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Current Opinion in Structural Biology

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https://www.readbyqxmd.com/read/27923209/recognition-of-ubiquitinated-nucleosomes
#1
REVIEW
Michael T Morgan, Cynthia Wolberger
Histone ubiquitination plays a non-degradative role in regulating transcription and the DNA damage response. A mechanistic understanding of this chromatin modification has lagged that of small histone modifications because of the technical challenges in preparing ubiquitinated nucleosomes. The recent structure of the DUB module of the SAGA coactivator complex bound to a nucleosome containing monoubiquitinated H2B has provided the first view of how specialized subunits target this enzyme to its substrate. Single particle electron microscopy of the intact SAGA coactivator suggests how the DUB module and histone acetyltransferase module engage a nucleosomal substrate...
December 3, 2016: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/27912110/structures-and-mechanisms-of-crispr-rna-guided-effector-nucleases
#2
REVIEW
Hiroshi Nishimasu, Osamu Nureki
In the prokaryotic CRISPR-Cas adaptive immune systems, a CRISPR RNA (crRNA) assembles with multiple or single Cas proteins to form crRNA ribonucleoprotein (crRNP) effector complexes, responsible for the destruction of invading genetic elements. Although the mechanisms of target recognition and cleavage by the crRNP effectors are quite diverse among the different types of CRISPR-Cas systems, the basic action principles of these crRNA-guided effector nucleases are highly conserved. In all of the crRNP effectors, the repeat-derived invariant and spacer-derived variable segments of the crRNA are recognized by the Cas protein(s) in sequence-dependent and sequence-independent manners, respectively, with the spacer-derived guide segment available for base pairing with target nucleic acids...
November 29, 2016: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/27908508/editorial-overview-biophysical-and-molecular-biological-methods
#3
EDITORIAL
Petra Fromme, Andrej Sali
No abstract text is available yet for this article.
November 28, 2016: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/27907886/strategies-for-the-photo-control-of-endogenous-protein-activity
#4
REVIEW
Katherine E Brechun, Katja M Arndt, G Andrew Woolley
Photo-controlled or 'optogenetic' effectors interfacing with endogenous protein machinery allow the roles of endogenous proteins to be probed. There are two main approaches being used to develop optogenetic effectors: (i) caging strategies using photo-controlled conformational changes, and (ii) protein relocalization strategies using photo-controlled protein-protein interactions. Numerous specific examples of these approaches have been reported and efforts to develop general methods for photo-control of endogenous proteins are a current focus...
November 28, 2016: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/27899244/editorial-overview-carbohydrate-protein-interactions-and-glycosylation-integrating-structural-biology-informatics-and-systems-modelling-to-understand-glycan-structure-and-glycan-protein-interactions
#5
EDITORIAL
Harry J Gilbert, Nagasuma Chandra
No abstract text is available yet for this article.
November 26, 2016: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/27894013/outer-membrane-protein-design
#6
REVIEW
Joanna Sg Slusky
Membrane proteins are the gateway to the cell. These proteins are also a control center of the cell, as information from the outside is passed through membrane proteins as signals to the cellular machinery. The design of membrane proteins seeks to harness the power of these gateways and signal carriers. This review will focus on the design of the membrane proteins that are in the outer membrane, a membrane which only exists for gram negative bacteria, mitochondria, and chloroplasts. Unlike other membrane proteins, outer membrane proteins are uniquely shaped as β-barrels...
November 25, 2016: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/27889113/editorial-overview-multi-protein-assemblies-in-signaling
#7
EDITORIAL
Arun K Shukla, Shoshana J Wodak
No abstract text is available yet for this article.
November 23, 2016: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/27886568/deep-sequencing-methods-for-protein-engineering-and-design
#8
REVIEW
Emily E Wrenbeck, Matthew S Faber, Timothy A Whitehead
The advent of next-generation sequencing (NGS) has revolutionized protein science, and the development of complementary methods enabling NGS-driven protein engineering have followed. In general, these experiments address the functional consequences of thousands of protein variants in a massively parallel manner using genotype-phenotype linked high-throughput functional screens followed by DNA counting via deep sequencing. We highlight the use of information rich datasets to engineer protein molecular recognition...
