Abstract:
:To probe the mechanism of the catalytic antibody NPN43C9, we have constructed a three-dimensional model of the NPN43C9 variable region using our antibody structural database (ASD), which takes maximal advantage of immunoglobulin sequence and structural information. The ASD contains separately superimposed variable light and variable heavy chains, which reveal not only conserved backbone structure, but also structurally conserved side-chain conformations. The NPN43C9 model revealed that the guanidinium group of light chain Arg L96 was positioned at the bottom of the antigen-binding site and formed a salt bridge with the antigen's phosphonamidate group, which mimics the negatively charged, tetrahedral transition states in the hydrolysis reaction. Thus, the model predicts both binding and catalytic functions for Arg L96, which previously had not been implicated in either. First, Arg L96 should enhance antigen binding by electrostatically complementing the negative charge of the antigen, which is buried upon complex formation. Second, Arg L96 should promote catalysis by electrostatically stabilizing the negatively charged transition states formed during catalysis. These hypotheses were tested experimentally by design and characterization of the R-L96-Q mutant, in which Arg L96 was replaced with Gln by site-directed mutagenesis. As predicted, antigen binding in the R-L96-Q mutant was decreased relative to that in the parent NPN43C9 antibody, but binding of antigen fragments lacking the phosphonamidate group was retained. In addition, the R-L96-Q mutant had no detectable esterase activity. Thus, the computational model and experimental results together suggest a mechanism by which the catalytic antibody NPN43C9 stabilizes high-energy transition states during catalysis.
journal_name
J Mol Bioljournal_title
Journal of molecular biologyauthors
Roberts VA,Stewart J,Benkovic SJ,Getzoff EDdoi
10.1006/jmbi.1994.1060subject
Has Abstractpub_date
1994-01-21 00:00:00pages
1098-116issue
3eissn
0022-2836issn
1089-8638pii
S0022-2836(84)71060-6journal_volume
235pub_type
杂志文章abstract::The sigma N class of sigma factors confer upon RNA polymerase the requirement for enhancer-binding activator proteins. The sigma-N (sigma N) protein of Klebsiella pneumoniae was analysed by the assay of purified peptides comprising domains or regions of sigma N defined by proteolysis or by homology alignment, respecti...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1995.0260
更新日期:1995-05-12 00:00:00
abstract::The powerful explanatory paradigm of molecular biology requiring form to co-evolve with function has again been proven successful when, over the recent two decades, a wealth of biological functions have been uncovered for RNA. Previously considered as a mere mediator of the genetic code, RNA is now acknowledged as a k...
journal_title:Journal of molecular biology
pub_type: 杂志文章,评审
doi:10.1006/jmbi.1999.3312
更新日期:1999-12-10 00:00:00
abstract::Clostridium botulinum C3 exoenzyme inactivates the small GTP-binding protein family Rho by ADP-ribosylating asparagine 41, which depolymerizes the actin cytoskeleton. C3 thus represents a major family of the bacterial toxins that transfer the ADP-ribose moiety of NAD to specific amino acids in acceptor proteins to mod...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.2000.4292
更新日期:2001-01-05 00:00:00
abstract::We have identified a novel family of proteins, in which the N-terminal cystathionine beta-synthase (CBS) domain is fused to the C-terminal Zn ribbon domain. Four proteins were overexpressed in Escherichia coli and purified: TA0289 from Thermoplasma acidophilum, TV1335 from Thermoplasma volcanium, PF1953 from Pyrococcu...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2007.10.060
更新日期:2008-01-04 00:00:00
abstract::Bloom syndrome protein (BLM) is one of five human RecQ helicases that participate in DNA metabolism. RecQ C-terminal (RQC) domain is the main DNA binding module of BLM and specifically recognizes G-quadruplex (G4) DNA structures. Because G4 processing by BLM is essential for regulating replication and transcription, b...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2019.01.010
更新日期:2019-02-15 00:00:00
abstract::In bacteria and lower eukaryotes, adaptation to changes in the environment is often mediated by two-component regulatory systems. Such systems provide the basis for chemotaxis, nitrogen and phosphate regulation and adaptation to osmotic stress, for example. In Escherichia coli, the sensor kinase EnvZ detects a change ...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.2000.3809
更新日期:2000-06-23 00:00:00
abstract::The trimeric TolC protein of Escherichia coli comprises an outer membrane beta-barrel and a contiguous alpha-helical barrel projecting across the periplasm. This provides a single 140 A long pore for multidrug efflux and protein export. We have previously reported that trivalent cations such as hexammine cobalt can se...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2004.07.088
更新日期:2004-09-17 00:00:00
abstract::Saccharomyces cerevisiae is an occasional host to an array of prions, most based on self-propagating, self-templating amyloid filaments of a normally soluble protein. [URE3] is a prion of Ure2p, a regulator of nitrogen catabolism, while [PSI+] is a prion of Sup35p, a subunit of the translation termination factor Sup35...
