Energy landscape of the Michaelis complex of lactate dehydrogenase: relationship to catalytic mechanism.


:Lactate dehydrogenase (LDH) catalyzes the interconversion between pyruvate and lactate with nicotinamide adenine dinucleotide (NAD) as a cofactor. Using isotope-edited difference Fourier transform infrared spectroscopy on the "live" reaction mixture (LDH·NADH·pyruvate ⇌ LDH·NAD(+)·lactate) for the wild-type protein and a mutant with an impaired catalytic efficiency, a set of interconverting conformational substates within the pyruvate side of the Michaelis complex tied to chemical activity is revealed. The important structural features of these substates include (1) electronic orbital overlap between pyruvate's C2═O bond and the nicotinamide ring of NADH, as shown from the observation of a delocalized vibrational mode involving motions from both moieties, and (2) a characteristic hydrogen bond distance between the pyruvate C2═O group and active site residues, as shown by the observation of at least four C2═O stretch bands indicating varying degrees of C2═O bond polarization. These structural features form a critical part of the expected reaction coordinate along the reaction path, and the ability to quantitatively determine them as well as the substate population ratios in the Michaelis complex provides a unique opportunity to probe the structure-activity relationship in LDH catalysis. The various substates have a strong variance in their propensity toward on enzyme chemistry. Our results suggest a physical mechanism for understanding the LDH-catalyzed chemistry in which the bulk of the rate enhancement can be viewed as arising from a stochastic search through an available phase space that, in the enzyme system, involves a restricted ensemble of more reactive conformational substates as compared to the same chemistry in solution.






Peng HL,Deng H,Dyer RB,Callender R




Has Abstract


2014-03-25 00:00:00












  • Properties of overlapping EREs: synergistic activation of transcription and cooperative binding of ER.

    abstract::We have designed a novel estrogen-responsive unit, overERE, which consists of two overlapping ERE separated by 5 bp (center-to-center). In gel retardation assays, this sequence forms a low-mobility complex that migrates like an estrogen receptor tetramer. The receptor-overERE complex was specific and was supershifted ...


    pub_type: 杂志文章


    authors: Massaad C,Coumoul X,Sabbah M,Garlatti M,Redeuilh G,Barouki R

    更新日期:1998-04-28 00:00:00

  • Evidence for the kinetic partitioning of polymerase activity on G-quadruplex DNA.

    abstract::We have investigated the action of the human DNA polymerase ε (hpol ε) and η (hpol η) catalytic cores on G-quadruplex (G4) DNA substrates derived from the promoter of the c-MYC proto-oncogene. The translesion enzyme hpol η exhibits a 6.2-fold preference for binding to G4 DNA over non-G4 DNA, while hpol ε binds both G4...


    pub_type: 杂志文章


    authors: Eddy S,Maddukuri L,Ketkar A,Zafar MK,Henninger EE,Pursell ZF,Eoff RL

    更新日期:2015-05-26 00:00:00

  • Organellar Na+/H+ exchangers: novel players in organelle pH regulation and their emerging functions.

    abstract::Mammalian Na+/H+ exchangers (NHEs) play a fundamental role in cellular ion homeostasis. NHEs exhibit an appreciable variation in expression, regulation, and physiological function, dictated by their dynamics in subcellular localization and/or interaction with regulatory proteins. In recent years, a subgroup of NHEs co...


    pub_type: 杂志文章,评审


    authors: Ohgaki R,van IJzendoorn SC,Matsushita M,Hoekstra D,Kanazawa H

    更新日期:2011-02-01 00:00:00

  • Retroviral nucleocapsid protein specifically recognizes the base and the ribose of mononucleotides and mononucleotide components.

    abstract::The interaction of the retroviral nucleocapsid protein (NC) with nucleic acids forms the basis of its varied roles in the replication cycle, which include binding and condensing the viral RNA within the virion, stimulation of the early steps in reverse transcription, and dissociation from RNA in the replication comple...


