abstract：:The folding of many globular proteins from the unfolded (U) to the native (N) state appears to be describable by a two-state N ↔ U model, which has led to the general belief that protein folding occurs in a highly cooperative manner. One reason for the widespread belief in "two-state folding" is that protein folding r...

journal_title：Biochemistry

authors： Jethva PN,Udgaonkar JB

更新日期：2018-10-09 00:00:00

abstract：:Cytochrome c binds to cardiolipin (CL) on the inner mitochondrial membrane during the initial stages of apoptosis where it oxidizes CL, promoting its release into the cytoplasm where it initiates apoptosis. Previous work has identified interaction sites on cytochrome c involved in the cytochrome c-CL interaction. The ...

journal_title：Biochemistry

authors： Elmer-Dixon MM,Bowler BE

更新日期：2018-10-02 00:00:00

abstract：:Members of the uracil-DNA glycosylase (UDG) enzyme family recognize and bind uracil, sequestering it within the binding site pocket and catalyzing the cleavage of the base from the deoxyribose, leaving an abasic site. The recognition and binding are passive and rely on innate dynamic motions of DNA wherein base pairs ...

journal_title：Biochemistry

authors： Carr CE,Khutsishvili I,Gold B,Marky LA

更新日期：2018-10-02 00:00:00

abstract：:Glycosylases specifically recognize and flip their target base out of the DNA helix into the enzyme's active site. Our simulations show that a partially flipped state, already present in free DNA carrying a T:G mispair, becomes the more probable state compared to the closed state after binding of thymine DNA glycosyla...

journal_title：Biochemistry

authors： Kanaan N,Imhof P

更新日期：2018-10-02 00:00:00

abstract：:We have previously designed and synthesized small-molecule inhibitors that reduce Vibrio cholerae virulence in vitro by targeting the transcription factor ToxT. Here we report the synthesis and biological activity of derivatives of our previous bicyclic, fatty acid-like inhibitors. All of the synthesized derivatives s...

journal_title：Biochemistry

authors： Woodbrey AK,Onyango EO,Kovacikova G,Kull FJ,Gribble GW

更新日期：2018-09-25 00:00:00

abstract：:A cutinase-type polyesterase from Saccharomonospora viridis AHK190 (Cut190) has been shown to degrade the inner block of polyethylene terephthalate. A unique feature of Cut190 is that its function and stability are regulated by Ca2+ binding. Our previous crystal structure analysis of Cut190S226P showed that one Ca2+ b...

journal_title：Biochemistry

authors： Numoto N,Kamiya N,Bekker GJ,Yamagami Y,Inaba S,Ishii K,Uchiyama S,Kawai F,Ito N,Oda M

更新日期：2018-09-11 00:00:00

abstract：:3-Deoxy-d- manno-2-octulosonate-8-phosphate (KDO8P) synthase catalyzes the first step of lipopolysaccharide biosynthesis, namely condensation of phosphoenolpyruvate (PEP) with arabinose 5-phosphate (A5P), to produce KDO8P. We have characterized Campylobacter jejuni KDO8P synthase and its inhibition by KDO8P oxime. It ...

journal_title：Biochemistry

authors： Gama SR,Balachandran N,Berti PJ

更新日期：2018-09-11 00:00:00

abstract：:RosB catalyzes the formation of 8-aminoriboflavin 5'-phosphate (AFP), the key intermediate in roseoflavin biosynthesis, from the metabolic precursors riboflavin 5'-phosphate (RP, also known as FMN) and glutamate. The conversion of the aromatic methyl group at position 8 in RP into the aromatic amine in AFP occurs via ...

journal_title：Biochemistry

authors： Kapoor I,Nair SK

更新日期：2018-09-11 00:00:00

abstract：:The ras oncogene products (H-Ras, K-Ras, and N-Ras) have been regarded as some of the most promising targets for anticancer drug discovery because their activating mutations are frequently found in human cancers. Nonetheless, molecular targeted therapy for them is currently unavailable. Here, we report the discovery o...

journal_title：Biochemistry

authors： Matsumoto S,Hiraga T,Hayashi Y,Yoshikawa Y,Tsuda C,Araki M,Neya M,Shima F,Kataoka T

