Abstract:
:High-throughput interaction discovery initiatives have revealed the existence of hundreds of multiprotein complexes whose functions are regulated through thousands of protein-protein interactions (PPIs). However, the structural details of these interactions, often necessary to understand their function, are only available for a tiny fraction, and the experimental difficulties surrounding complex structure determination make computational modeling techniques paramount. In this manuscript, we critically review some of the most recent developments in the field of structural bioinformatics applied to the modeling of protein interactions and complexes, from large macromolecular machines to domain-domain and peptide-mediated interactions. In particular, we place a special emphasis on those methods that can be applied in a proteome-wide manner, and discuss how they will help in the ultimate objective of building 3D interactome networks.
journal_name
Curr Opin Struct Bioljournal_title
Current opinion in structural biologyauthors
Stein A,Mosca R,Aloy Pdoi
10.1016/j.sbi.2011.01.005subject
Has Abstractpub_date
2011-04-01 00:00:00pages
200-8issue
2eissn
0959-440Xissn
1879-033Xpii
S0959-440X(11)00007-8journal_volume
21pub_type
杂志文章,评审abstract::ATP-binding cassette (ABC) transporters are central to many physiological processes, including the uptake of nutrients, the non-classical secretion of signaling molecules and toxins, multidrug resistance and the development of human disease. As one might expect from this spectrum of translocation events, these ubiquit...
journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/s0959-440x(02)00399-8
更新日期:2002-12-01 00:00:00
abstract::The past decade has seen a revolution in our ability to engineer designer enzymes using genetic tools that mimic evolution on a laboratory timescale. Many excellent examples of directed evolution applied to a wide range of enzymes have clearly demonstrated its future role in adapting enzymes for use in the chemical in...
journal_title:Current opinion in structural biology
pub_type: 杂志文章
doi:10.1016/s0959-440x(03)00101-5
更新日期:2003-08-01 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::This review focuses on pharmacophore approaches in researching protein interfaces that bind protein ligands. Pharmacophore descriptions of binding interfaces that employ molecular dynamics simulation can account for effects of solvation and conformational flexibility. In addition, these calculations provide an approxi...
journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2020.12.016
更新日期:2021-01-21 00:00:00
abstract::Advances in electron microscopes, detectors and data processing algorithms have greatly facilitated the structural determination of many challenging integral membrane proteins that have been evasive to crystallization. These breakthroughs facilitate the application and development of various membrane protein solubiliz...
journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2019.05.022
更新日期:2019-10-01 00:00:00
abstract::Glycosylation is a common post-translational protein modification, in which glycans are built onto proteins through the sequential addition of monosaccharide units, in reactions catalysed by glycosyltransferases. Glycosylation influences the physicochemical and biological properties of proteins, with subsequent effect...
journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2016.08.007
更新日期:2016-10-01 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::Few biological macromolecular complexes exhibit the combination of massive size and hierarchical, symmetrical architecture embodied in icosahedral viruses. X-ray crystallography, electron cryomicroscopy and small-angle X-ray scattering provide complementary approaches to studying these remarkable structures. Through a...
journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2003.09.007
更新日期:2003-10-01 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
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2015.03.007
更新日期:2015-04-01 00:00:00
abstract::A novel ligand-binding domain, named the 'ACT domain', was recently identified by a PSI-BLAST search. The archetypical ACT domain is the C-terminal regulatory domain of 3-phosphoglycerate dehydrogenase (3PGDH), which folds with a ferredoxin-like betaalphabetabetaalphabeta topology. A pair of ACT domains form an eight-...
journal_title:Current opinion in structural biology
pub_type: 杂志文章
doi:10.1016/s0959-440x(01)00272-x
更新日期:2001-12-01 00:00:00
abstract::Antibody engineering has been an extremely intensive research area for many years. Recent achievements discussed in this review include: (i) significant improvements in the field of selection of antigen-specific antibody fragments on bacteriophages; (ii) new structural work, in particular using NMR; (iii) the cloning ...
journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/0959-440x(95)80028-x
更新日期:1995-08-01 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
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2015.01.003
更新日期:2015-06-01 00:00:00
abstract::The exponential growth in the amount of genomic data published in recent years has led to increased efforts in analysing genomes for the presence of repeated sequences, which has in turn fostered the development of novel repeat recognition methods. This has resulted in a deepened understanding of the importance and ab...
journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/s0959-440x(98)80068-7
更新日期:1998-06-01 00:00:00
abstract::Gamma-tubulin is as ubiquitous in eukaryotes as alpha- and beta-tubulin. Rather than forming part of the microtubule wall, however, gamma-tubulin is involved in microtubule nucleation. Although gamma-tubulin concentrates at microtubule-organizing centers, it also exists in a cytoplasmic complex whose size and complexi...
journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/S0959-440X(99)80035-9
更新日期:1999-04-01 00:00:00
abstract::Demand for novel GPCR modulators is increasing as the association between the GPCR signaling pathway and numerous diseases such as cancers, psychological and metabolic disorders continues to be established. In silico structure-based drug design (SBDD) offers an outlet where researchers could exploit the accumulating s...
journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2019.03.015
更新日期:2019-04-01 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::The past year has witnessed a tremendous increase in our understanding of the structures and interactions of the GTPases. The highlights include crystal structures of G alpha subunits, as well as the first complex between a GTPase (Rap1A) and an effector molecule (c-Raf1 Ras-binding domain). In the field of elongation...
journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/0959-440x(95)80015-8
更新日期:1995-12-01 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
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2013.11.002
更新日期:2014-04-01 00:00:00
abstract::Salt-dependent electrostatic effects are a major factor in determining the stability, structure, reactivity, and binding behavior of nucleic acids. Increasingly detailed theoretical methods, especially those based on Monte Carlo and Poisson-Boltzmann methodologies, combined with powerful computational algorithms are b...
journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/0959-440x(95)80093-x
更新日期:1995-06-01 00:00:00
abstract::Molecular dynamics simulation studies of protein-nucleic acid complexes are more complicated than studies of either component alone-the force field has to be properly balanced, the systems tend to become very large, and a careful treatment of solvent and of electrostatic interactions is necessary. Recent investigation...
journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2007.12.012
更新日期:2008-04-01 00:00:00
abstract::Hydrogen-deuterium exchange (HDX) mass spectrometry (MS) can provide information about proteins that can be challenging to obtain by other means. Structure/function relationships, binding interactions, and the effects of modification have all been measured with HDX MS for a diverse and growing array of signaling prote...
journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2016.08.003
更新日期:2016-12-01 00:00:00
abstract::Mechanisms for making and breaking the heme b cofactor (heme) are more diverse than previously expected. Biosynthetic pathways have diverged at least twice along taxonomic lines, reflecting differences in membrane organization and O2 utilization among major groups of organisms. At least three families of heme degradas...
journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2019.01.006
更新日期:2019-12-01 00:00:00
abstract::As the fundamental packing units of DNA in eukaryotes, nucleosomes play a central role in governing DNA accessibility in a variety of cellular processes. Our understanding of the mechanisms underlying this complex regulation has been aided by unique structural and dynamic perspectives offered by single molecule techni...
journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2011.11.003
更新日期:2012-02-01 00:00:00
abstract::Achieving the goals of structural genomics initiatives depends on the outcomes of two groups of factors: the number and distribution of experimentally determined protein structures, and our ability to assign novel proteins to known structures (fold recognition) and use them to build models (modeling). The quality of t...
journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2004.04.005
更新日期:2004-06-01 00:00:00
abstract::Emerging data suggest that the mechanisms by which RNA-binding proteins (RBPs) interact with RNA and the rules governing specificity might be substantially more complex than those underlying their DNA-binding counterparts. Even our knowledge of what constitutes the RNA-bound proteome is contentious; recent studies sug...
journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2016.05.005
更新日期:2016-06-01 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
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2014.07.006
更新日期:2014-12-01 00:00:00
abstract::Advances in the crystallization of biological macromolecules have come not only from the application of biochemical, molecular biological and immunological principles and techniques, but also from continued efforts to understand the crystallization process. Developments in crystallization methodologies, protocols, and...
journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/s0959-440x(96)80024-8
更新日期:1996-10-01 00:00:00
abstract::Newly synthesized proteins leave the ribosome through a narrow tunnel in the large subunit. During ongoing synthesis, nascent protein chains are particularly sensitive to aggregation and degradation because they emerge from the ribosome in an unfolded state. In bacteria, the first protein to interact with nascent chai...
journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2005.03.005
更新日期:2005-04-01 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::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