Showing papers in "Current Opinion in Structural Biology in 2017"

TL;DR: The goal of this review is to show the roles of intrinsic disorder in the magic behind biological liquid-liquid phase transitions that lead to the formation of PMLOs, which are crucially dependent on intrinsic disorder.

TL;DR: The growing literature of recent methods that combine experimental and computational information to model structural ensembles are reviewed, highlighting their similarities and differences and defining future goals towards the establishment of objective criteria for the comparison, validation, visualization and dissemination of such ensemble.

TL;DR: Some of the developments in simulation and theory in recent years, which have been driven by the desire to better capture IDP properties at different time- and length-scales, are summarized.

TL;DR: An overview of the structural basis of the different mechanisms by which TFs can cooperate is presented, focusing on insight from recent functional studies and structural analyses of specific TF-TF-DNA complexes.

TL;DR: The number of available LPMO structures has increased rapidly, including the first structure of an enzyme-substrate complex and the insights gained are reviewed below.

TL;DR: Recent developments are reviewed, including a variational principle to find optimal approximations to slow collective variables from simulation data, and algorithms such as the time-lagged independent component analysis.

TL;DR: Heavy-chain only isotypes (HcAb) devoid of light chains, where antigen-binding is mediated exclusively by one variable domain, evolved as promising candidates for biomedical applications of which many have already proven to be successful in early stage clinical trials.

TL;DR: A snapshot of the current state of knowledge of the molecular bases of thermal and cold stability and adaptation is presented, whose resolution would enable large-scale rational protein design.

TL;DR: New high-throughput approaches have significantly advanced the ability to identify Promiscuous activities, setting the stage for synthetic biology efforts to construct novel pathways using catalysts derived from promiscuous enzymes via directed evolution.

TL;DR: This review focuses on computational aspects of predicting the best native-like complex structure and binding affinities and provides the latest developments on protein- protein docking and binding affinity studies along with a list of available computational resources for understanding protein-protein interactions.

TL;DR: This review surveys screening and rational design methods for identifying peptides to inhibit protein-protein interactions, as well as methods for stabilizing peptide to effectively mimic protein surfaces.

TL;DR: This review summarizes recent advances in structural biological and mechanistic studies on the core autophagy machinery and discusses the molecular mechanisms of autophagosome formation.

TL;DR: It is suggested how novel structural and biophysical approaches can help to probe the interplay between the ribosome and the emerging peptide and present future challenges in understanding co-translational folding.

TL;DR: Recent structural studies of pseudoenzymes are highlighted, which have revealed the molecular basis for roles as allosteric regulators of conventional enzymes, as molecular switches and integrators, as hubs for assembling protein complexes, and as competitors of substrate availability and holoenzyme assembly.

TL;DR: Quantitative mass spectrometry of glycopeptides together with structures of the trimeric viral-spike define the steric principles controlling processing and provide a detailed map of the glycan shield.

TL;DR: Results from both, electron cryo-tomography and single particle analysis (SPA), have demonstrated the benefits of using a phase plate and improvements in phase plate technology are possible and new designs are already under development.

TL;DR: 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 to engineer protein molecular recognition.

TL;DR: Fundamental aspects of the process of catalytic optimization are discussed, practical solutions with respect to overcoming optimization plateaus are offered, and the maximal catalytic efficiency of the enzyme is reached.

TL;DR: Key open issues that could be tackled with either or both approaches are finally pointed out.

TL;DR: Recent advances in the application of SAS to disordered proteins and highly flexible complexes are described and current challenges are discussed.

TL;DR: Recent advances in FRET methods for examining biomolecular interactions and dynamics are described, including phasor plot analysis for quantitative analysis of protein interactions, single-molecule FRET measurement for detecting conformational dynamics in live cells, and data assimilation using molecular dynamics simulation to evaluate conformation of the whole protein.

TL;DR: This work states that path sampling approaches have been in use for nearly 20 years in biomolecular systems and enabled the generation of pathways and calculation of rate constants for ms processes, including large protein conformational changes, protein folding, and protein (un)binding.

TL;DR: Overall, this review aims to mechanistically explain the reversible and dynamic nature of this unique RNA internal modification that contributes to the complexity of RNA-mediated gene regulation, and inspire new studies in epitranscriptomics.

TL;DR: The bHLH-PAS proteins must form heterodimeric complexes to function as transcription factors as mentioned in this paper, which can give rise to unique patterns of heteroderimization.

TL;DR: This review focuses on computer simulations of disordered protein structures, functions, assemblies, and emerging questions that, taken together, give an overview of the field as it exists today.

TL;DR: Genetic and chemical technologies that enable targeted degradation of proteins of interest, namely small-molecule dependent inducible degrons and chemical degraders, for example, proteolysis-targeting chimeras (PROTACs) are presented.

TL;DR: The current understanding of transport, ligand promiscuity and regulation within the POT family is reviewed, including peptide-based pro-drugs that use PepT1 and PepT2, the mammalian homologues, to improve oral drug delivery.

TL;DR: How PPI networks (PPINs) inferred from experimentally characterized PPI data have been utilized for knowledge discovery and how in silico approaches to PPI characterization can contribute to PPIN-based biological research are discussed.

TL;DR: The recent advances in theory, computer simulations, and experiments that advance the understanding of the links between various physical scales in biology are summarized.

TL;DR: Recent work with Potts Hamiltonian models of protein sequence co-variation 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 is reviewed.