    pub_type: 杂志文章


    authors: Secnik J,Gelfand CA,Jentoft JE

    更新日期:1992-03-24 00:00:00

  • Evidence for rapid inter- and intramolecular chlorine transfer reactions of histamine and carnosine chloramines: implications for the prevention of hypochlorous-acid-mediated damage.

    abstract::Hypochlorous acid (HOCl) is a powerful oxidant generated from H(2)O(2) and Cl(-) by the heme enzyme myeloperoxidase, which is released from activated leukocytes. HOCl possesses potent antibacterial properties, but excessive production can lead to host tissue damage that is implicated in a wide range of human diseases ...


    pub_type: 杂志文章


    authors: Pattison DI,Davies MJ

    更新日期:2006-07-04 00:00:00

  • The swapping of terminal arms in ribonucleases: comparison of the solution structure of monomeric bovine seminal and pancreatic ribonucleases.

    abstract::Bovine seminal ribonuclease (BS-RNase), the only dimeric protein among the pancreatic-like ribonucleases, is endowed with special structural features and with biological functions beyond enzymatic activity. In solution, the protein exists as an equilibrium mixture of two forms, with or without exchange (or swapping) o...


    pub_type: 杂志文章


    authors: Avitabile F,Alfano C,Spadaccini R,Crescenzi O,D'Ursi AM,D'Alessio G,Tancredi T,Picone D

    更新日期:2003-07-29 00:00:00

  • Decreased amyloidogenicity caused by mutational modulation of surface properties of the immunoglobulin light chain BRE variable domain.

    abstract::Amyloid formation by immunoglobulin light chain (LC) proteins is associated with amyloid light chain (AL) amyloidosis. Destabilization of the native state of the variable domain of the LC (VL) is known to be one of the critical factors in promoting the formation of amyloid fibrils. However, determining the key residue...


    pub_type: 杂志文章


    authors: Kobayashi Y,Tsutsumi H,Abe T,Ikeda K,Tashiro Y,Unzai S,Kamikubo H,Kataoka M,Hiroaki H,Hamada D

    更新日期:2014-08-12 00:00:00

  • Limited proteolysis of human von Willebrand factor by Staphylococcus aureus V-8 protease: isolation and partial characterization of a platelet-binding domain.

    abstract::Purified human von Willebrand factor (vWF) was digested with Staphylococcus aureus V-8 protease, and specific domains interacting with platelets were isolated and characterized. Amino acid sequence analysis and sodium dodecyl sulfate gel electrophoresis demonstrated that the digestion proceeded primarily by a single c...


    pub_type: 杂志文章


    authors: Girma JP,Chopek MW,Titani K,Davie EW

    更新日期:1986-06-03 00:00:00

  • Tying up the Ends: Plasticity in the Recognition of Single-Stranded DNA at Telomeres.

    abstract::Telomeres terminate nearly exclusively in single-stranded DNA (ssDNA) overhangs comprised of the G-rich 3' end. This overhang varies widely in length from species to species, ranging from just a few bases to several hundred nucleotides. These overhangs are not merely a remnant of DNA replication but rather are the res...


    pub_type: 杂志文章


    authors: Lloyd NR,Dickey TH,Hom RA,Wuttke DS

    更新日期:2016-09-27 00:00:00

  • Essential cysteines in 3-deoxy-D-manno-octulosonic acid 8-phosphate synthase from Escherichia coli: analysis by chemical modification and site-directed mutagenesis.

    abstract::The enzyme 3-deoxy-D-manno-octulosonic acid 8-phosphate synthase (EC 4.1. 2.16) (KDO 8-P synthase) that catalyzes the condensation of D-arabinose 5-phosphate (A 5-P) with phosphoenolpyruvate (PEP) to give 3-deoxy-D-manno-octulosonic acid 8-phosphate (KDO 8-P) and inorganic phosphate (Pi) was inactivated by the thiol-m...


    pub_type: 杂志文章


    authors: Salleh HM,Patel MA,Woodard RW

    更新日期:1996-07-09 00:00:00

  • Microfibril-associated glycoprotein: characterization of the bovine gene and of the recombinantly expressed protein.

