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Current Opinion in Structural Biology

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https://www.readbyqxmd.com/read/28189794/the-lectin-self-of-complement-factor-h
#1
REVIEW
Bärbel S Blaum
Complement, a part of the humoral innate immune system, is divided into three pathways. The classical and mannose-binding lectin pathways are triggered by specific recognition of foreign targets. Conversely, the alternative pathway (AP) is actively down-regulated on host tissue. Glycosaminoglycans (GAGs) and sialylated glycans mediate host recognition of the AP as self-associated molecular patterns (SAMPs) to the regulatory protein factor H (FH). This review summarizes the more recent years of research on SAMP recognition by FH from a structural biology point of view and discusses implications for two complement-associated conditions, age-related macular degeneration (AMD) and atypical hemolytic uremic syndrome (aHUS)...
February 9, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28160724/exploring-the-relationships-between-protein-sequence-structure-and-solubility
#2
REVIEW
Kyle Trainor, Aron Broom, Elizabeth M Meiering
Aggregation can be thought of as a form of protein folding in which intermolecular associations lead to the formation of large, insoluble assemblies. Various types of aggregates can be differentiated by their internal structures and gross morphologies (e.g., fibrillar or amorphous), and the ability to accurately predict the likelihood of their formation by a given polypeptide is of great practical utility in the fields of biology (including the study of disease), biotechnology, and biomaterials research. Here we review aggregation/solubility prediction methods and selected applications thereof...
February 1, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28157627/modeling-and-simulation-of-bacterial-outer-membranes-and-interactions-with-membrane-proteins
#3
REVIEW
Dhilon S Patel, Yifei Qi, Wonpil Im
The outer membrane (OM) of Gram-negative bacteria is composed of phospholipids in the periplasmic leaflet and lipopolysaccharides (LPS) in the external leaflet, along with β-barrel OM proteins (OMPs) and lipidated periplasmic lipoproteins. As a defensive barrier to toxic compounds, an LPS molecule has high antigenic diversity and unique combination of OM-anchored lipid A with core oligosaccharides and O-antigen polysaccharides, creating dynamic protein-LPS and LPS-LPS interactions. Here, we review recent efforts on modeling and simulation of native-like bacterial OMs to explore structures, dynamics, and interactions of different OM components and their roles in transportation of ions, substrates, and antibiotics across the OM and accessibility of monoclonal antibodies (mAbs) to surface epitopes...
January 31, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28130986/recognition-of-substrate-degrons-by-e3-ubiquitin-ligases-and-modulation-by-small-molecule-mimicry-strategies
#4
REVIEW
Xavier Lucas, Alessio Ciulli
The ubiquitin-proteasome system is a master regulator of protein homeostasis, by which proteins are initially targeted for poly-ubiquitination by E3 ligases and then degraded into short peptides by the proteasome. Nature evolved diverse peptidic motifs, termed degrons, to signal substrates for degradation. We discuss degrons of the N-end rule pathway and also degrons characterized by post-translational modifications, including phosphorylation and hydroxylation. In each case we detail the structural basis of E3 ligase:degron recognition and small-molecule mimicry approaches that disrupt those protein-protein interactions...
January 25, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28126529/comparing-protein-behaviour-in-vitro-and-in-vivo-what-does-the-data-really-tell-us
#5
REVIEW
Jens Danielsson, Mikael Oliveberg
The recent advancement in moving 'biophysical' analysis of proteins in vivo has finally brought us to a position where we can start to make quantitative comparisons with existing in-vitro data. A striking observation is that protein behaviour in live cells seems, after all, not that different from in test tubes, not even at the level of complex mechanisms like protein aggregation. The example examined in this review is the ALS associated protein SOD1 that apparently retains its in-vitro properties in vivo. Does this mean that the protocols for studying proteins in vivo are somehow oversimplified, or that the macromolecular properties and interplay - despite being intrinsically malleable - are more evolutionary more 'streamlined' than previously anticipated? Whatever the answer may be the time is now right to put these data to critical biological test...
January 23, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28109980/carbohydrate-recognition-and-lysis-by-bacterial-peptidoglycan-hydrolases
#6
REVIEW
Martín Alcorlo, Siseth Martínez-Caballero, Rafael Molina, Juan A Hermoso
The major component of bacterial cell wall is peptidoglycan (PG), a complex polymer formed by long glycan chains cross-linked by peptide stems. PG is in constant equilibrium requiring well-orchestrated coordination between synthesis and degradation. The resulting cell-wall fragments can be recycled, act as messengers for bacterial communication, as effector molecules in immune response or as signaling molecules triggering antibiotics resistance. Tailoring and recycling of PG requires the cleavage of different covalent bonds of the PG sacculi by a diverse set of specific enzymes whose activities are strictly regulated...