更新日期：2018-09-11 00:00:00

abstract：:Chemoenzymatic glycan remodeling by endoglycosidase-catalyzed deglycosylation and reglycosylation is emerging as an attractive approach for producing homogeneous glycoforms of antibodies, and the success of this approach depends on the discovery of efficient endoglycosidases and their glycosynthase mutants. We report ...

journal_title：Biochemistry

authors： Tong X,Li T,Li C,Wang LX

更新日期：2018-09-04 00:00:00

abstract：:Inexpensive, straightforward, and rapid medical diagnostics are becoming increasingly important for disease identification in time- and resource-limited settings. Previous attempts to link oligonucleotide-based aptamers and hammerhead ribozymes to form ligand-induced ribozymes have been successful in identifying a var...

journal_title：Biochemistry

authors： Liao AM,Pan W,Benson JC,Wong AD,Rose BJ,Caltagirone GT

更新日期：2018-08-28 00:00:00

abstract：:Fom3, the antepenultimate enzyme in the fosfomycin biosynthetic pathway in Streptomyces spp., is a class B cobalamin-dependent radical SAM methyltransferase that catalyzes methylation of (5'-cytidylyl)-2-hydroxyethylphosphonate (2-HEP-CMP) to form (5'-cytidylyl)-2-hydroxypropylphosphonate (2-HPP-CMP). Previously, the ...

journal_title：Biochemistry

authors： McLaughlin MI,van der Donk WA

更新日期：2018-08-21 00:00:00

abstract：:DB2277, a heterocyclic diamidine, is a successful design for mixed base pair (bp) DNA sequence recognition. The compound has a central aza-benzimidazole group that forms two H-bonds with a GC bp that has flanking AT bps. The nuclear magnetic resonance structure of the DB2277-DNA complex with an AAGATA recognition site...

journal_title：Biochemistry

authors： Harika NK,Wilson WD

更新日期：2018-08-21 00:00:00

abstract：:In fosfomycin biosynthesis, the hydrolysis of cytidylyl ( S)-2-hydroxypropylphosphonate [( S)-HPP-CMP] to afford ( S)-HPP is the only uncharacterized step. Because FomD is an uncharacterized protein with a DUF402 domain that is encoded in the fosfomycin biosynthetic gene cluster, FomD was hypothesized to be responsibl...

journal_title：Biochemistry

authors： Sato S,Miyanaga A,Kim SY,Kuzuyama T,Kudo F,Eguchi T

更新日期：2018-08-14 00:00:00

abstract：:To test for on target toxicity of a new chemical entity, it is important to have comparable binding affinities of the compound in the target proteins from humans and the test species. To evaluate our myeloid cell leukemia-1 (Mcl-1) inhibitors, we tested them against rodent Mcl-1 and found a significant loss of binding...

journal_title：Biochemistry

authors： Zhao B,Arnold AL,Coronel MA,Lee JH,Lee T,Olejniczak ET,Fesik SW

更新日期：2018-08-14 00:00:00

abstract：:Protein-protein interactions mediate the vast majority of cellular processes. Though protein interactions obey basic chemical principles also within the cell, the in vivo physiological environment may not allow for equilibrium to be reached. Thus, in vitro measured thermodynamic affinity may not provide a complete pic...

journal_title：Biochemistry

authors： Cohen-Khait R,Schreiber G

更新日期：2018-08-07 00:00:00

abstract：:In recent years, there has been dramatic growth in the study of RNA. RNA has gone from being known as an intermediate in the central dogma of molecular biology to a molecule with a large diversity of structure and function that is involved in all aspects of biology. As new functions are rapidly discovered, it has beco...

journal_title：Biochemistry

authors： Moon MH,Hilimire TA,Sanders AM,Schneekloth JS Jr

更新日期：2018-08-07 00:00:00

abstract：:Kinases play a critical role in cellular signaling and are dysregulated in a number of diseases, such as cancer, diabetes, and neurodegeneration. Therapeutics targeting kinases currently account for roughly 50% of cancer drug discovery efforts. The ability to explore human kinase biochemistry and biophysics in the lab...

journal_title：Biochemistry

authors： Albanese SK,Parton DL,Işık M,Rodríguez-Laureano L,Hanson SM,Behr JM,Gradia S,Jeans C,Levinson NM,Seeliger MA,Chodera JD

更新日期：2018-08-07 00:00:00

abstract：:The dehaloperoxidase-hemoglobin (DHP) from the terebellid polychaete Amphitrite ornata is a multifunctional hemoprotein that catalyzes the oxidation of a wide variety of substrates, including halo/nitrophenols, haloindoles, and pyrroles, via peroxidase and/or peroxygenase mechanisms. To probe whether substrate substit...