    abstract::Microfibrils having a diameter of 10-12 nm, found either in association with elastin or independently, are an important component of the extracellular matrix of many tissues. Because isolation of native proteins composing the microfibrils has proven difficult, information on structure/function relationships is limited...


    pub_type: 杂志文章


    authors: Bashir MM,Abrams WR,Rosenbloom J,Kucich U,Bacarra M,Han MD,Brown-Augsberger P,Mecham R,Rosenbloom J

    更新日期:1994-01-18 00:00:00

  • Solution structure of the biologically relevant G-quadruplex element in the human c-MYC promoter. Implications for G-quadruplex stabilization.

    abstract::The nuclease hypersensitivity element III(1) (NHE III(1)) of the c-MYC promoter strongly controls the transcriptional activity of the c-MYC oncogene. The purine-rich strand of the NHE III(1) element has been shown to be a silencer element for c-MYC transcription upon formation of a G-quadruplex structure. We have dete...


    pub_type: 杂志文章


    authors: Ambrus A,Chen D,Dai J,Jones RA,Yang D

    更新日期:2005-02-15 00:00:00

  • Conformation of myosin interdomain interactions during contraction: deductions from muscle fibers using polarized fluorescence.

    abstract::Myosin cross-bridge subfragment 1 (S1) is the ATP catalyzing motor protein in muscle. It consists of three domains that catalyze ATP and bind actin (catalytic), conduct energy transduction (converter), and transport the load (lever arm). Force development during contraction is thought to result from rotary lever arm m...


    pub_type: 杂志文章


    authors: Burghardt TP,Cruz-Walker AR,Park S,Ajtai K

    更新日期:2001-04-17 00:00:00

  • Peptidyl aldehydes as reversible covalent inhibitors of SRC homology 2 domains.

    abstract::Src homology 2 (SH2) domains are phosphotyrosine- (pY-) binding modules found in a variety of signal-transducing proteins and constitute an important class of drug targets for the treatment of signaling related diseases/conditions. To date, a large number of peptidic as well as nonpeptidic SH2 domain inhibitors have b...


    pub_type: 杂志文章


    authors: Park J,Fu H,Pei D

    更新日期:2003-05-06 00:00:00

  • Model for general acid-base catalysis by the hammerhead ribozyme: pH-activity relationships of G8 and G12 variants at the putative active site.

    abstract::We have used nucleobase substitution and kinetic analysis to test the hypothesis that hammerhead catalysis occurs by a general acid-base mechanism, in which nucleobases are directly involved in deprotonation of the attacking 2'-hydroxyl group and protonation of the 5'-oxygen that serves as the leaving group in the cle...


    pub_type: 杂志文章


    authors: Han J,Burke JM

    更新日期:2005-05-31 00:00:00

  • Carbohydrate chains of human thyrotropin are differentially susceptible to endoglycosidase removal on combined and free polypeptide subunits.

    abstract::The accessibility of the asparagine-linked carbohydrate chains of human thyrotropin (hTSH) and free alpha and beta subunits was investigated by their susceptibility to endoglycosidases H and F as well as to peptide:N-glycosidase F. Iodinated hTSH or subunits were incubated with a commercial enzyme preparation containi...


    pub_type: 杂志文章


    authors: Ronin C,Papandreou MJ,Canonne C,Weintraub BD

    更新日期:1987-09-08 00:00:00

  • Effects of exposure to low pH on the lateral mobility of influenza hemagglutinin expressed at the cell surface: correlation between mobility inhibition and inactivation.

    abstract::To investigate the possible role of viral glycoprotein mobility in membrane fusion, fluorescence photobleaching recovery was employed to study the effects of exposure to mildly acidic pH (required to convert many viral fusion proteins to the fusion-active form) on the lateral mobility of influenza hemagglutinin (HA) p...


    pub_type: 杂志文章


    authors: Gutman O,Danieli T,White JM,Henis YI

    更新日期:1993-01-12 00:00:00

  • Human CD4 Metastability Is a Function of the Allosteric Disulfide Bond in Domain 2.

