Abstract：
:The evolution of protein interactions cannot be deciphered without a detailed analysis of interaction interfaces and binding modes. We performed a large-scale study of protein homooligomers in terms of their symmetry, interface sizes, and conservation of binding modes. We also focused specifically on the evolution of protein binding modes from nine families of homooligomers and mapped 60 different binding modes and oligomerization states onto the phylogenetic trees of these families. We observed a significant tendency for the same binding modes to be clustered together and conserved within clades on phylogenetic trees; this trend is especially pronounced for close homologs with 70% sequence identity or higher. Some binding modes are conserved among very distant homologs, pointing to their ancient evolutionary origin, while others are very specific for a certain phylogenetic group. Moreover, we found that the most ancient binding modes have a tendency to involve symmetrical (isologous) homodimer binding arrangements with larger interfaces, while recently evolved binding modes more often exhibit asymmetrical arrangements and smaller interfaces.
journal_name
J Mol Bioljournal_title
Journal of molecular biologyauthors
Dayhoff JE,Shoemaker BA,Bryant SH,Panchenko ARdoi
10.1016/j.jmb.2009.10.052subject
Has Abstractpub_date
2010-01-29 00:00:00pages
860-70issue
4eissn
0022-2836issn
1089-8638pii
S0022-2836(09)01311-4journal_volume
395pub_type
杂志文章abstract：:Using simple design and selective pressure, we have evolved an artificial M13 bacteriophage coat protein. M13 coat proteins first reside in the bacterial inner membrane and subsequently surround the DNA core of the assembled virus. The artificial coat protein (ACP) was designed and evolved to mimic both functions of t...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.2000.3845
更新日期：2000-06-30 00:00:00
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pub_type： 杂志文章
doi：10.1016/j.jmb.2009.07.086
更新日期：2009-10-23 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(87)90612-7
更新日期：1987-09-05 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.2002.5433
更新日期：2002-03-29 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1994.1336
更新日期：1994-05-20 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/S0022-2836(05)80096-8
更新日期：1990-09-05 00:00:00
abstract：:The yeast a1 and alpha 2 proteins are examples of homeodomain proteins that display cell-type-specific expression. They are co-expressed in only one type of cell, the a/alpha cell, where they repress the expression of a group of target genes. Using purified proteins, we demonstrate that a1 and alpha 2 form a highly sp...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1993.1517
更新日期：1993-10-05 00:00:00
abstract：:Transcription in all cellular organisms is performed by multisubunit, DNA-dependent RNA polymerases that synthesize RNA from DNA templates. Previous sequence and structural studies have elucidated the importance of shared regions common to all multisubunit RNA polymerases. In addition, RNA polymerases contain multiple...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2009.10.062
更新日期：2010-01-29 00:00:00
abstract：:The three-dimensional structure of a site-directed mutant of the bacterially expressed Fv fragment from monoclonal antibody D1.3, complexed to the specific antigen lysozyme has been determined to a nominal resolution of 1.8 A using X-ray diffraction data. The replacement of VL Trp92 by Asp allows two water molecules t...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1994.1309
更新日期：1994-05-13 00:00:00
abstract：:The preferred DNase I cleavage sites within the 160 bp tyrT DNA fragment were identified by studying the initial rate of cleavage of individual bonds. The results show that there is no correlation between the rate of cleavage and the identity of the dinucleotide sequence that is cleaved. Examination of the sequences s...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1994.1152
更新日期：1994-02-18 00:00:00
abstract：:Monoclinic P2(1) crystals of the bacteriophage phi X174 have been incubated with calcium ions (Ca2+) and the induced structural conformational changes studied to 3 A resolution with X-ray crystallographic methods. Three different types of Ca2+ binding sites have been located within the asymmetric unit of the virion. T...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1994.1730
更新日期：1994-12-02 00:00:00
abstract：:Staphyloferrin B is a hydroxycarboxylate siderophore that is crucial for the invasion and virulence of Staphylococcus aureus in mammalian hosts where free iron ions are scarce. The assembly of staphyloferrin B involves four enzymatic steps, in which SbnH, a pyridoxal 5'-phosphate (PLP)-dependent decarboxylase, catalyz...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2019.10.009
更新日期：2019-12-06 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2014.11.011
更新日期：2015-01-30 00:00:00
abstract：:The Sto12a protein, from the thermoacidophilic archaeon Sulfolobus tokodaii, has been identified as a small putative DNA-binding protein. Most of the proteins with a high level of amino acid sequence homology to this protein are derived from members of the Sulfolobaceae family, including a transcriptional regulator. W...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2007.07.051
更新日期：2007-10-05 00:00:00
abstract：:Members of the Bcl-2 protein family regulate apoptosis by controlling the release of apoptogenic proteins such as cytochrome c from the mitochondrial intermembrane space. Proapoptotic members induce release by increasing outer membrane permeability, while antiapoptotic members prevent this. The activity of Bcl-2 prote...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2003.10.028
更新日期：2004-01-02 00:00:00