November 22, 2016: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/27884574/corrigendum-to-unveiling-the-functional-diversity-of-the-alpha-beta-hydrolase-superfamily-in-the-plant-kingdom-curr-opin-struct-biol-2016-41-233-246
#9
Jeffrey T Mindrebo, Charisse M Nartey, Yoshiya Seto, Michael D Burkart, Joseph P Noel
No abstract text is available yet for this article.
November 21, 2016: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/27883951/survey-of-adaptive-biasing-potentials-comparisons-and-outlook
#10
REVIEW
Bradley M Dickson
Adaptive biasing potentials are becoming a standard tool of the trade for problems in chemistry, material science, biology, and drug discovery. These methods are easy to use, easy to distribute, reliable, and make otherwise impossible simulations possible. In this review we survey a number of adaptive bias potentials, and take a critical look at how they work. The biases fall into two basic classes, each having distinct attributes and levels of complexity. The vantage point from which the biases are discussed has only emerged in the last couple of years, and allows for a unified treatment of all the biases...
November 21, 2016: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/27871057/mechanistic-insights-into-gpcr-g-protein-interactions
#11
REVIEW
Jacob P Mahoney, Roger K Sunahara
G protein-coupled receptors (GPCRs) respond to extracellular stimuli and interact with several intracellular binding partners to elicit cellular responses, including heterotrimeric G proteins. Recent structural and biophysical studies have highlighted the dynamic nature of GPCRs and G proteins and have identified specific conformational changes important for receptor-mediated nucleotide exchange on Gα. While domain separation within Gα is necessary for GDP release, opening the inter-domain interface is insufficient to stimulate nucleotide exchange...
November 18, 2016: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/27870991/potts-hamiltonian-models-of-protein-co-variation-free-energy-landscapes-and-evolutionary-fitness
#12
REVIEW
Ronald M Levy, Allan Haldane, William F Flynn
Potts Hamiltonian models of protein sequence co-variation are statistical models constructed from the pair correlations observed in a multiple sequence alignment (MSA) of a protein family. These models are powerful because they capture higher order correlations induced by mutations evolving under constraints and help quantify the connections between protein sequence, structure, and function maintained through evolution. We review recent work with Potts models to predict protein structure and sequence-dependent conformational free energy landscapes, to survey protein fitness landscapes and to explore the effects of epistasis on fitness...
November 18, 2016: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/27866112/protein-protein-interactions-scoring-schemes-and-binding-affinity
#13
REVIEW
M Michael Gromiha, K Yugandhar, Sherlyn Jemimah
Protein-protein interactions mediate several cellular functions, which can be understood from the information obtained using the three-dimensional structures of protein-protein complexes and binding affinity data. This review focuses on computational aspects of predicting the best native-like complex structure and binding affinities. The first part covers the prediction of protein-protein complex structures and the advantages of conformational searching and scoring functions in protein-protein docking. The second part is devoted to various aspects of protein-protein interaction thermodynamics, such as databases for binding affinities and other thermodynamic parameters, computational methods to predict the binding affinity using either the three-dimensional structures of complexes or amino acid sequences, and change in binding affinities of the complexes upon mutations...
November 17, 2016: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/27866084/engineering-cell-signaling-modulators-from-native-protein-protein-interactions
#14
REVIEW
Wei Zhang, Moshe Ben-David, Sachdev S Sidhu
Recent studies on genome sequencing and genetic screens with RNAi and CRISPR technology have revolutionized our understanding of aberrant signaling networks in human diseases. A strategy combining both genetic and protein-based technologies should be at the heart of modern drug-development efforts, particularly in the era of precision medicine. Thus, there is an urgent need for efficient platforms to develop probes that can modulate protein function in cells to validate drug targets and to develop therapeutic leads...
