Abstract:
:Methods that compare a protein sequence directly to a structure can be divided into those that construct a molecular model (threading methods) and those that perform a sequence alignment with the structure encoded as a sequence of structural states (one-dimensional/three-dimensional (1D/3D) matching). The former take into account the internal packing of the molecule but the latter do not. On the other hand, it is simple to include multiple sequence data in a 1D/3D comparison but difficult in a threading method. Here, a protein sequence/structure alignment method is described that uses a combination of matching predicted and observed residue exposure, predicted and observed secondary structure (1D/3D) together with pairwise packing interactions in the core (threading). Using a variety of distantly related and analogous protein structures, the multiple sequence threading (MST) method was compared to a single sequence threading (SST) method (that uses complex potentials of mean-force) and also to a multiple sequence alignment (MSA) program. It was found that the MST method produced alignments that were better than the best that could be obtained with either the SST or MSA method. The method was found to be stable to error in both secondary structure prediction and predicted exposure and also under variation of the key parameters (fully described in an Appendix). The contribution of the pairwise term was found to be small but without it, the correct alignments were less stable and structurally unreasonable deletions were observed when matching against larger structures. Using the parameters derived for alignment, the method was able to recognise related folds in the structure databank with a specificity comparable to other methods.
journal_name
J Mol Bioljournal_title
Journal of molecular biologyauthors
Taylor WRdoi
10.1006/jmbi.1997.1008subject
Has Abstractpub_date
1997-06-27 00:00:00pages
902-43issue
5eissn
0022-2836issn
1089-8638pii
S0022-2836(97)91008-1journal_volume
269pub_type
杂志文章abstract::The small (40 S) subunit of the eukaryotic ribosome may have to scan more than 2000 nucleotides (>600 nm) from its 5'cap recruiting point on an mRNA molecule before initiating on a translation start codon. As with many other processes in living cells, including transcription, editing, mRNA splicing, pre-rRNA processin...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2006.06.016
更新日期:2006-08-11 00:00:00
abstract::An essential consequence of growth factor-mediated signal transduction is the generation of intracellular H(2)O(2). It operates as a second messenger in the control of actin microfilament dynamics, causing rapid and dramatic changes in the morphology and motile activity of stimulated cells. Little is understood about ...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2007.04.056
更新日期:2007-07-06 00:00:00
abstract::The central domain is an evolutionarily conservative region that is invariant in length in the A and Hc-A families of silkmoth chorion proteins. This domain shows strong sixfold periodicities for various amino acid residues, such as glycine and large non-polar residues. The periodicities and their phase relationships,...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/0022-2836(85)90132-9
更新日期:1985-12-05 00:00:00
abstract::The crystal structure of desulforedoxin from Desulfovibrio gigas, a new homo-dimeric (2 x 36 amino acids) non-heme iron protein, has been solved by the SIRAS method using the indium-substituted protein as the single derivative. The structure was refined to a crystallographic R-factor of 16.9% at 1.8 A resolution. Nati...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1995.0465
更新日期:1995-09-01 00:00:00
abstract::Human serum amyloid P component (SAP) is a normal plasma glycoprotein and the precursor of amyloid P component which is a universal constituent of the abnormal tissue deposits in amyloidosis. X-ray and neutron scattering data showed that pentameric or decameric ring structures for SAP in solution are readily distingui...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1997.1271
更新日期:1997-09-26 00:00:00
abstract::The structure of goose egg-white lysozyme (GEWL) has been refined to an R-value of 15.9% at 1.6 A resolution. Details of the structure determination, the refinement and the structure itself are presented. The structure of a complex of the enzyme with the trisaccharide of N-acetyl glucosamine has also been determined a...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/s0022-2836(95)80038-7
更新日期:1995-01-06 00:00:00
abstract::Mycobacteriophage Brujita is an unusual temperate phage in which establishment of superinfection immunity is dependent on chromosomal integration. Integration is mediated by a non-canonical tyrosine integrase (Int) lacking an N-terminal domain typically associated with binding to arm-type sites within the phage attach...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2016.04.023
