Abstract：
:We have identified independently folding units, so called "foldons", from non-homologous proteins representing different folds. We applied simple statistical arguments in order to estimate the size of the foldon universe required to construct all foldable proteins. Various alignment procedures yield about 2600 foldons in the natural protein universe but this estimate is shown to be rather sensitive to the chosen cut-off value for structural similarity. We showed that foldon matching-modelling can reproduce the major part of the main chain of several proteins with a structural similarity measure Q-score of about 0.4 and an r.m.s. error of about 5 A, although the accuracy of structure prediction has been limited so far by the small size of foldon data set. The prediction score may be increased if one uses the set of protein fragments with optimized sequence-structure relationships, in other works, minimally frustrated segments. To quantify the degree of frustration of the structures of foldons from our database, we searched for those foldons which recognize their own sequence and structure upon threading. As a result we found that about half of the foldons from our data set recognize themselves as the best choice upon threading and therefore are individually minimally frustrated. We showed that there is a close connection between the Q-score of self recognition and the relative foldability (Theta) of the folding units. Foldons having high Q-score and Theta values are expected to be formed in the early phase of the folding process and be observed as stable intermediates under appropriate experimental conditions.
journal_name
J Mol Bioljournal_title
Journal of molecular biologyauthors
Panchenko AR,Luthey-Schulten Z,Cole R,Wolynes PGdoi
10.1006/jmbi.1997.1205subject
Has Abstractpub_date
1997-09-12 00:00:00pages
95-105issue
1eissn
0022-2836issn
1089-8638pii
S0022-2836(97)91205-5journal_volume
272pub_type
杂志文章abstract：:Profile hidden Markov models (HMMs) are used to model protein families and for detecting evolutionary relationships between proteins. Such a profile HMM is typically constructed from a multiple alignment of a set of related sequences. Transition probability parameters in an HMM are used to model insertions and deletio...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2004.03.023
更新日期：2004-05-07 00:00:00
abstract：:Phospholamban (PLB) is a pentameric transmembrane protein that regulates the Ca(2+)-dependent ATPase SERCA2a in sarcoplasmic reticulum membranes. We previously described the computational design of a water-soluble variant of phospholamban, WSPLB, which reproduced many of the structural and functional properties of the...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2005.02.040
更新日期：2005-05-06 00:00:00
abstract：:Tissue deposition of normally soluble proteins as insoluble amyloid fibrils is associated with serious diseases including the systemic amyloidoses, maturity onset diabetes, Alzheimer's disease and transmissible spongiform encephalopathy. Although the precursor proteins in different diseases do not share sequence homol...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1997.1348
更新日期：1997-10-31 00:00:00
abstract：:The X-ray crystal structure of the Escherichia coli stress response protein HDEA has been determined at 2.0 A resolution. The single domain alpha-helical protein is found in the periplasmic space, where it supports an acid resistance phenotype essential for infectivity of enteric bacterial pathogens, such as Shigella ...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1999.3347
更新日期：2000-01-21 00:00:00
abstract：:Bacterial cell shape is dictated by the cell wall, a plastic structure that must adapt to growth and division whilst retaining its function as a selectively permeable barrier. The modulation of cell wall structure is achieved by a variety of enzymatic functions, all of which must be spatially regulated in a precise ma...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2007.07.022
更新日期：2007-09-28 00:00:00
abstract：:Penicillin G acylase is a periplasmic protein, cytoplasmically expressed as a precursor polypeptide comprising a signal sequence, the A and B chains of the mature enzyme (209 and 557 residues respectively) joined by a spacer peptide of 54 amino acid residues. The wild-type AB heterodimer is produced by proteolytic rem...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.2000.4105
更新日期：2000-09-29 00:00:00
abstract：:The energetic profiles of a significant number of protein-DNA systems at 20 degrees C reveal that, despite comparable Gibbs free energies, association with the major groove is primarily an enthalpy-driven process, whereas binding to the minor groove is characterized by an unfavorable enthalpy that is compensated by fa...
