abstract：:2D-IR spectroscopy has matured to a powerful technique to study the structure and dynamics of peptides, but its extension to larger proteins is still in its infancy, the major limitations being sensitivity and selectivity. Site-selective information requires measuring single vibrational probes at sub-millimolar concen...

journal_title：Current opinion in structural biology

authors： Koziol KL,Johnson PJ,Stucki-Buchli B,Waldauer SA,Hamm P

更新日期：2015-10-01 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

authors： Woolfson DN,Bartlett GJ,Burton AJ,Heal JW,Niitsu A,Thomson AR,Wood CW

更新日期：2015-08-01 00:00:00

abstract：:This review emphasizes the effects of naturally occurring mutations on structural features and physico-chemical properties of proteins. The basic protein characteristics considered are stability, dynamics, and the binding of proteins and methods for assessing effects of mutations on these macromolecular characteristic...

journal_title：Current opinion in structural biology

authors： Kucukkal TG,Petukh M,Li L,Alexov E

更新日期：2015-06-01 00:00:00

abstract：:Connecting dynamics to structural data from diverse experimental sources, molecular dynamics simulations permit the exploration of biological phenomena in unparalleled detail. Advances in simulations are moving the atomic resolution descriptions of biological systems into the million-to-billion atom regime, in which n...

journal_title：Current opinion in structural biology

authors： Perilla JR,Goh BC,Cassidy CK,Liu B,Bernardi RC,Rudack T,Yu H,Wu Z,Schulten K

更新日期：2015-04-01 00:00:00

abstract：:Bacterial transcription initiation is controlled by sigma factors, the RNA polymerase (RNAP) subunits responsive for promoter specificity. While the primary sigma factor ensures the bulk of transcription during growth, a major strategy used by bacteria to regulate gene expression consists of modifying the RNAP promote...

journal_title：Current opinion in structural biology

authors： Campagne S,Allain FH,Vorholt JA

更新日期：2015-02-01 00:00:00

abstract：:Force can drive conformational changes in proteins, as well as modulate their stability and the affinity of their complexes, allowing a mechanical input to be converted into a biochemical output. These properties have been utilised by nature and force is now recognised to be widely used at the cellular level. The effe...

journal_title：Current opinion in structural biology

authors： Chen Y,Radford SE,Brockwell DJ

更新日期：2015-02-01 00:00:00

abstract：:Conformational dynamics is a hallmark of diverse non-coding RNA functions. During these functional processes, RNA molecules almost ubiquitously undergo conformational transitions that are tuned to meet distinct structural and kinetic requirements for proper function. A complete mechanistic understanding of RNA functio...

journal_title：Current opinion in structural biology

authors： Zhao B,Zhang Q

更新日期：2015-02-01 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

authors： Cherfils J

更新日期：2014-12-01 00:00:00

abstract：:The past years have seen tremendous progress towards understanding how arrestins recognize phosphorylated G protein-coupled receptors (GPCRs). Two arrestin crystal structures, one of a pre-activated splice variant and one bound to a GPCR phosphopeptide, provided insights into the conformational changes upon phosphate ...

journal_title：Current opinion in structural biology

authors： Ostermaier MK,Schertler GF,Standfuss J

更新日期：2014-12-01 00:00:00

abstract：:Generally, non-catalytic carbohydrate binding module (CBM) specificity has been shown to parallel the catalytic activity of the carbohydrate active enzyme (CAZyme) module it is appended to. With the rapid expansion in metagenomic sequence space for the potential discovery of new CBMs in addition to the recent emergenc...

journal_title：Current opinion in structural biology

authors： Abbott DW,van Bueren AL

更新日期：2014-10-01 00:00:00

abstract：:Integrative structural modeling uses multiple types of input information and proceeds in four stages: (i) gathering information, (ii) designing model representation and converting information into a scoring function, (iii) sampling good-scoring models, and (iv) analyzing models and information. In the first stage, unc...

journal_title：Current opinion in structural biology

authors： Schneidman-Duhovny D,Pellarin R,Sali A

更新日期：2014-10-01 00:00:00

abstract：:Transmembrane helix-helix interactions mediate the folding and assembly of membrane proteins. Recognition motifs range from GxxxG and leucine zippers to polar side chains and salt bridges. Some canonical membrane proteins contain local charge clusters that are important for folding and function, and which have to be c...

journal_title：Current opinion in structural biology

authors： Walther TH,Ulrich AS

更新日期：2014-08-01 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

authors： Flock T,Weatheritt RJ,Latysheva NS,Babu MM

更新日期：2014-06-01 00:00:00

abstract：:Recently, atomic models of the mammalian, fungal and the bacterial fatty acid synthases type I (FAS I) were reported. Now, a wealth of functional data, collected during the last decades, can be embedded into structural frames. But there is more, which remains to be done! Our current considerations are implicitly very ...