abstract：:We describe a method for probing the integrity and relative orientation of structural elements that are indirectly linked by ligands in protein complexes during protein folding. The effect of 3'-GMP on the rate constants of unfolding of wild-type barnase and several mutants has been studied. By comparing the rates of ...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(91)80188-z
更新日期：1991-10-05 00:00:00
abstract：:The work reported here describes insertion-deletion (Indel) polymorphisms in two internally eliminated sequences (IESs, that are deleted during development in Tetrahymena): a 1.8 kb Indel at one end of the 1.1 kb H1 IES and a 0.5 kb Indel inside the 1.4 kb calmodulin (C) IES. These two IESs are located in the proximit...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2003.12.065
更新日期：2004-03-05 00:00:00
abstract：:The human signal recognition particle (SRP) is a large RNA-protein complex that targets secretory and membrane proteins to the endoplasmic reticulum membrane. The S domain of SRP is composed of roughly half of the 7SL RNA and four proteins (SRP19, SRP54, and the SRP68/72 heterodimer). In order to understand how the bi...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2006.12.056
更新日期：2007-03-16 00:00:00
abstract：:Current clinical anti-CD40 biologic agents include both antagonist molecules for the treatment of autoimmune diseases and agonist molecules for immuno-oncology, yet the relationship between CD40 epitope and these opposing biological outcomes is not well defined. This report describes the identification of potent antag...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2016.05.014
更新日期：2016-07-17 00:00:00
abstract：:Ebolaviruses are causative agents of lethal hemorrhagic fever in humans and nonhuman primates. Among the filoviruses characterized thus far, Reston Ebola virus (REBOV) is the only Ebola virus that is nonpathogenic to humans despite the fact that REBOV can cause lethal disease in nonhuman primates. Previous studies als...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2010.04.022
更新日期：2010-06-11 00:00:00
abstract：:A Xenopus laevis complementary DNA (cDNA) library prepared from messenger RNAs extracted from embryos has been screened for actin-coding sequences. Two cDNA clones corresponding to an alpha cardiac and an alpha skeletal muscle actin mRNA have been identified and characterized. From a genomic library, we have furthermo...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(86)90438-9
更新日期：1986-02-05 00:00:00
abstract：:Catalase-1, one of four catalase activities of Neurospora crassa, is associated with non-growing cells and accumulates in asexual spores. It is a large, tetrameric, highly efficient, and durable enzyme that is active even at molar concentrations of hydrogen peroxide. Catalase-1 is oxidized at the heme by singlet oxyge...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2004.07.027
更新日期：2004-09-17 00:00:00
abstract：:Amber suppressors previously isolated from the yeast Saccharomyces cerevisiae and belonging to the same phenotypic class (Liebman et al., 1976) were assigned to nine different linkage groups named SUP52 through SUP60. One of these suppressors, SUP52, had been shown to cause the insertion of leucine and had been geneti...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(84)90140-2
更新日期：1984-09-15 00:00:00
abstract：:The tyrosine residues adjacent to the C termini of the hemoglobin (Hb) subunits, alphaY140 and betaY145, are expected to play important structural roles, because the C termini are the loci of T-state quaternary salt-bridges, and because the tyrosine side-chains bridge the H and F helices via H bonds to the alphaV93 an...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2005.11.006
更新日期：2006-02-17 00:00:00
abstract：:The majority of archaeal viral genes are of unknown function hindering our understanding of the virus life cycle and viral interactions with their host. Here, we first describe functional characterization of ORF131b (gp17) and ORF436 (gp18) of Sulfolobus islandicus rod-shaped virus 2 (SIRV2), both encoding proteins of...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2015.03.013
更新日期：2015-06-19 00:00:00
abstract：:The effect of GT/CA dinucleotide repeat tracts on RecA-dependent homologous recombination was examined in vitro. By measuring the binding of RecA protein to oligonucleotides containing GT or CA repeats using the surface plasmon resonance (BIAcore), we show that the efficiency of RecA protein binding is sequence depend...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1997.1293
更新日期：1997-10-17 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2008.05.029
更新日期：2008-07-18 00:00:00
abstract：:The formation of two-dimensional crystals of the membrane-bound enzyme microsomal glutathione transferase is sensitive to fractional changes in the lipid-to-protein ratio. Variation of this parameter results in crystal polymorphism. The projection structure of a p6 crystal form of the enzyme has been determined by the...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1999.2683
更新日期：1999-04-30 00:00:00
abstract：:The positive control protein NifA of Klebsiella pneumoniae activates transcription by RNA polymerase containing sigma 54 by catalysing open promoter complex formation. We show that the integrity of the putative ATP-binding pocket in the central domain of NifA is necessary for the positive control function of NifA, but...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(92)90921-6
更新日期：1992-05-20 00:00:00
abstract：:Protein domains represent the basic evolutionary units that form proteins. Domain duplication and shuffling by recombination are probably the most important forces driving protein evolution and hence the complexity of the proteome. While the duplication of whole genes as well as domain-encoding exons increases the abu...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2004.11.050
更新日期：2005-02-11 00:00:00