    abstract::CD4 is expressed on the surface of specific leukocytes where it plays a key role in the activation of immunostimulatory T-cells and acts as a primary receptor for HIV-1 entry. CD4 has four ecto-domains (D1-D4) of which D1, D2, and D4 contain disulfide bonds. Although disulfide bonds commonly serve structural or cataly...


    pub_type: 杂志文章


    authors: Owen GR,Channell JA,Forsyth VT,Haertlein M,Mitchell EP,Capovilla A,Papathanasopoulos M,Cerutti NM

    更新日期:2016-04-19 00:00:00

  • Importance of asparagine-61 and asparagine-109 to the angiogenic activity of human angiogenin.

    abstract::Two distinct regions of angiogenin are critical for angiogenic activity: a catalytic site capable of cleaving RNA and a noncatalytic site, encompassing residues 60-68, which may bind to an endothelial cell-surface receptor [Hallahan, T. W., Shapiro, R., & Vallee, B. L. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 2222-222...


    pub_type: 杂志文章


    authors: Hallahan TW,Shapiro R,Strydom DJ,Vallee BL

    更新日期:1992-09-01 00:00:00

  • Crystal structure analysis of a mutant Escherichia coli thioredoxin in which lysine 36 is replaced by glutamic acid.

    abstract::The structure of a mutant Escherichia coli thioredoxin with a glutamic acid substituted for a conserved lysine at position 36 adjacent to the active site has been solved using molecular replacement and refined at 2.0-A resolution to a crystallographic residual of 19.9%. The mutant was crystallized in an orthorhombic s...


    pub_type: 杂志文章


    authors: Nikkola M,Gleason FK,Fuchs JA,Eklund H

    更新日期:1993-05-18 00:00:00

  • Probing the communication between the regulatory and catalytic domains of a protein tyrosine kinase, Csk.

    abstract::Protein tyrosine kinases (PTKs) are important regulators of mammalian cell function and their own activities are tightly regulated. Underlying their tight regulation, all PTKs contain multiple regulatory domains in addition to a catalytic domain. C-terminal Src kinase (Csk) contains a catalytic domain and a regulatory...


    pub_type: 杂志文章


    authors: Lin X,Ayrapetov MK,Lee S,Parang K,Sun G

    更新日期:2005-02-08 00:00:00

  • Conformational changes of HIV reverse transcriptase subunits on formation of the heterodimer: correlation with kcat and Km.

    abstract::The reverse transcriptase (RT) from the human immunodeficiency virus (HIV) is initially expressed as a 66-kDa protein and is subsequently proteolytically processed in vivo to form a 66-kDa/51-kDa heterodimer. Comparison of circular dichroism spectra of the 66-kDa, 51-kDa, and heterodimeric forms of RT indicates that t...


    pub_type: 杂志文章


    authors: Anderson SF,Coleman JE

    更新日期:1992-09-08 00:00:00

  • Stability and reversibility of higher ordered structure of interphase chromatin: continuity of deoxyribonucleic acid is not required for maintenance of folded structure.

    abstract::The organization of the higher order structure of chromatin has been examined in chicken erythrocyte. Chromatin solubilized during the time course of a gentle micrococcal nuclease digestion of nuclei shows a continuous variation in the distribution of molecular weights. Electron microscopy studies of large chromatin f...


    pub_type: 杂志文章


    authors: Ruiz-Carrillo A,Puigdomènech P,Eder G,Lurz R

    更新日期:1980-06-10 00:00:00

  • Human erythrocytic purine nucleoside phosphorylase: reaction with sugar-modified nucleoside substrates.

    abstract::The kinetic parameters (Km and Vmax) of sugar-modified analogues of inosine and guanosine have been determined with human erythrocytic purine nucleoside phosphorylase (PNP). Steric alterations at the 2' and 3' positions greatly lessened or abolished substrate activity. However, the 5'-deoxy- and 2',5'-dideoxy-beta-D-r...