journal_title：Current opinion in structural biology

authors： Grininger M

更新日期：2014-04-01 00:00:00

abstract：:The folding and assembly of myosin motor proteins is essential for most movement processes at the cellular, but also at the organism level. Importantly, myosins, which represent a very diverse family of proteins, require the activity of general and specialized folding factors to develop their full motor function. The ...

journal_title：Current opinion in structural biology

authors： Hellerschmied D,Clausen T

更新日期：2014-04-01 00:00:00

abstract：:Ring-shaped nucleic acid translocases and helicases catalyze the directed and processive movement of nucleic acid strands to support essential transactions such as replication, transcription, and chromosome partitioning. Assembled typically as hexamers, ring helicase/translocase systems use coordinated cycles of nucle...

journal_title：Current opinion in structural biology

authors： O'Shea VL,Berger JM

更新日期：2014-04-01 00:00:00

abstract：:Protein biogenesis integrates multiple finely regulated mechanisms, ensuring nascent polypeptide chains are correctly enzymatically processed, targeted to membranes and folded to native structure. Recent studies show that the cellular translation machinery serves as hub that coordinates the maturation events in space ...

journal_title：Current opinion in structural biology

authors： Gloge F,Becker AH,Kramer G,Bukau B

更新日期：2014-02-01 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

authors： Bartholomew B

更新日期：2014-02-01 00:00:00

abstract：:Caspases are a family of aspartate-specific cysteine proteases that regulate cellular homeostasis through the mediation of apoptosis and inflammation. Despite keen interest in caspases as therapeutic targets for cancer, inflammatory, and neurodegenerative diseases, no active-site directed small molecule has yet succee...

journal_title：Current opinion in structural biology

authors： Murray J,Renslo AR

更新日期：2013-12-01 00:00:00

abstract：:Connecting three dimensional structure and affinity is analogous to seeking the 'Archimedean point', a vantage point from where any observer can quantitatively perceive the subject of inquiry. Here we review current knowledge and challenges that lie ahead of us in the quest for this Archimedean point. We argue that cu...

journal_title：Current opinion in structural biology

authors： Kastritis PL,Bonvin AM

更新日期：2013-12-01 00:00:00

abstract：:The encounter complex of two proteins is a dynamic intermediate state that guides proteins to their binding site, thus enhancing the rate of complex formation. It is particularly useful for complexes that must balance a biological requirement for high turnover with the need for specific binding, such as electron trans...

journal_title：Current opinion in structural biology

authors： Schilder J,Ubbink M

更新日期：2013-12-01 00:00:00

abstract：:Peptide-mediated interactions are gaining increased attention due to their predominant roles in the many regulatory processes that involve dynamic interactions between proteins. The structures of such interactions provide an excellent starting point for their characterization and manipulation, and can provide leads fo...

journal_title：Current opinion in structural biology

authors： London N,Raveh B,Schueler-Furman O

更新日期：2013-12-01 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

authors： Moal IH,Moretti R,Baker D,Fernández-Recio J

更新日期：2013-12-01 00:00:00

abstract：:Here we review mechanisms of protein evolution leading to structural changes in protein complexes. These mechanisms include mutations directly within protein interfaces, as well as the effects of mutations that propagate from distant regions of the protein. We also discuss the constraints protein complex structures im...

journal_title：Current opinion in structural biology

authors： Zhang X,Perica T,Teichmann SA

更新日期：2013-12-01 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

authors： McGowan S

更新日期：2013-12-01 00:00:00

abstract：:Molecular flexibility over a wide time range is of central importance to the function of many proteins, both soluble and membrane. Revealing the modes of flexibility, their amplitudes, and time scales under physiological conditions is the challenge for spectroscopic methods, one of which is site-directed spin labeling...

journal_title：Current opinion in structural biology

authors： Hubbell WL,López CJ,Altenbach C,Yang Z

更新日期：2013-10-01 00:00:00

abstract：:Transmembrane proton gradients, known as Proton Motive Force (PMF), serve important physiological functions. In addition to driving ATP synthesis, PMF is harnessed by a large variety of secondary transporters to achieve 'uphill' translocation of specific substrates across the membrane. Proton-coupled secondary transpo...

journal_title：Current opinion in structural biology

authors： Yan N

更新日期：2013-08-01 00:00:00

abstract：:In all contemporary organisms, the active site of the ribosome--the peptidyl transferase center--catalyzes two distinct reactions, peptide bond formation between peptidyl-tRNA and aminoacyl-tRNA as well as the hydrolysis of peptidyl-tRNA with the help of a release factor. However, when provided with appropriate substr...