journal_title：Journal of molecular biology
pub_type： 杂志文章,评审
doi：10.1016/j.jmb.2006.09.059
更新日期：2007-01-05 00:00:00
abstract：:The protein/protein interaction between SinI and SinR has been studied by analytical ultracentrifugation and gel electrophoresis in an attempt to understand how these proteins contribute to developmental control of sporulation in Bacillus subtilis. SinR was found to be tetrameric, while SinI was found to exist as mono...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1999.3221
更新日期：1999-11-12 00:00:00
abstract：:What energetic and solvation effects underlie the remarkable two-state thermodynamics and folding/unfolding kinetics of small single-domain proteins? To address this question, we investigate the folding and unfolding of a hierarchy of continuum Langevin dynamics models of chymotrypsin inhibitor 2. We find that residue...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/s0022-2836(02)01434-1
更新日期：2003-02-21 00:00:00
abstract：:The fragment crystallizable (Fc) region links the key pathogen identification and destruction properties of immunoglobulin G (IgG). Pathogen opsonization positions Fcs to activate pro-inflammatory Fcγ receptors (FcγRs) on immune cells. The cellular response and committal to a damaging, though protective, immune respon...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2014.01.011
更新日期：2014-04-17 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1999.3025
更新日期：1999-08-27 00:00:00
abstract：:We report here the isolation and primary structure of two genes encoding rat U3 small nuclear RNA. One of the genes encodes U3B RNA; the other encodes an RNA which is almost identical to U3A RNA. Both genes are expressed after microinjection into the nuclei of Xenopus laevis oocytes and can direct the accumulation of ...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(85)90372-9
更新日期：1985-07-20 00:00:00
abstract：:The papillomavirus E1 protein is essential for viral DNA replication, and phosphorylation of E1 appears to regulate protein function and DNA replication. Serine 584 of bovine papillomavirus E1 is in a conserved motif resembling a CK2 consensus site, and is phosphorylated by CK2 in vitro. Mutation of serine 584 to alan...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.2001.5375
更新日期：2002-02-22 00:00:00
abstract：:Quantitatively describing RNA structure and conformational elements remains a formidable problem. Seven standard torsion angles and the sugar pucker are necessary to characterize the conformation of an RNA nucleotide completely. Progress has been made toward understanding the discrete nature of RNA structure, but clas...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2007.06.058
更新日期：2007-09-28 00:00:00
abstract：:In phylogenetic reconstructions by the parsimony method, utilizing 62 sequenced globin genes and pseudogenes (including 34 of the beta-globin gene family from eutherian orders Primates, Lagomorpha, Artiodactyla and Rodentia), the branch of primate psi beta pseudogenes and the goat embryonically expressed epsilon II ge...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(84)90258-4
更新日期：1984-12-25 00:00:00
abstract：:The molecular mechanism by which the microtubule-associated protein (MAP) tau regulates the formation of microtubules (MTs) is poorly understood. The activity of tau is controlled via phosphorylation at specific Ser/Thr sites. Of those phosphorylation sites, 17 precede a proline, making them potential recognition site...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2016.03.010
更新日期：2016-05-08 00:00:00
abstract：:The region of bacteriophage P1 DNA containing a lytic (vegetative) replicon has been identified by cloning P1 fragments into a phage lambda vector. We present the sequence of that replicon. Using a novel fusion vector containing two P1 loxP recombination sites, we have developed a transformation assay for replicon fun...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(89)90444-0
更新日期：1989-05-05 00:00:00
abstract：:Toxin-antitoxin systems consist of a stable toxin, frequently with endonuclease activity, and a small, labile antitoxin, which sequesters the toxin into an inactive complex. Under unfavorable conditions, the antitoxin is degraded, leading to activation of the toxin and resulting in growth arrest, possibly also in bact...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2007.07.016
更新日期：2007-09-28 00:00:00
abstract：:The DNA hexamer d(CACGPG), in which dP is the ambivalent pyrimidine nucleoside analogue 2'-deoxy-beta-d-ribofuranosyl-(6H,8H-3, 4-dihydropyrimido[4,5-c][1,2]oxazin-7-one), crystallises as a left-handed Z-DNA duplex. X-ray analysis at 1.5 A shows that both P. A base-pairs are of the wobble type. This result appears inc...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1998.2080
