Abstract：
:The recent and growing evidence that the efficacy of a drug can be correlated to target binding kinetics has seeded the development of a multitude of novel methods aimed at computing rate constants for receptor-ligand binding processes, as well as gaining an understanding of the binding and unbinding pathways and the determinants of structure-kinetic relationships. These new approaches include various types of enhanced sampling molecular dynamics simulations and the combination of energy-based models with chemometric analysis. We assess these approaches in the light of the varying levels of complexity of protein-ligand binding processes.
journal_name
Curr Opin Struct Bioljournal_title
Current opinion in structural biologyauthors
Bruce NJ,Ganotra GK,Kokh DB,Sadiq SK,Wade RCdoi
10.1016/j.sbi.2017.10.001subject
Has Abstractpub_date
2018-04-01 00:00:00pages
1-10eissn
0959-440Xissn
1879-033Xpii
S0959-440X(17)30109-4journal_volume
49pub_type
杂志文章,评审abstract：:The past twelve months have seen a renewal of interest in the therapeutic potential of members of the tumour necrosis factor receptor family and their cytokine ligands. This biomedical interest has spawned a number of structural studies, which have significantly deepened our understanding of the molecular basis for th...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/s0959-440x(00)00149-4
更新日期：2000-12-01 00:00:00
abstract：:Recent studies from several laboratories have provided evidence that cell surface complex carbohydrates play key roles in the regulation of developmentally relevant signal transduction events. The demonstration that Fringe, a known modifier of Notch function, is a fucose-specific N-acetylglucosaminyltransferase provid...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/s0959-440x(02)00371-8
更新日期：2002-10-01 00:00:00
abstract：:Eukaryotic mRNAs contain a 5' cap structure that protects the transcript against rapid exonucleolytic degradation. The regulation of cellular mRNA levels therefore depends on a precise control of the mRNA decapping pathways. The major mRNA decapping enzyme in eukaryotic cells is Dcp2. It is regulated by interactions w...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2019.07.009
更新日期：2019-12-01 00:00:00
abstract：:Biology has, and continues to be, shaped by evolutionary mechanisms. Within the past decade, local fitness landscapes have become experimentally tractable and are providing new perspectives on evolutionary mechanisms. Powered by next-generation sequencing, the impacts of all individual amino acid substitutions on func...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2018.01.001
更新日期：2018-02-01 00:00:00
abstract：:The utility of mass spectrometry for the analysis of proteins has grown enormously in the past decade. Significant advances in detection and ionization techniques are allowing questions about noncovalent assembly to be addressed by the direct observation of gas phase complexes, their assembly in real time and their di...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/s0959-440x(00)00137-8
更新日期：2000-10-01 00:00:00
abstract：:Force spectroscopy has developed into an indispensable tool for studying folding and binding of proteins on a single molecule level in real time. Design of the pulling geometry allows tuning the reaction coordinate in a very precise manner. Many recent experiments have taken advantage of this possibility and have prov...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2012.11.007
更新日期：2013-02-01 00:00:00
abstract：:Rapid advances in the cloning and expression of glycosyltransferase genes, especially from bacteria, could open the way to overcoming difficulties in the mass production of oligosaccharides. The large-scale production of oligosaccharides using either glycosyltransferases isolated from engineered microorganisms or whol...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/s0959-440x(00)00127-5
更新日期：2000-10-01 00:00:00
abstract：:Eukaryotes possess a variety of translational control mechanisms which function in the surveillance of mRNAs, discriminating between normal and aberrant translation elongation and termination, triggering mRNA decay. The three major evolutionarily conserved eukaryotic pathways are No-Go, Non-Stop and Nonsense-Mediated ...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2020.06.011
更新日期：2020-12-01 00:00:00
abstract：:All domains of life make carbohydrate polymers and by anchoring them to lipid molecules they can decorate the outside of the cell. Polysaccharides are linked to proteins by glycosylation, a process found in both bacteria and in higher organisms. Bacteria do have other distinct uses for carbohydrate polymers; in gram-n...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2016.07.016
更新日期：2016-10-01 00:00:00
abstract：:Arf GTPases are major regulators of membrane traffic and organelle structure in eukaryotes where they recruit many different effectors, including components of vesicular coats, proteins that tether membranes, sort lipids or have diverse other functions in vesicular traffic, and bacterial proteins that divert Arf funct...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2014.09.007
更新日期：2014-12-01 00:00:00
abstract：:Aromatic polyketides are secondary metabolites that afford some of the most common antibiotics and anti-cancer drugs currently in clinical use. Not least because of their medical importance, the biosynthesis of these compounds has attracted considerable interest during the past few years; important advances have been ...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2005.10.002
更新日期：2005-12-01 00:00:00
abstract：:The small multidrug resistance proteins constitute a family of bacterial antiporters that confer multidrug resistance by H(+)-linked drug efflux across the bacterial cytoplasmic membrane. The structure of EmrE, the family archetype, has been determined by electron crystallography and shows that EmrE in the membrane is...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2006.06.005
更新日期：2006-08-01 00:00:00
abstract：:Protein scientists are paving the way to a new phase in protein design and engineering. Approaches and methods are being developed that could allow the design of proteins beyond the confines of natural protein structures. This possibility of designing entirely new proteins opens new questions: What do we build? How do...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2015.05.009
更新日期：2015-08-01 00:00:00
abstract：:Computational protein design - the search for amino acids that adopt defined structures and functions - has achieved significant successes in recent years. Design is often approached from the perspective of targeting the design objective one structure-sequence pair at a time. Here we summarize studies that take an alt...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2010.02.004