journal_title：Current opinion in structural biology

authors： Rodnina MV

更新日期：2013-08-01 00:00:00

abstract：:Protein engineering strategies for increasing stability can be improved by replacing random mutagenesis and high-throughput screening by approaches that include bioinformatics and computational design. Mutations can be focused on regions in the structure that are most flexible and involved in the early steps of therma...

journal_title：Current opinion in structural biology

authors： Wijma HJ,Floor RJ,Janssen DB

更新日期：2013-08-01 00:00:00

abstract：:There has been significant recent progress in the computational design of protein interactions including the creation of novel heterodimers, homodimers, nanohedra, fibril caps and a protein crystal. Essential to these successes has been the use of innovative strategies for finding binding modes that are achievable, th...

journal_title：Current opinion in structural biology

authors： Der BS,Kuhlman B

更新日期：2013-08-01 00:00:00

abstract：:Many proteins are composed of protein domains, functional units of common descent. Multidomain forms are common in all eukaryotes making up more than half of the proteome and the evolution of novel domain architecture has been accelerated in metazoans. It is also becoming increasingly clear that alternative splicing i...

journal_title：Current opinion in structural biology

authors： Light S,Elofsson A

更新日期：2013-06-01 00:00:00

abstract：:Alternatively spliced protein segments tend to be intrinsically disordered and contain linear interaction motifs and/or post-translational modification sites. An emerging concept is that differential inclusion of such disordered segments can mediate new protein interactions, and hence change the context in which the b...

journal_title：Current opinion in structural biology

authors： Buljan M,Chalancon G,Dunker AK,Bateman A,Balaji S,Fuxreiter M,Babu MM

更新日期：2013-06-01 00:00:00

abstract：:During protein evolution, novel domain arrangements are continuously formed. Rearrangements are important for the creation of molecular biodiversity and for functional molecular changes which underlie developmental shifts in the bauplan of organisms. Here we review the mechanisms by which new arrangements arise and th...

journal_title：Current opinion in structural biology

authors： Bornberg-Bauer E,Albà MM

更新日期：2013-06-01 00:00:00

abstract：:Purification from a source enriched in large macromolecular machines with basic cellular function is still the method of choice in many cases. Such complexes occur in sufficiently high copy numbers in the cell and can be isolated using classical protein purification protocols. Although advanced DNA recombinant technol...

journal_title：Current opinion in structural biology

authors： Mesa P,Deniaud A,Montoya G,Schaffitzel C

更新日期：2013-06-01 00:00:00

abstract：:While there have been impressive advances in understanding protein folding over the past few decades, we are still far from the goal of solving the protein folding problem: predicting the folding pathway and final structure entirely from the amino acid sequence. One reason for this shortcoming may be the lack of under...

journal_title：Current opinion in structural biology

authors： Lapidus LJ

更新日期：2013-02-01 00:00:00

abstract：:The 'Fold Approach' involves a detailed analysis of the folding of several topologically, structurally and/or evolutionarily related proteins. Such studies can reveal determinants of the folding mechanism beyond the gross topology, and can dissect the residues required for folding from those required for stability or ...

journal_title：Current opinion in structural biology

authors： Nickson AA,Wensley BG,Clarke J

更新日期：2013-02-01 00:00:00

abstract：:ATP-dependent initiation factors help process replication origins and coordinate replisome assembly to control the onset of DNA synthesis. Although the specific properties and regulatory mechanisms of initiator proteins can vary greatly between different organisms, certain nucleotide-binding elements and assembly patt...

journal_title：Current opinion in structural biology

authors： Duderstadt KE,Berger JM

更新日期：2013-02-01 00:00:00

abstract：:Historically it has been virtually impossible to experimentally determine the contribution of residual protein entropy to fundamental protein activities such as the binding of ligands. Recent progress has illuminated the possibility of employing NMR relaxation methods to quantitatively determine the role of changes in...

journal_title：Current opinion in structural biology

authors： Wand AJ

更新日期：2013-02-01 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

authors： Zoldák G,Rief M

更新日期：2013-02-01 00:00:00

abstract：:The ribosome undergoes numerous large-scale conformational changes during protein synthesis, but the molecular basis for these changes have been unclear. Recent cryo-electron microscopic and X-ray crystallographic structures of both the bacterial and eukaryotic ribosome now provide snapshots of the wide range of motio...

journal_title：Current opinion in structural biology

authors： Noeske J,Cate JH

更新日期：2012-12-01 00:00:00