have been undertaken to better understand the formation of signaling complexes at cellular membranes. Since the preparation of proteins containing a transmembrane domain or a prenylation motif is generally challenging an alternative membrane anchoring unit that is easy to attach, water-soluble and binds to different membrane mimetics would find broad application. The 33-residue long FATC domain of yeast TOR1 (y1fatc) fulfills these criteria and binds to neutral and negatively charged micelles, bicelles and liposomes...
October 12, 2017: Protein Science: a Publication of the Protein Society
Adam Kazimierz Górka, Andrzej Górecki, Marta Dziedzicka-Wasylewska
Site-specific labeling of proteins with fluorescent dyes allows the study of protein structure and function using a wide variety of fluorescent techniques. However, specific labeling is not trivial in the case of proteins containing multiple cysteine residues. An example of such a protein is transcription factor Yin Yang 1, which comprises eight cysteine residues in four C2H2 type zinc fingers in the C-terminal region. Kinetic measurements of the labeling process allowed us to develop preparative labeling of three cysteine residues differently introduced to the N-terminal, disordered fragment of the protein...
October 12, 2017: Protein Science: a Publication of the Protein Society
Kathryn M Schultz, Candice S Klug
Lipopolysaccharide (LPS, endotoxin) is the major component of the outer leaflet of the outer membrane of Gram-negative bacteria such as Escherichia coli and Salmonella typhimurium. LPS is a large lipid containing several acyl chains as its hydrophobic base and numerous sugars as its hydrophilic core and O-antigen domains, and is an essential element of the organisms' natural defenses in adverse environmental conditions. LptC is one of seven members of the lipopolysaccharide transport (Lpt) protein family that functions to transport LPS from the inner membrane (IM) to the outer leaflet of the outer membrane of the bacterium...
October 12, 2017: Protein Science: a Publication of the Protein Society
Melanie H Dietrich, Christina Harprecht, Thilo Stehle
Numerous viruses rely on glycan receptor binding as the initial step in host cell infection. Engagement of specific glycan receptors such as sialylated carbohydrates, glycosaminoglycans, or histo-blood group antigens can determine host range, tissue tropism, and pathogenicity. Glycan receptor binding sites are typically located in exposed regions on viral surfaces - sites that are also generally prone to binding of neutralizing antibodies that directly interfere with virus-glycan receptor interactions. In this review, we examine the locations and architecture of the glycan- and antibody binding sites in four different viruses with stalk-like attachment proteins (reovirus, influenza virus, norovirus, and coronavirus) and investigate the mechanisms by which antibodies block glycan recognition...
October 7, 2017: Protein Science: a Publication of the Protein Society
Jiayi Dou, Lindsey Doyle, Per Jr Greisen, Alberto Schena, Hahnbeom Park, Kai Johnsson, Barry L Stoddard, David Baker
The steroid hormone 17α-hydroxylprogesterone (17-OHP) is a biomarker for congenital adrenal hyperplasia and hence there is considerable interest in sensor development towards this compound. We used computational protein design to generate protein models with binding sites for 17-OHP containing an extended, nonpolar, shape-complementary binding pocket corresponding to the four-ring core of the compound, and hydrogen bonding residues at the base of the pocket to interact with carbonyl and hydroxyl groups at the more polar end of the ligand...
October 4, 2017: Protein Science: a Publication of the Protein Society
Elin Teppa, Diego Javier Zea, Cristina Marino-Buslje
Protein-protein interactions are essential to all aspects of life. Specific interactions result from evolutionary pressure at the interacting interfaces of partner proteins. However, evolutionary pressure is not homogeneous within the interface: for instance, each residue does not contribute equally to the binding energy of the complex. To understand functional differences between residues within the interface, we analyzed their properties in the core and rim regions. Here, we characterized protein interfaces with two evolutionary measures, conservation and coevolution, using a comprehensive dataset of 896 protein complexes...
October 4, 2017: Protein Science: a Publication of the Protein Society
Pablo Conesa Mingo, José Gutierrez, Adrián Quintana, José Miguel de la Rosa Trevín, Airén Zaldívar-Peraza, Jesús Cuenca Alba, Moshen Kazemi, Javier Vargas, Laura Del Cano, Joan Segura, Carlos Oscar S Sorzano, Jose María Carazo
Macromolecular structural determination by Electron Microscopy under cryogenic conditions is revolutionizing the field of structural biology, interesting a large community of potential users. Still, the path from raw images to density maps is complex, and sophisticated image processing suites are required in this process, often demanding the installation and understanding of different software packages. Here we present Scipion Web Tools, a web-based set of tools/workflows derived from the Scipion image processing framework, specially tailored to non-expert users in need of very precise answers at several key stages of the structural elucidation process...