更新日期:2016-06-05 00:00:00
abstract::Recently, the absence of a thermally induced transition has been offered as proof that the unfolded and the molten globule states of apo-alpha-lactalbumin are enthalpically equivalent. In this paper we demonstrate that that argument is thermodynamically incorrect. In addition, it is shown that the absence of a thermal...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1993.1364
更新日期:1993-07-05 00:00:00
abstract::HscA, a specialized bacterial Hsp70-class molecular chaperone, interacts with the iron-sulfur cluster assembly protein IscU by recognizing a conserved LPPVK sequence motif. We report the crystal structure of the substrate-binding domain of HscA (SBD, residues 389-616) from Escherichia coli bound to an IscU-derived pep...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2004.07.025
更新日期:2004-09-24 00:00:00
abstract::The enzyme penicillin acylase (penicillin amidohydrolase EC 3.5.1. 11) catalyses the cleavage of the amide bond in the benzylpenicillin (penicillin G) side-chain to produce phenylacetic acid and 6-aminopenicillanic acid (6-APA). The enzyme is of great pharmaceutical importance, as the product 6-APA is the starting poi...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1998.2180
更新日期:1998-11-27 00:00:00
abstract::The Myosin A-tail interacting protein (MTIP) of the malaria parasite links the actomyosin motor of the host cell invasion machinery to its inner membrane complex. We report here that at neutral pH Plasmodium falciparum MTIP in complex with Myosin A adopts a compact conformation, with its two domains completely surroun...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2007.06.016
更新日期:2007-09-07 00:00:00
abstract::While the disulfide bridge is highly conserved within the immunoglobulin fold, a few antibody variable domains lack one of the essential cysteine residues. In the levan binding antibody ABPC48 one of the essential cysteine residues (Cys H92) of the heavy chain variable domain is replaced by tyrosine. We expressed scFv...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1996.0726
更新日期:1997-01-17 00:00:00
abstract::The pentameric ATPase motor gp16 packages double-stranded DNA into the bacteriophage phi29 virus capsid. On the basis of the results of single-molecule experimental studies, we propose a push and roll mechanism to explain how the packaging motor translocates the DNA in bursts of four 2.5 bp power strokes, while rotati...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2010.05.002
更新日期:2010-07-09 00:00:00
abstract::Enhanced structural insights into the folding energy landscape of the N-terminal dimerization domain of Escherichia coli tryptophan repressor, [2-66]2 TR, were obtained from a combined experimental and theoretical analysis of its equilibrium folding reaction. Previous studies have shown that the three intertwined heli...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2006.07.080
更新日期:2006-10-13 00:00:00
abstract::The nine polyglutamine (polyQ) neurodegenerative diseases are caused in part by a gain-of-function mechanism involving protein misfolding, the deposition of β-sheet-rich aggregates and neuronal toxicity. While previous experimental evidence suggests that the polyQ-induced misfolding mechanism is context dependent, the...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2011.09.014
更新日期:2011-11-04 00:00:00
abstract::Proteorhodopsin (PR) is a recently discovered ubiquitous eubacterial retinal-binding light-driven proton pump. Almost 1000 PR variants are widely distributed in species of marine and freshwater bacteria, suggesting PR's important photobiological role. PR is a typical seven-transmembrane alpha-helical membrane protein ...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2009.01.011
更新日期:2009-03-06 00:00:00
abstract::The Janus kinases (JAKs) are a pivotal family of protein tyrosine kinases (PTKs) that play prominent roles in numerous cytokine signaling pathways, with aberrant JAK activity associated with a variety of hematopoietic malignancies, cardiovascular diseases and immune-related disorders. Whereas the structures of the JAK...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2009.01.041
更新日期:2009-03-20 00:00:00
abstract::Major histocompatibility complex (MHC) class I proteins are expressed on the cell surface where they present foreign and self-peptides to effector cells of the immune system. While an understanding of the structural prerequisites for antigen presentation has already been achieved, insight into subtype- or peptide-depe...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2011.11.021
更新日期:2012-01-13 00:00:00