November 17, 2016: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/27865209/protein-function-machinery-from-basic-structural-units-to-modulation-of-activity
#15
REVIEW
Igor N Berezovsky, Enrico Guarnera, Zejun Zheng, Birgit Eisenhaber, Frank Eisenhaber
Contemporary protein structure is a result of the trade off between the laws of physics and the evolutionary selection. The polymer nature of proteins played a decisive role in establishing the basic structural and functional units of soluble proteins. We discuss how these elementary building blocks work in the hierarchy of protein domain structure, co-translational folding, as well as in enzymatic activity and molecular interactions. Next, we consider modulators of the protein function, such as intermolecular interactions, disorder-to-order transitions, and allosteric signaling, acting via interference with the protein's structural dynamics...
November 16, 2016: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/27865208/what-evolution-tells-us-about-protein-physics-and-protein-physics-tells-us-about-evolution
#16
REVIEW
Ugo Bastolla, Yves Dehouck, Julian Echave
The integration of molecular evolution and protein biophysics is an emerging theme that steadily gained importance during the last 15 years, significantly advancing both fields. The central integrative concept is the stability of the native state, although non-native conformations are increasingly recognized to play a major role, concerning, for example, aggregation, folding kinetics, or functional dynamics. Besides molecular requirements on fitness, the stability of native and alternative conformations is modulated by a variety of factors, including population size, selective pressure on the replicative system, which determines mutation rates and biases, and epistatic effects...
November 16, 2016: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/27865112/recent-advances-in-understanding-proton-coupled-peptide-transport-via-the-pot-family
#17
REVIEW
Simon Newstead
The POT family of membrane transporters use the inwardly directed proton electrochemical gradient to drive the uptake of essential nutrients into the cell. Originally discovered in bacteria, members of the family have been found in all kingdoms of life except the archaea. A remarkable feature of the family is their diverse substrate promiscuity. Whereas in mammals and bacteria they are predominantly di- and tri-peptide transporters, in plants the family has diverged to recognize nitrate, plant defence compounds and hormones...
November 16, 2016: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/27865111/camelid-and-shark-single-domain-antibodies-structural-features-and-therapeutic-potential
#18
REVIEW
Doreen Könning, Stefan Zielonka, Julius Grzeschik, Martin Empting, Bernhard Valldorf, Simon Krah, Christian Schröter, Carolin Sellmann, Björn Hock, Harald Kolmar
In addition to canonical antibodies composed of heavy and light chains, the adaptive immune systems of camelids and cartilaginous fish comprise heavy-chain only isotypes (HcAb) devoid of light chains, where antigen-binding is mediated exclusively by one variable domain. Due to their inherent favorable attributes, such as high affinity and specificity for their cognate antigen, extraordinary stability, small size and, most importantly, the possibility to complement classical antibodies in terms of 'drugable' target-space, HcAb-derived entities evolved as promising candidates for biomedical applications of which many have already proven to be successful in early stage clinical trials...
November 16, 2016: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/27838525/intrinsically-disordered-proteins-in-overcrowded-milieu-membrane-less-organelles-phase-separation-and-intrinsic-disorder
#19
REVIEW
Vladimir N Uversky
Although the cellular interior is crowded with various biological macromolecules, the distribution of these macromolecules is highly inhomogeneous. Eukaryotic cells contain numerous proteinaceous membrane-less organelles (PMLOs), which are condensed liquid droplets formed as a result of the reversible and highly controlled liquid-liquid phase transitions. The interior of these cellular bodies represents an overcrowded milieu, since their protein concentrations are noticeably higher than those of the crowded cytoplasm and nucleoplasm...
November 10, 2016: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/27835803/free-energy-analysis-of-protein-solvation-with-all-atom-molecular-dynamics-simulation-combined-with-a-theory-of-solutions
#20
REVIEW
Nobuyuki Matubayasi
The structure of a protein is strongly influenced by solvation. In the present review, the solvation effect is treated within the framework of statistical thermodynamics. The key quantity is the solvation free energy of protein and a fast method for its computation with explicit solvent is introduced. The applications of the method to the structural fluctuation of protein in water, structure determination of protein-protein complex, and urea effect on protein structure are then described, and the roles of solvent water and cosolvent are discussed from the standpoint of energetics...
November 8, 2016: Current Opinion in Structural Biology
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