January 19, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28092811/towards-the-structure-of-the-tir-domain-signalosome
#7
REVIEW
Surekha Nimma, Thomas Ve, Simon J Williams, Bostjan Kobe
TIR (Toll/interleukin-1 receptor/resistance protein) domains feature in animal, plant and bacterial proteins involved in innate immunity pathways and associated processes. They function through protein:protein interactions, in particular self-association and homotypic association with other TIR domains. Structures of TIR domains from all phyla have been determined, but common association modes have only emerged for plant and bacterial TIR domains, and not for mammalian TIR domains. Numerous attempts involving hybrid approaches, which have combined structural, computational, mutagenesis and biophysical data, have failed to converge onto common models of how these domains associate and function...
January 13, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28088125/computational-methods-for-analyzing-conformational-variability-of-macromolecular-complexes-from-cryo-electron-microscopy-images
#8
REVIEW
Slavica Jonić
Thanks to latest technical advances in cryo-electron microscopy (cryo-EM), structures of macromolecular complexes (viruses, ribosomes, etc.) are now often obtained at near-atomic resolution. Also, studies of conformational changes of complexes, in connection with their function, are gaining ground. Conformational variability analysis is usually done by classifying images in a number of discrete classes supposedly representing all conformational states present in the specimen. However, discrete classes cannot be meaningfully defined when the conformational change is continuous (the specimen contains a continuum of states instead of a few discrete states)...
January 11, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28088083/specificity-and-stability-of-transient-protein-protein-interactions
#9
REVIEW
Sneha Vishwanath, Anshul Sukhwal, Ramanathan Sowdhamini, Narayanaswamy Srinivasan
Remarkable features that are achieved in a protein-protein complex to precise levels are stability and specificity. Deviation from the normal levels of specificity and stability, which is often caused by mutations, could result in disease conditions. Chemical nature, 3-D arrangement and dynamics of interface residues code for both specificity and stability. This article reviews roles of interfacial residues in transient protein-protein complexes. It is proposed that aside from hotspot residues conferring stability to the complex, a small set of 'rigid' residues at the interface that maintain conformation between complexed and uncomplexed forms, play a major role in conferring specificity...
January 11, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28087119/editorial-overview-proteins-bridging-theory-and-experiment
#10
EDITORIAL
Igor N Berezovsky, Ugo Bastolla
No abstract text is available yet for this article.
January 10, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28086105/structural-diversity-of-lytic-polysaccharide-monooxygenases
#11
REVIEW
Gustav Vaaje-Kolstad, Zarah Forsberg, Jennifer Sm Loose, Bastien Bissaro, Vincent Gh Eijsink
Lytic polysaccharide monooxygenases (LPMOs) catalyze the oxidative cleavage of glycosidic bonds and represent a promising resource for development of industrial enzyme cocktails for biomass processing. LPMOs show high sequence and modular diversity and are known, so far, to cleave insoluble substrates such as cellulose, chitin and starch, as well as hemicelluloses such as beta-glucan, xyloglucan and xylan. All LPMOs share a catalytic histidine brace motif to bind copper, but differ strongly when it comes to the nature and arrangement of residues on the substrate-binding surface...
January 10, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28063303/peptides-and-peptidomimetics-as-regulators-of-protein-protein-interactions
#12
REVIEW
Anna D Cunningham, Nir Qvit, Daria Mochly-Rosen
Protein-protein interactions are essential for almost all intracellular and extracellular biological processes. Regulation of protein-protein interactions is one strategy to regulate cell fate in a highly selective manner. Specifically, peptides are ideal candidates for inhibition of protein-protein interactions because they can mimic a protein surface to effectively compete for binding. Additionally, peptides are synthetically accessible and can be stabilized by chemical modifications. In this review, we survey screening and rational design methods for identifying peptides to inhibit protein-protein interactions, as well as methods for stabilizing peptides to effectively mimic protein surfaces...
January 4, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28063280/principles-of-protein-structural-ensemble-determination
#13
REVIEW
Massimiliano Bonomi, Gabriella T Heller, Carlo Camilloni, Michele Vendruscolo
The biological functions of protein molecules are intimately dependent on their conformational dynamics. This aspect is particularly evident for disordered proteins, which constitute perhaps one-third of the human proteome. Therefore, structural ensembles often offer more useful representations of proteins than individual conformations. Here, we describe how the well-established principles of protein structure determination should be extended to the case of protein structural ensembles determination. These principles concern primarily how to deal with conformationally heterogeneous states, and with experimental measurements that are averaged over such states and affected by a variety of errors...
