Protein topology and allostery.

Abstract:

:Allostery plays important roles in many biological processes. Although all non-fibrous proteins may be allosteric, currently only a limited number of allosteric proteins are known. How allosteric regulation depends on protein topology and what are the preferred folds in allosteric proteins need to be explored. Allosteric sites are found more often between chains or domains in multimeric or multi-domain proteins, while they often occur on the opposite side of the structure of the protein from the orthosteric site in monomeric single domain proteins. Although most folds are found in allosteric proteins, the immunoglobulin-like fold is rarely used. Typical regulatory domains include alpha-beta plaits, PDZ, WW domains, and so on. According to the understandings of allosteric regulations, novel allosteric proteins and materials have been rationally designed.

journal_name

Curr Opin Struct Biol

authors

Xie J,Lai L

doi

10.1016/j.sbi.2020.01.011

subject

Has Abstract

pub_date

2020-06-01 00:00:00

pages

158-165

eissn

0959-440X

issn

1879-033X

pii

S0959-440X(20)30011-7

journal_volume

62

pub_type

杂志文章,评审
  • Automatic annotation of protein function.

    abstract::The annotation of protein function at genomic scale is essential for day-to-day work in biology and for any systematic approach to the modeling of biological systems. Currently, functional annotation is essentially based on the expansion of the relatively small number of experimentally determined functions to large co...

    journal_title:Current opinion in structural biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.sbi.2005.05.010

    authors: Valencia A

    更新日期:2005-06-01 00:00:00

  • Activation and regulation of H2B-Ubiquitin-dependent histone methyltransferases.

    abstract::Covalent modifications of histone proteins regulate a wide variety of cellular processes. Methylation of histone H3K79 and H3K4 is associated with active transcription and is catalyzed by Dot1L and Set1, respectively. Both Dot1L and Set1 are activated by prior ubiquitination of histone H2B on K120 in a process termed ...

    journal_title:Current opinion in structural biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.sbi.2019.05.009

    authors: Worden EJ,Wolberger C

    更新日期:2019-12-01 00:00:00

  • Structure and function of restriction endonucleases.

    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

    authors: Aggarwal AK

    更新日期:1995-02-01 00:00:00

  • Core-directed protein design.

    abstract::For various reasons, it seems sensible to redesign or design proteins from the inside out. Past approaches in this field have involved iterations of mutagenesis and characterisation to 'evolve' designs. Increasingly, combinatorial approaches are being taken to select 'fit' sequences from libraries of variant proteins....

    journal_title:Current opinion in structural biology

    pub_type: 杂志文章,评审

    doi:10.1016/s0959-440x(00)00234-7

    authors: Woolfson DN

    更新日期:2001-08-01 00:00:00

  • Covalently circularized nanodiscs; challenges and applications.

    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

    authors: Nasr ML,Wagner G

    更新日期:2018-08-01 00:00:00

  • Structural investigation of the proton-coupled secondary transporters.

    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

    pub_type: 杂志文章,评审

    doi:10.1016/j.sbi.2013.04.011

    authors: Yan N

    更新日期:2013-08-01 00:00:00

  • Electron crystallography--the waking beauty of structural biology.

    abstract::Since its debut in the mid 1970s, electron crystallography has been a valuable alternative in the structure determination of biological macromolecules. Its reliance on single-layered or double-layered two-dimensionally ordered arrays and the ability to obtain structural information from small and disordered crystals m...

    journal_title:Current opinion in structural biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.sbi.2012.03.006

    authors: Pope CR,Unger VM

    更新日期:2012-08-01 00:00:00

  • Predicting protein function from sequence and structural data.

    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

    authors: Watson JD,Laskowski RA,Thornton JM

    更新日期:2005-06-01 00:00:00

  • Regulatory GTPases.

    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

    authors: Hilgenfeld R

    更新日期:1995-12-01 00:00:00

  • Transmembrane helix assembly and the role of salt bridges.

    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

    pub_type: 杂志文章,评审

    doi:10.1016/j.sbi.2014.05.003

    authors: Walther TH,Ulrich AS

    更新日期:2014-08-01 00:00:00

  • Enzymatic methylation of the amide bond.

    abstract::The amide bond with its planarity and lack of chemical reactivity is at the heart of protein structure. Chemical methylation of amides is known but was considered too harsh to be accessible to biology. Until last year there was no protein structure in the data bank with an enzymatically methylated amide. The discovery...

    journal_title:Current opinion in structural biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.sbi.2020.06.004

    authors: Song H,Naismith JH

    更新日期:2020-12-01 00:00:00

  • Protein-biotin interactions.