更新日期：2010-06-01 00:00:00
abstract：:DNA photolyases are extremely efficient light-driven DNA repair enzymes that use the energy of a blue-light photon to 'inject' an electron onto UV-damaged DNA, catalyzing the splitting of mutagenic pyrimidine dimers. By contrast, cryptochromes use blue light to trigger signaling cascades in multicellular organisms, fu...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2006.01.004
更新日期：2006-02-01 00:00:00
abstract：:Viruses with an icosahedrally symmetric protein capsid and a membrane infect hosts from all three domains of life. Similar architectural principles are shared by different viral families, as exemplified by double-stranded DNA viruses such as PRD1 and STIV. During virus assembly, the membrane lipids are selectively acq...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2007.03.005
更新日期：2007-04-01 00:00:00
abstract：:G-protein-coupled receptors (GPCRs) participate in virtually all physiological processes. They constitute the largest and most structurally conserved family of signaling molecules. Several class C GPCRs have been shown to exist as dimers in their active form and growing evidence indicates that many, if not all, class ...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2006.03.013
更新日期：2006-04-01 00:00:00
abstract：:The sema domain was first defined from sequence by Kolodkin and colleagues in the early 1990s, and constitutes the distinctive structural and functional element of semaphorins, their plexin receptors and the receptor tyrosine kinases MET and RON, three protein families with major roles in development, tissue regenerat...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2004.10.010
更新日期：2004-12-01 00:00:00
abstract：:The past year has seen some major advances in the area of carbohydrate synthesis using chemical methods. Progress in all areas of synthetic methodology, including new protecting groups and coupling methods, has been reported. A number of complex carbohydrate structures have been prepared using known, as well as new, m...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/s0959-440x(00)00252-9
更新日期：2001-10-01 00:00:00
abstract：:A coherent view of the structure and function of DNA polymerase processivity factors (sliding clamps and clamp loaders) is emerging from recent structural studies. Crystal structures of sliding clamps from the T4 and RB69 bacteriophages, and from an archaebacterium expand the gallery of ring-shaped processivity factor...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/s0959-440x(02)00313-5
更新日期：2002-04-01 00:00:00
abstract：:Intrinsically disordered regions (IDRs) are fundamental units of protein function and regulation. Despite their inability to form a unique stable tertiary structure in isolation, many IDRs adopt a defined conformation upon binding and achieve their function through their interactions with other biomolecules. However, ...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2014.05.007
更新日期：2014-06-01 00:00:00
abstract：:Malaria remains the world's most prevalent human parasitic disease. Because of the rapid spread of drug resistance in parasites, there is an urgent need to identify diverse new drug targets. One group of proteases that are emerging as targets for novel antimalarials are the metalloaminopeptidases. These enzymes cataly...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2013.07.015
更新日期：2013-12-01 00:00:00
abstract：:A large body of work has gone into understanding the effect of mutations on protein structure and function. Conventional treatments have involved quantifying the change in stability, activity and relaxation rates of the mutants with respect to the wild-type protein. However, it is now becoming increasingly apparent th...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2018.09.004
更新日期：2019-02-01 00:00:00
abstract：:Transition states in protein folding are being analyzed experimentally and by computer simulation to reveal the sequence of events in the folding and unfolding of proteins at high resolution. Results of this analysis have enabled the reconstruction of folding pathways in vitro and open the prospect of analyzing pathwa...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/0959-440x(95)80012-p
更新日期：1995-02-01 00:00:00
abstract：:The ISWI family of ATP-dependent chromatin remodelers regulates transcription of coding and noncoding RNA by mobilizing nucleosomes and controlling the length of linker DNA separating nucleosomes (spacing). Nucleosome movement is tightly coupled to the DNA translocation activity of the helicase domain in the catalytic...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2014.01.010
更新日期：2014-02-01 00:00:00
abstract：:Helical filaments were the first structures to be reconstructed in three dimensions from electron microscopic images, and continue to be extensively studied due to the large number of such helical polymers found in biology. In principle, a single image of a helical polymer provides all of the different projections nee...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2007.07.006
更新日期：2007-10-01 00:00:00
abstract：:When a protein's function cannot be experimentally determined, it can often be inferred from sequence similarity. Should this process fail, analysis of the protein structure can provide functional clues or confirm tentative functional assignments inferred from the sequence. Many structure-based approaches exist (e.g. ...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2005.04.003
更新日期：2005-06-01 00:00:00
abstract：:Covalently circularized nanodiscs (cNDs) represent a significant advance in the durability and applicability of nanodisc technology. The new cNDs demonstrate higher size homogeneity and improved stability compared with that of non-circularized forms. Moreover, cNDs can be prepared at various defined sizes up to 80-nm ...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2018.03.014
更新日期：2018-08-01 00:00:00
abstract：:The computational evaluation of protein-protein interactions will play an important role in organising the wealth of data being generated by high-throughput initiatives. Here we discuss future applications, report recent developments and identify areas requiring further investigation. Many functions have been develope...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2013.06.017
更新日期：2013-12-01 00:00:00
abstract：:ATP- and NAD(+)-dependent DNA ligases, ATP-dependent RNA ligases and GTP-dependent mRNA capping enzymes comprise a superfamily of proteins that catalyze nucleotidyl transfer to polynucleotide 5' ends via covalent enzyme-(lysyl-N)-NMP intermediates. The superfamily is defined by five peptide motifs that line the nucleo...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2004.10.006
更新日期：2004-12-01 00:00:00