journal_title:Journal of molecular biology
pub_type: 杂志文章,评审
doi:10.1016/j.jmb.2018.04.022
更新日期:2018-10-12 00:00:00
abstract::A pseudoknot-containing aptamer isolated from a pool of random sequence molecules has been shown previously to represent an optimal RNA solution to the problem of binding biotin. The affinity of this RNA molecule is nonetheless orders of magnitude weaker than that of its highly evolved protein analogs, avidin and stre...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.2000.3539
更新日期:2000-03-10 00:00:00
abstract::The observed propeller twist in base-pairs of crystalline double-helical DNA oligomers improves the stacking overlap along each individual helix strand. But, as proposed by Calladine, it also leads to clash or steric hindrance between purines at adjacent base-pairs on opposite strands of the helix. This clash can be r...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/s0022-2836(83)80093-x
更新日期:1983-05-25 00:00:00
abstract::The expression of the gene thrS encoding threonyl-tRNA synthetase is under the control of two apparently different regulatory loops: translational feedback regulation and growth rate-dependent control. The translational feedback regulation is due to the binding of threonyl-tRNA synthetase to a site located in the lead...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1996.0445
更新日期:1996-08-16 00:00:00
abstract::The nuclear pore complex is the sole mediator of bidirectional transport between the nucleus and cytoplasm. Nup358 is a metazoan-specific nucleoporin that localizes to the cytoplasmic filaments and provides several binding sites for the mobile nucleocytoplasmic transport machinery. Here we present the crystal structur...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2013.01.021
更新日期:2013-04-26 00:00:00
abstract::Specificity engineering is challenging and particularly difficult for enzymes that have the catalytic machinery and specificity determinants in close proximity. Restriction endonucleases have been used as a paradigm for protein engineering, but successful cases are rare. Here, we present the results of a directed evol...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2019.04.010
更新日期:2019-05-17 00:00:00
abstract::Interactions of polymerase X from African swine fever virus with single-stranded DNA (ssDNA) have been studied, using quantitative fluorescence titration and analytical ultracentrifugation techniques. Experiments were performed with a fluorescent etheno-derivative of ssDNA oligomers. Studies of unmodified ssDNA oligom...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2005.10.061
更新日期:2006-02-10 00:00:00
abstract::Polycystin-1 is a large membrane-associated protein that interacts with polycystin-2 in the primary cilia of renal epithelial cells to form a mechanosensitive ion channel. Bending of the cilia induces calcium flow into the cells, mediated by the polycystin complex. Antibodies to polycystin-1 and polycystin-2 abolish t...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2005.04.008
更新日期:2005-06-17 00:00:00
abstract::A library of variant enzymes was created by combined shuffling of the DNA encoding the human Mu class glutathione transferases GST M1-1 and GST M2-2. The parental GSTs are 84 % sequence identical at the protein level, but their specific activities with the substrates aminochrome and 2-cyano-1,3-dimethyl-1-nitrosoguani...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1999.2607
更新日期:1999-03-26 00:00:00
abstract::Isoprenoids, most of them synthesized by prenyltransferases (PTSs), are a class of important biologically active compounds with diverse functions. The mint geranyl pyrophosphate synthase (GPPS) is a heterotetramer composed of two LSU·SSU (large/small subunit) dimers. In addition to C(10)-GPP, the enzyme also produces ...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2010.10.011
更新日期:2010-12-17 00:00:00
abstract::Exotoxin A of Pseudomonas aeruginosa asserts its cellular toxicity through ADP-ribosylation of translation elongation factor 2, predicated on binding to specific cell surface receptors and intracellular trafficking via a complex pathway that ultimately results in translocation of an enzymatic activity into the cytopla...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.2001.5195
更新日期:2001-12-07 00:00:00
abstract::Human pancreatic alpha-amylase has been isolated using a glycogen affinity precipitation procedure and crystallized in a form suitable for high resolution three-dimensional X-ray crystallographic analyses. Crystals are of the orthorhombic space group P2(1)2(1)2(1), with unit cell dimensions of a = 53.04 A, b = 74.80 A...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1993.1221