    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

    pub_type: 杂志文章,评审

    doi:10.1016/s0959-440x(96)80010-8

    authors: Lindqvist Y,Schneider G

    更新日期:1996-12-01 00:00:00

  • The morphology of lipid membranes.

    abstract::Current research into the morphology of lipid membranes focuses on three areas: first, the transformations and fluctuations of the shape of freely suspended vesicles; second, the morphology of membranes that experience mutual interactions or external forces arising, for example, from a macroscopic surface or from opti...

    journal_title:Current opinion in structural biology

    pub_type: 杂志文章,评审

    doi:10.1016/0959-440x(95)80040-9

    authors: Lipowsky R

    更新日期:1995-08-01 00:00:00

  • MAD contortions: conformational dimerization boosts spindle checkpoint signaling.

    abstract::Almost two decades after their identification, the components of the mitotic checkpoint are finally revealing their structural secrets. The activation of Mad2, a central piece of the checkpoint protein machinery, is linked to the rare ability of this protein to adopt two distinct topologies. Current models of checkpoi...

    journal_title:Current opinion in structural biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.sbi.2007.08.011

    authors: Mapelli M,Musacchio A

    更新日期:2007-12-01 00:00:00

  • Fast infrared spectroscopy of protein dynamics: advancing sensitivity and selectivity.

    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

    pub_type: 杂志文章,评审

    doi:10.1016/j.sbi.2015.03.012

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

    更新日期:2015-10-01 00:00:00

  • Small-angle scattering studies of intrinsically disordered proteins and their complexes.

    abstract::Intrinsically Disordered Proteins (IDPs) perform a broad range of biological functions. Their relevance has motivated intense research activity seeking to characterize their sequence/structure/function relationships. However, the conformational plasticity of these molecules hampers the application of traditional struc...

    journal_title:Current opinion in structural biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.sbi.2016.10.011

    authors: Cordeiro TN,Herranz-Trillo F,Urbanek A,Estaña A,Cortés J,Sibille N,Bernadó P

    更新日期:2017-02-01 00:00:00

  • What can we learn about protein folding from Ising-like models?

    abstract::Ising-like models have been remarkably successful in reproducing all the experimental data available on the equilibrium and kinetics of secondary structure formation in short peptides. Over the past two years, very similar models have been used to predict the folding of complete proteins, with encouraging results. Alt...

    journal_title:Current opinion in structural biology

    pub_type: 杂志文章,评审

    doi:10.1016/s0959-440x(00)00192-5

    authors: Muñoz V

    更新日期:2001-04-01 00:00:00

  • Aminoacyl-tRNA synthetases.

    abstract::Crystallographic studies of a number of aminoacyl-tRNA synthetases and their complexes with ATP, amino acid and cognate tRNA are leading to an increasingly detailed picture of how these sophisticated enzymes function. Within the two distinct structural classes of ten synthetases, many common features are apparent, alt...

    journal_title:Current opinion in structural biology

    pub_type: 杂志文章,评审

    doi:10.1016/s0959-440x(97)80161-3

    authors: Cusack S

    更新日期:1997-12-01 00:00:00

  • Elucidating ligand-bound structures of membrane proteins using solid-state NMR spectroscopy.

    abstract::Magic-angle-spinning (MAS) solid-state NMR spectroscopy is a versatile technique to elucidate functionally important protein-ligand interactions in lipid membranes. Here, we review recent solid-state NMR studies of membrane protein interactions with cholesterol, lipids, transported substrates, and peptide ligands. The...

    journal_title:Current opinion in structural biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.sbi.2019.02.002

    authors: Elkins MR,Hong M

    更新日期:2019-08-01 00:00:00

  • Structure and function of the small ribozymes.

    abstract::Recently, major advances have been made toward increasing our understanding of small ribozyme structure and function. The first general acid-base catalytic mechanism for a ribozyme has been defined. Shifted nucleotide pK(a) values have been found to be surprisingly frequent structural elements. Finally, the dynamic na...

    journal_title:Current opinion in structural biology

    pub_type: 杂志文章,评审

    doi:10.1016/s0959-440x(00)00207-4

    authors: Butcher SE

    更新日期:2001-06-01 00:00:00

  • Interactions of the ribosome with mRNA and tRNA.