January 4, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28056362/structures-of-biomolecular-complexes-by-combination-of-nmr-and-cryoem-methods
#14
REVIEW
Philippe Cuniasse, Paulo Tavares, Elena V Orlova, Sophie Zinn-Justin
CryoEM is presently providing structures of biocomplexes considered intractable to analysis by other structural techniques. NMR is playing an important role in delivering structural information on dynamics events and conformational heterogeneity. Impressive results were obtained by combining cryoEM and either liquid- or solid-state NMR, revealing the structures of cellular machines, filaments and amyloid fibrils. NMR solution structures of proteins and nucleic acids were fitted, together with crystallographic structures, into cryoEM maps of large complexes, to decipher their assembly mechanisms and describe their functional dynamics...
January 2, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28043017/evolution-and-structural-dynamics-of-bacterial-glycan-binding-adhesins
#15
REVIEW
Kristof Moonens, Han Remaut
Infectious disease processes like bacterial adherence or the activity of secreted toxins frequently gain host and tissue specificity by glycan binding interactions with the host glycome. Recent functional and structural studies highlight the high niche specialization of bacterial lectins, but also reveal a remarkable plasticity in their glycan binding sites and mechanisms, to adapt to host glycome dynamics or changing environmental conditions at the site of infection. In this review we put emphasis on new structural insights in host adaptation and dynamics of bacterial carbohydrate binding adhesins and toxins in human pathogens like uropathogenic and enteropathogenic Escherichia coli, Helicobacter pylori, Yersinia pestis or Vibrio cholerae...
December 30, 2016: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28040640/physical-and-molecular-bases-of-protein-thermal-stability-and-cold-adaptation
#16
REVIEW
Fabrizio Pucci, Marianne Rooman
The molecular bases of thermal and cold stability and adaptation, which allow proteins to remain folded and functional in the temperature ranges in which their host organisms live and grow, are still only partially elucidated. Indeed, both experimental and computational studies fail to yield a fully precise and global physical picture, essentially because all effects are context-dependent and thus quite intricate to unravel. We present a snapshot of the current state of knowledge of this highly complex and challenging issue, whose resolution would enable large-scale rational protein design...
December 29, 2016: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28040636/protein-engineering-approaches-for-regulating-blood-brain-barrier-transcytosis
#17
REVIEW
Loukas I Goulatis, Eric V Shusta
The blood brain barrier (BBB) presents a challenge for the delivery of brain therapeutics. Trans-BBB delivery methods that use targeting vectors to coopt the vesicle trafficking machinery of BBB endothelial cells have been developed, but these are often hampered by limited flux through the BBB. A solution to this problem lies in the semi-rational engineering of BBB targeting vectors. Leveraging knowledge of intracellular trafficking, researchers have begun to tune selected binding properties of the vector-receptor interaction...
December 29, 2016: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28040635/alternating-access-mechanisms-of-leut-fold-transporters-trailblazing-towards-the-promised-energy-landscapes
#18
REVIEW
Kelli Kazmier, Derek P Claxton, Hassane S Mchaourab
Secondary active transporters couple the uphill translocation of substrates to electrochemical ion gradients. Transporter conformational motion, generically referred to as alternating access, enables a central ligand binding site to change its orientation relative to the membrane. Here we review themes of alternating access and the transduction of ion gradient energy to power this process in the LeuT-fold class of transporters where crystallographic, computational and spectroscopic approaches have converged to yield detailed models of transport cycles...
December 29, 2016: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28038355/structure-guided-rational-design-of-red-fluorescent-proteins-towards-designer-genetically-encoded-fluorophores
#19
REVIEW
Matthew G Eason, Adam M Damry, Roberto A Chica
Red fluorescent proteins (RFPs) have become an integral part of modern biological research due to their longer excitation and emission wavelengths. Protein engineering efforts have improved many key properties of RFPs for their practical use in imaging. Even so, continued engineering is required to overcome the shortcomings of the red chromophore and create RFPs with photophysical properties rivalling those of their optimized green and yellow counterparts. Here, we highlight recent examples of structure-guided rational design of RFPs to improve brightness, monomerization, maturation, and photostability, and discuss possible pathways for the future engineering of designer RFPs tailored to specific applications...
December 27, 2016: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28038331/protein-unfolding-under-isometric-tension-what-force-can-integrins-generate-and-can-it-unfold-fniii-domains
#20
REVIEW
Harold P Erickson
Extracellular matrix fibrils of fibronectin (FN) are highly elastic, and are typically stretched three to four times their relaxed length. The mechanism of stretching has been controversial, in particular whether it involves tension-induced unfolding of FNIII domains. Recent studies have found that ∼5pN is the threshold isometric force for unfolding various protein domains. FNIII domains should therefore not be unfolded until the tension approaches 5pN. Integrins have been reported to generate forces ranging from 1 to >50pN, but I argue that studies reporting 1-2pN are the most convincing...
December 27, 2016: Current Opinion in Structural Biology
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