更新日期:1993-04-05 00:00:00
abstract::Many medically relevant Gram-negative bacteria use the type III secretion system (T3SS) to translocate effector proteins into the host for their invasion and intracellular survival. A multi-protein complex located at the cytosolic interface of the T3SS is proposed to act as a sorting platform by selecting and targetin...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2019.07.004
更新日期:2019-09-06 00:00:00
abstract::Integrins, which are heterodimeric (α and β subunits) signal-transducer proteins, are essential for cell adhesion and migration. β cytosolic tails (β-CTs) of integrins interact with a number of cytosolic proteins including talin, Dok1, and 14-3-3ζ. The formation of multiprotein complexes with β-CTs is involved in the ...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2016.08.014
更新日期:2016-10-09 00:00:00
abstract::Human prostate-specific antigen (PSA or KLK3) is an important marker for the diagnosis and management of prostate cancer. This is an androgen-regulated glycoprotein of the kallikrein-related protease family secreted by prostatic epithelial cells. Its physiological function is to cleave semenogelins in the seminal coag...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2007.11.052
更新日期:2008-02-29 00:00:00
abstract::In the crowded cell, a strong selective pressure operates on the proteome to limit the competition between functional and non-functional protein-protein interactions. We developed an original theoretical framework in order to interrogate how this competition constrains the behavior of proteins with respect to their pa...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2019.12.047
更新日期:2020-02-14 00:00:00
abstract::The bacteriophage P1 recombinase Cre mediates site-specific recombination between loxP sites. The loxP site consists of two 13 base-pair inverted repeats separated by an eight base-pair spacer region. When DNA containing the loxP site is incubated with Cre, specific cleavages occur within the spacer region, creating a...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/0022-2836(85)90224-4
更新日期:1985-02-05 00:00:00
abstract::When influenza A virus infects host cells, its integral matrix protein M2 forms a proton-selective channel in the viral envelope. Although X-ray crystallography and NMR studies using fragment peptides have suggested that M2 stably forms a tetrameric channel irrespective of pH, the oligomeric states of the full-length ...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2014.05.002
更新日期:2014-07-15 00:00:00
abstract::An explanation is suggested for the roll alternation between low and high values in A-type nucleic acid duplexes containing alternating sequences of purine and pyrimidine residues. The explanation combines two points. (1) Roll inevitably occurs in A-type duplexes due to geometrical reasons. (2) Intrastrand base stacki...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/0022-2836(91)80172-q
更新日期:1991-10-05 00:00:00
abstract::An analysis by electron microscopy in amorphous ice and X-ray diffraction of four types of three-dimensional crystals of adenovirus fibre is presented. Fibre from adenovirus type 2 (Ad2) crystallizes in two forms depending on whether it is native or cleaved near the N terminus at Tyr17. Fibre from Ad5 also crystallize...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/S0022-2836(05)80169-X
更新日期:1990-10-20 00:00:00
abstract::We have investigated the translational and rotational diffusion of two proteins, bovine pancreatic trypsin inhibitor and hen egg white lysozyme, using molecular dynamics simulations in explicit solvent. The translational diffusion constants obtained from the simulations compare favourably with results from experiments...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1994.1172
更新日期:1994-02-18 00:00:00
abstract::Crystal structures of two complexes between recombinant MS2 capsids and RNA operator fragments have been determined at 2.7 A resolution. The coat protein of the RNA bacteriophage MS2 is bifunctional; it forms the icosahedral virus shell to protect the viral nucleic acid and it acts as a translational repressor by bind...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1997.1144
更新日期:1997-08-01 00:00:00
abstract::Translating ribosomes often stall during elongation. The stalled ribosomes are known to be recycled by tmRNA (SsrA)-mediated trans-translation. Another process that recycles the stalled ribosomes is characterized by peptidyl-tRNA release. However, the mechanism of peptidyl-tRNA release from the stalled ribosomes is no...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2008.05.033
更新日期:2008-07-11 00:00:00