更新日期：1998-10-09 00:00:00
abstract：:The mechanisms for de novo protein folding differ significantly between bacteria and eukaryotes, as evidenced by the often observed poor yields of native eukaryotic proteins upon recombinant production in bacterial systems. Polypeptide synthesis rates are faster in bacteria than in eukaryotes, but the effects of gener...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2009.12.042
更新日期：2010-03-12 00:00:00
abstract：:Recent studies indicate that binding of the urokinase-type plasminogen activator (uPA) to its high-affinity receptor (uPAR) orchestrates uPAR interactions with other cellular components that play a pivotal role in diverse (patho-)physiological processes, including wound healing, angiogenesis, inflammation, and cancer ...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2006.08.063
更新日期：2006-10-20 00:00:00
abstract：:We have sequenced the heavy and light chain genes from 365 IgG(+) B cells and found that 24 (6.5 %) contain somatically introduced insertions or deletions. These insertions and deletions are clustered at "hot-spots" in the antigen-binding site and frequently result in the creation of new combinations of canonical loop...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1999.3289
更新日期：1999-12-03 00:00:00
abstract：:Cholera toxin (CT) holotoxin must be activated to intoxicate host cells. This process requires the intracellular dissociation of the enzymatic CTA1 domain from the holotoxin components CTA2 and B5, followed by subsequent interaction with the host factor ADP ribosylation factor 6 (ARF6)-GTP. We report the first NMR-bas...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2007.12.075
更新日期：2008-03-28 00:00:00
abstract：:The temperature dependence of processing of precursor tRNA(Gly) (ptRNA(Gly)) variants carrying a single 2'-OCH(3) or locked nucleic acid (LNA) modification at G+1 by Escherichia coli endoribonuclease P RNA was studied at rate-limiting chemistry. We show, for the first time, that these ribose modifications at nucleotid...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2008.03.042
更新日期：2008-05-23 00:00:00
abstract：:The interaction of archaeal family B DNA polymerases with deaminated bases has been examined. As determined previously by our group, the polymerase binds tightly to uracil (the deamination product of cytosine), in single-stranded DNA, and stalls replication on encountering this base. DNA polymerisation was also inhibi...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2007.07.015
更新日期：2007-09-28 00:00:00
abstract：:Recent experimental results suggest that the native fold, or topology, plays a primary role in determining the structure of the transition state ensemble, at least for small, fast-folding proteins. To investigate the extent of the topological control of the folding process, we studied the folding of simplified models ...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.2000.3693
更新日期：2000-05-19 00:00:00
abstract：:Thiol peroxidases (Tpxs) are dimeric 2-Cys peroxiredoxins from bacteria that preferentially reduce alkyl hydroperoxides. Catalysis requires two conserved residues, the peroxidatic cysteine and the resolving cysteine, which are located in helix alpha(2) and helix alpha(3), respectively. The partial unraveling of helice...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2009.08.040
更新日期：2009-11-06 00:00:00
abstract：:The tandemly repeated sea urchin alpha-histone genes are developmentally regulated. These genes are transcribed up to the early blastula stage and permanently silenced as the embryos approach gastrulation. As previously described, expression of the alpha-H2A gene depends on the binding of the MBF-1 activator to the 5'...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2006.10.098
更新日期：2007-02-02 00:00:00
abstract：:The discovery that RNA molecules can fold into complex structures and carry out diverse cellular roles has led to interest in developing tools for modeling RNA tertiary structure. While significant progress has been made in establishing that the RNA backbone is rotameric, few libraries of discrete conformations specif...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2012.03.002
更新日期：2012-08-03 00:00:00
abstract：:A 144 amino acid residue cts-52 mutant repressor (mtc phi 105) located in the EcoRI-F immunity region (immF) of Bacillus subtilis phage phi 105 is involved in the control mechanism of a thermo-inducible expression system. Adjacent to the repressor gene, an open-reading frame, designated ORF4, encodes a polypeptide of ...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2003.08.017
更新日期：2003-10-10 00:00:00