    abstract::Recent collection of high-resolution crystal structures of the 70S ribosome with mRNA and tRNA substrates enhances our knowledge of protein synthesis principles. A novel network of interactions between the ribosome in the elongation state and mRNA downstream from the A codon suggests that mRNA is stabilized and aligne...

    journal_title:Current opinion in structural biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.sbi.2010.03.002

    authors: Demeshkina N,Jenner L,Yusupova G,Yusupov M

    更新日期:2010-06-01 00:00:00

  • Additivity-based prediction of equilibrium constants for some protein-protein associations.

    abstract::For many protein families, such as serine proteinases or serine proteinase inhibitors, the family assignment predicts reactivity only in general terms. Both detailed specificity and quantitative reactivity are lacking. We believe that, for many such protein families, algorithms can be devised by defining the subset of...

    journal_title:Current opinion in structural biology

    pub_type: 杂志文章

    doi:10.1016/s0959-440x(03)00013-7

    authors: Laskowski M Jr,Qasim MA,Yi Z

    更新日期:2003-02-01 00:00:00

  • Insights into biomolecular function from small-angle scattering.

    abstract::Recent advances in neutron and X-ray sources and instrumentation, new and improved scattering techniques, and molecular biology techniques, which have permitted facile preparation of samples, have each led to new opportunities in using small-angle scattering to study the conformations and interactions of biological ma...

    journal_title:Current opinion in structural biology

    pub_type: 杂志文章,评审

    doi:10.1016/s0959-440x(97)80081-4

    authors: Trewhella J

    更新日期:1997-10-01 00:00:00

  • Combining structural genomics and enzymology: completing the picture in metabolic pathways and enzyme active sites.

    abstract::An important goal of structural genomics is to complete the structural analysis of all the enzymes in metabolic pathways and to understand the structural similarities and differences. A preliminary glimpse of this type of analysis was achieved before structural genomics efforts with the glycolytic pathway and efforts ...

    journal_title:Current opinion in structural biology

    pub_type: 杂志文章,评审

    doi:10.1016/s0959-440x(00)00154-8

    authors: Erlandsen H,Abola EE,Stevens RC

    更新日期:2000-12-01 00:00:00

  • Macromolecular assemblages. Theory and simulation.

    abstract::A selection of World Wide Web sites relevant to papers published in this issue of Current Opinion in Structural Biology. ...

    journal_title:Current opinion in structural biology

    pub_type:

    doi:10.1016/s0959-440x(00)00182-2

    authors: Lakey JH,Reddy BV,Murray-Rust J

    更新日期:2001-04-01 00:00:00

  • Evolution of protein structures and interactions from the perspective of residue contact networks.

    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

    pub_type: 杂志文章,评审

    doi:10.1016/j.sbi.2013.07.004

    authors: Zhang X,Perica T,Teichmann SA

    更新日期:2013-12-01 00:00:00

  • Theory of biomolecular recognition.

    abstract::Specific, noncovalent binding of biomolecules can only be understood by considering structural, thermodynamic, and kinetic issues. The theoretical foundations for such analyses have been clarified in the past year. Computational techniques for both particle-based and continuum models continue to improve and to yield u...

    journal_title:Current opinion in structural biology

    pub_type: 杂志文章,评审

    doi:10.1016/s0959-440x(98)80046-8

    authors: McCammon JA

    更新日期:1998-04-01 00:00:00

  • Mass spectrometry: come of age for structural and dynamical biology.

    abstract::Over the past two decades, mass spectrometry (MS) has emerged as a bone fide approach for structural biology. MS can inform on all levels of protein organization, and enables quantitative assessments of their intrinsic dynamics. The key advantages of MS are that it is a sensitive, high-resolution separation technique ...

    journal_title:Current opinion in structural biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.sbi.2011.08.002

    authors: Benesch JL,Ruotolo BT

    更新日期:2011-10-01 00:00:00

  • Single-particle reconstruction from EM images of helical filaments.

    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

    authors: Egelman EH

    更新日期:2007-10-01 00:00:00

  • Co-translational mechanisms of protein maturation.

    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

    pub_type: 杂志文章,评审

    doi:10.1016/j.sbi.2013.11.004

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

    更新日期:2014-02-01 00:00:00