abstract::Dof is a large molecule essential for signal transduction by the two FGF receptors in Drosophila. It contains two ankyrin repeats and a coiled-coil region, but has no other recognisable structural motif. Dof shares these features with its closest vertebrate relatives, the B-cell signalling molecules BCAP and BANK. In ...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/s0022-2836(03)00489-3
更新日期:2003-06-06 00:00:00
abstract::Bovine enterovirus (BEV) strain VG-5-27 derived from an infectious cDNA clone has been crystallized as extended hexagonal plates. Virus recovered from crystals produced cytopathic effect in BHK cells. These crystals diffract X-rays from high energy synchrotron sources to beyond 2.7 A. The crystal system is monoclinic,...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1993.1339
更新日期:1993-06-05 00:00:00
abstract::Aminoacylation and editing by leucyl-tRNA synthetases (LeuRS) require migration of the tRNA acceptor stem end between the canonical aminoacylation core and a separate domain called CP1 that is responsible for amino acid editing. The LeuRS CP1 domain can also support group I intron RNA splicing in the yeast mitochondri...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2006.12.051
更新日期:2007-03-23 00:00:00
abstract::In the filamentous fungus Podospora anserina, the unavoidable phenomenon of senescence is associated with specific mitochondrial rearrangements and particularly with the amplification of some regions of the mitochondrial chromosome. Mechanisms responsible for these rearrangements are still unknown. The implication in ...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1993.1558
更新日期:1993-11-05 00:00:00
abstract::The majority of cell surface receptors involved in antigen recognition by T cells and in the orchestration of the subsequent cell signalling events are glycoproteins. The length of a typical N-linked sugar is comparable with that of an immunoglobulin domain (30 A). Thus, by virtue of their size alone, oligosaccharides...
journal_title:Journal of molecular biology
pub_type: 杂志文章,评审
doi:10.1006/jmbi.1999.3104
更新日期:1999-10-22 00:00:00
abstract::NADH:ubiquinone oxidoreductase (complex I) is the first and largest complex in the electron transport chain of mitochondria. The bovine complex purified from cardiac muscle consists of at least 42 different subunits with a combined molecular mass of about 890 kDa. The three-dimensional structure of the complex was det...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1998.1668
更新日期:1998-04-17 00:00:00
abstract::Escherichia coli nitroreductase (NTR) is a flavoprotein that reduces a variety of quinone and nitroaromatic substrates. Among these substrates is the prodrug 5-[aziridin-1-yl]-2,4-dinitrobenzamide (CB1954) that is activated by NTR to form two products, one of which is highly cytotoxic. NTR in combination with CB1954 h...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2007.02.012
更新日期:2007-04-27 00:00:00
abstract::Molecular aspects of thermal adaptation of proteins were studied by following the co-evolution of temperature dependence, conformational stability, and substrate specificity in a cold-active lipase modified via directed evolution. We found that the evolution of kinetic stability was accompanied by a relaxation in subs...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2009.10.026
更新日期:2010-01-08 00:00:00
abstract::The effect of temperature on the velocity of rhodamine phalloidin-labelled F-actin moving in vitro on rabbit skeletal myosin has been studied. Translating actin filaments were visualized by epi-fluorescence in an inverted microscope, equipped with temperature control (+/- 0.2 K) of the stage and objective. Images were...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/0022-2836(92)90467-x
更新日期:1992-04-20 00:00:00
abstract::Solution NMR structures for sperm whale carbonmonoxy myoglobin have been calculated using 1301 distance restraints determined from nuclear Overhauser enhancement (NOE) measurements on 15N-labeled protein and chemical shift calculations for 385 protons. Starting structures included four crystal forms of myoglobin and 1...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1994.1718
更新日期:1994-11-25 00:00:00
abstract::Reverse transcription coupled with DNA amplification has become a well-established and powerful molecular technique for studying ribonucleic acids. However, the efficiency of those reactions is largely dependent on the molecular properties of currently used reverse transcriptases (RTs). Engineered and natural RT varia...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2009.07.081
更新日期:2009-10-02 00:00:00
abstract::The structure of filamentous bacteriophage Pf1 has been studied using neutron diffraction from magnetically oriented gels of native and valine-deuterated phage. Neutron diffraction intensities were measured to approximately 8 A resolution along the equator and first six layer-lines, and differences due to the deuterat...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/0022-2836(88)90387-7
更新日期:1988-01-05 00:00:00