October 3, 2017: Protein Science: a Publication of the Protein Society
Luis C Acosta, Gerardo M Perez Goncalves, Gary J Pielak, Annelise H Gorensek-Benitez
Protein enzymes are the main catalysts in the crowded and complex cellular interior, but their activity is almost always studied in dilute buffered solutions. Studies that attempt to recreate the cellular interior in vitro often utilize synthetic polymers as crowding agents. Here, we report the effects of the synthetic polymer cosolutes Ficoll, dextran and polyvinylpyrrolidone, as well as their respective monomers, sucrose, glucose and 1-ethyl-2-pyrrolidone, on the activity of the 18-kDa monomeric enzyme, Escherichia coli dihydrofolate reductase...
October 3, 2017: Protein Science: a Publication of the Protein Society
Jimin Wang, Gary W Brudvig, Victor S Batista, Peter B Moore
In 2012, Karplus and Diederichs demonstrated that the Pearson correlation coefficient CC1/2 is a far better indicator of the quality and resolution of crystallographic data sets than more traditional measures like merging R-factor or signal-to-noise ratio. More specifically, they proposed that CC1/2 be computed for data sets in thin shells of increasing resolution so that the resolution dependence of that quantity can be examined. Recently, however, the CC1/2 values of entire data sets, i.e. cumulative correlation coefficients, have been used as a measure of data quality...
September 29, 2017: Protein Science: a Publication of the Protein Society
Rocco Moretti, Sergey Lyskov, Rhiju Das, Jens Meiler, Jeffrey J Gray
The Rosetta molecular modeling software package provides a large number of experimentally validated tools for modeling and designing proteins, nucleic acids, and other biopolymers, with new protocols being added continually. While freely available to academic users, external usage is limited by the need for expertise in the Unix command line environment. To make Rosetta protocols available to a wider audience, we previously created a web server called ROSIE (Rosetta Online Server that Includes Everyone), which provides a common environment for hosting web-accessible Rosetta protocols...
September 28, 2017: Protein Science: a Publication of the Protein Society
Yannick Mesrouze, Marco Meyerhofer, Fedir Bokhovchuk, Patrizia Fontana, Catherine Zimmermann, Typhaine Martin, Clara Delaunay, Aude Izaac, Joerg Kallen, Tobias Schmelzle, Dirk Erdmann, Patrick Chène
The Hippo pathway is deregulated in various cancers, and the discovery of molecules that modulate this pathway may open new therapeutic avenues in oncology. TEAD transcription factors are the most distal elements of the Hippo pathway and their transcriptional activity is regulated by the YAP protein. Amongst the various possibilities for targeting this pathway, inhibition of the YAP:TEAD interaction is an attractive strategy. It has been shown recently that TEAD proteins are covalently linked via a conserved cysteine to a fatty acid molecule (palmitate) that binds to a deep hydrophobic cavity present in these proteins...
September 28, 2017: Protein Science: a Publication of the Protein Society
Benjamin Webb, Shruthi Viswanath, Massimiliano Bonomi, Riccardo Pellarin, Charles H Greenberg, Daniel Saltzberg, Andrej Sali
Building models of a biological system that are consistent with the myriad data available is one of the key challenges in biology. Modeling the structure and dynamics of macromolecular assemblies, for example, can give insights into how biological systems work, evolved, might be controlled, and even designed. Integrative structure modeling casts the building of structural models as a computational optimization problem, for which information about the assembly is encoded into a scoring function that evaluates candidate models...
September 28, 2017: Protein Science: a Publication of the Protein Society
Meng Gao, Jingjing Zhou, Zhengding Su, Yongqi Huang
Azurin secreted by Pseudomonas aeruginosa is an anticancer bacteriocin, which preferentially enters human cancer cells and induces apoptosis or growth inhibition. It turns out that azurin is a multi-target anticancer agent interfering in the p53 signaling pathway and the non-receptor tyrosine kinases signaling pathway. This suggests that azurin exerts its anticancer activity by interacting with multiple targets and interfering in multiple steps in disease progression. Therefore, azurin could overcome resistance to therapy...
September 27, 2017: Protein Science: a Publication of the Protein Society
Manajit Hayer-Hartl
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) mediates the fixation of atmospheric CO2 in photosynthesis by catalyzing the carboxylation of the 5-carbon sugar ribulose-1,5-bisphosphate (RuBP). Despite its pivotal role, Rubisco is an inefficient enzyme and thus has been a key target for bioengineering. However, efforts to increase crop yields by Rubisco engineering remain unsuccessful, due in part to the complex machinery of molecular chaperones required for Rubisco biogenesis and metabolic repair...
September 27, 2017: Protein Science: a Publication of the Protein Society
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