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-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
pub_type: 杂志文章,评审
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abstract::Phage display is the longest-standing platform among molecular display technologies. Recent developments have extended its utility to proteins that were previously recalcitrant to phage display. The technique has played a dominant role in forming the field of synthetic binding protein engineering, where novel interfac...
journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
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abstract::The winged helix proteins constitute a subfamily within the large ensemble of helix-turn-helix proteins. Since the discovery of the winged helix/fork head motif in 1993, a large number of topologically related proteins with diverse biological functions have been characterized by X-ray crystallography and solution NMR ...
journal_title:Current opinion in structural biology
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abstract::Structure-specific DNA nucleases play important roles in various DNA transactions such as DNA replication, repair and recombination. These enzymes recognize loops and branched DNA structures. Recent structural studies have provided detailed insights into the functions of these enzymes. Structures of Holliday junction ...
journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2006.01.009
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abstract::Diverse glycans on proteins impact cell and organism physiology, along with drug activity. Since many protein-based biotherapeutics are glycosylated and these glycans have biological activity, there is a desire to engineer glycosylation for recombinant protein-based biotherapeutics. Engineered glycosylation can impact...
journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2016.08.008
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abstract::O-GlcNAcylation is an enzymatic post-translational modification occurring in hundreds of protein substrates. This modification occurs through the addition of the monosaccharide N-acetylglucosamine to serine and threonine residues on intracellular proteins in the cytosol, nucleus, and mitochondria. As a highly dynamic ...
journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2020.12.005
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journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
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journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
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更新日期:1997-12-01 00:00:00
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journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
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abstract::PUF proteins are RNA-binding proteins named for founding members PUMILIO and fem-3 binding factor (FBF). Together these proteins represent the range of known RNA recognition properties. PUMILIO is a prototypical PUF protein whose RNA sequence specificity is simple, elegant, and predictable. FBF displays differences in...
journal_title:Current opinion in structural biology
pub_type: 杂志文章
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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::Structures of two restriction endonucleases, BamHI and PvuII, were reported in the past year. This doubles the number of restriction endonuclease structures now known from two to four, and enables a comparative analysis of their structures and modes of DNA recognition. Despite a lack of sequence homology between the e...
journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/0959-440x(95)80004-k
更新日期:1995-02-01 00:00:00
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journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2019.07.010
更新日期:2019-12-01 00:00:00
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journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2009.04.002
更新日期:2009-06-01 00:00:00
abstract::The observed distribution of protein structures can give us important clues about the underlying evolutionary process, imposing important constraints on possible models. The availability of results from an increasing number of genome projects has made the development of these models an active area of research. Models ...
journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2008.01.006
更新日期:2008-04-01 00:00:00
abstract::Asymmetric cell division (ACD) is a strategy for achieving cell diversity. Research carried out over the last two decades has shown that in some cell types that divide asymmetrically, mother and daughter centrosomes are noticeably different from one another in structure, behaviour, and fate, and that robust ACD depend...
journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
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更新日期:2020-12-03 00:00:00
abstract::Can a stereochemical recognition code explain sequence-specific protein-nucleic acid interactions? Whereas a code that is generally applicable to DNA-binding proteins of all known structural families is unattainable, the indications are that a code can describe at least some of the interactions of classical zinc finge...
journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/s0959-440x(97)80015-2
更新日期:1997-02-01 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
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journal_title:Current opinion in structural biology
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journal_title:Current opinion in structural biology
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journal_title:Current opinion in structural biology
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journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
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abstract::Functional conformational changes of proteins can facilitate numerous biological events in cells. The Markov state model (MSM) built from molecular dynamics simulations provide a powerful approach to study them. We here introduce a protocol that is tailor-made for constructing MSMs to study the functional conformation...
journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
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abstract::RNA structure underpins many essential functions in biology. New chemical reagents and techniques for probing RNA structure in living cells have emerged in recent years. High-throughput, genome-wide techniques such as Structure-seq2 and DMS-MaPseq exploit nucleobase modification by dimethylsulfate (DMS) to obtain comp...
journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
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journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
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abstract::The three-dimensional structures of several biotin-binding proteins are now known, giving insights into the molecular architecture of the binding sites for biotin. In combination with biochemical and computational approaches, these structural insights provide the basis for our present understanding of biotin-protein i...
journal_title:Current opinion in structural biology
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journal_title:Current opinion in structural biology
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journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
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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
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