    pub_type: 杂志文章


    authors: Stoeckler JD,Cambor C,Parks RE Jr

    更新日期:1980-01-08 00:00:00

  • Reactions of isocytochrome c2 in the photosynthetic electron transfer chain of Rhodobacter sphaeroides.

    abstract::Rhodobacter sphaeroides strains lacking cytochrome c2 (cyt c2), the normal electron donor to P870+ in light-oxidized reaction center (RC) complexes, are unable to grow photosynthetically. However, spd mutations that suppress the photosynthetic deficiency of cyt c2 mutants elevate levels of the cyt c2 isoform, isocyt c...


    pub_type: 杂志文章


    authors: Witthuhn VC Jr,Gao J,Hong S,Halls S,Rott MA,Wraight CA,Crofts AR,Donohue TJ

    更新日期:1997-01-28 00:00:00

  • GTP hydrolysis of cell division protein FtsZ: evidence that the active site is formed by the association of monomers.

    abstract::The essential prokaryotic cell division protein FtsZ is a tubulin homologue that forms a ring at the division site. FtsZ forms polymers in a GTP-dependent manner. Recent biochemical evidence has shown that FtsZ forms multimeric structures in vitro and in vivo and functions as a self-activating GTPase. Structural analy...


    pub_type: 杂志文章


    authors: Scheffers DJ,de Wit JG,den Blaauwen T,Driessen AJ

    更新日期:2002-01-15 00:00:00

  • Stereochemical studies of the beta-elimination reactions at aldehydic abasic sites in DNA: endonuclease III from Escherichia coli, sodium hydroxide, and Lys-Trp-Lys.

    abstract::The DNA strand cleavage reaction catalyzed by endonuclease III from Escherichia coli (endo III) on the 3'-side of aldehyde abasic sites proceeds by a syn beta-elimination involving abstraction of the 2'-pro-S proton and formation of a trans alpha,beta-unsaturated aldose product; we previously reported the same stereoc...


    pub_type: 杂志文章


    authors: Mazumder A,Gerlt JA,Absalon MJ,Stubbe J,Cunningham RP,Withka J,Bolton PH

    更新日期:1991-01-29 00:00:00

  • Interactions of poly(N epsilon, N epsilon, N epsilon-trimethyllysine) and poly(N delta, N delta, N delta-trimethylornithine) with polynucleotides: salt dissociation and thermal denaturation.

    abstract::The interaction of poly(N epsilon, N epsilon, N epsilon-trimethyl-L-lysine) ([Lys(Me3)]n) and poly(N delta, N delta, N delta-trimethyl-L-ornithine) ([Orn(Me3)]n) with polynucleotides was studied by thermal denaturation, viscosity, and dissociation by salt. The methylated polymers decrease the viscosity of DNA in propo...


    pub_type: 杂志文章


    authors: Granados EN,Bello J

    更新日期:1980-07-08 00:00:00

  • Differential scanning calorimetric study of a homologous series of fully hydrated saturated mixed-chain C(X):C(X + 6) phosphatidylcholines.

    abstract::The successive high-resolution differential scanning calorimetric (DSC) thermograms for aqueous dispersions of a homologous series of mixed-chain phosphatidylcholines, C(X):C(X + 6)PC, have been recorded and analyzed. In this series of saturated mixed-chain phosphatidylcholines, the total number of carbon atoms in the...


    pub_type: 杂志文章


    authors: Wang ZQ,Lin HN,Huang CH

    更新日期:1990-07-31 00:00:00

  • Differential effects on energy transduction processes by fluorescamine derivatives in rat liver mitochondria.

    abstract::Intact rat liver mitochondria were treated with compounds derived from the reaction of fluorescamine with various types of primary amines, including the mycosamine-containing antibiotics amphotericin B and nystatin. The effect of varying amounts of these compounds on ATPase-linked inorganic phosphate (Pi) formation on...


    pub_type: 杂志文章


    authors: Ramirez F,Shiuan D,Tu SI,Marecek JF

    更新日期:1980-04-29 00:00:00