journal_title：Biochemistry

authors： McGuire AH,Carey LM,de Serrano V,Dali S,Ghiladi RA

更新日期：2018-07-31 00:00:00

abstract：:Pyrrolocytosine (PC) and 2-aminopurine (2AP) are fluorescent nucleobase analogues of the DNA nucleobases cytosine and adenine, respectively, and form base pairs with guanine and thymine. Both fluorescent nucleobases are used extensively as probes for local structure in nucleic acids as the fluorescence properties of P...

journal_title：Biochemistry

authors： Bull GD,Thompson KC

更新日期：2018-07-31 00:00:00

abstract：:Protein binding specificities can be manipulated by redesigning contacts that already exist at an interface or by expanding the interface to allow interactions with residues adjacent to the original binding site. Previously, we developed a strategy, called AnchorDesign, for expanding interfaces around linear binding e...

journal_title：Biochemistry

authors： Hussain M,Angus SP,Kuhlman B

更新日期：2018-07-31 00:00:00

abstract：:Our previous studies revealed that interaction of fibrin with the very low density lipoprotein (VLDL) receptor plays a prominent role in transendothelial migration of leukocytes and thereby inflammation. The major goal of our subsequent studies is to establish the structural basis for this interaction. As the first st...

journal_title：Biochemistry

authors： Banerjee K,Yakovlev S,Gruschus JM,Medved L,Tjandra N

更新日期：2018-07-31 00:00:00

abstract：:A subgroup of enzymes in the NAD(P)H:FMN reductase family is comprised of flavin reductases from two-component monooxygenase systems. The diverging structural feature in these FMN reductases is a π-helix centrally located at the tetramer interface that is generated by the insertion of an amino acid in a conserved α4 h...

journal_title：Biochemistry

authors： Musila JM,L Forbes D,Ellis HR

更新日期：2018-07-31 00:00:00

abstract：:Large primary deuterium kinetic isotope effects (1° DKIEs) on enzyme-catalyzed hydride transfer may be observed when the transferred hydride tunnels through the energy barrier. The following 1° DKIEs on kcat/ Km and relative reaction driving force are reported for wild-type and mutant glycerol-3-phosphate dehydrogenas...

journal_title：Biochemistry

authors： Reyes AC,Amyes TL,Richard JP

更新日期：2018-07-24 00:00:00

abstract：:Protein prenylation involves the attachment of a hydrophobic isoprenoid moiety to the C-terminus of proteins. Several small GTPases, including members of the Ras and Rho subfamilies, require prenylation for their normal and pathological functions. Recent work has suggested that SmgGDS proteins regulate the prenylation...

journal_title：Biochemistry

authors： Jennings BC,Lawton AJ,Rizk Z,Fierke CA

更新日期：2018-07-24 00:00:00

abstract：:While two-component systems (TCSs), composed of a sensor histidine kinase (HK) and a response regulator, are the main signaling pathways in bacteria, global TCS activity remains poorly described. Here, we report the kinetic parameters of the HK autophosphorylation reaction using previously uncharacterized γ-phosphate-...

journal_title：Biochemistry

authors： Chase OM,Espinasse A,Wilke KE,Carlson EE

更新日期：2018-07-24 00:00:00

abstract：:Phospholipids and sterols play multiple roles in cells. In addition to establishing barriers between compartments, they also provide the matrix for assembly and function of a large variety of catalytic processes. Lipid composition is a highly regulated feature of biological membranes, yet its implications for membrane...

journal_title：Biochemistry

authors： Autzen HE,Koldsø H,Stansfeld PJ,Gourdon P,Sansom MSP,Nissen P

更新日期：2018-07-17 00:00:00

abstract：:Duplication of a single β-strand that forms part of a β-sheet in photoactive yellow protein (PYP) was found to produce two approximately isoenergetic protein conformations, in which either the first or the second copy of the duplicated β-strand participates in the β-sheet. Whereas one conformation (big-loop) is more s...

journal_title：Biochemistry

authors： Kumar A,Nokhrin S,Woloschuk RM,Woolley GA

更新日期：2018-07-17 00:00:00

abstract：:Nonribosomal peptide synthetases (NRPSs) are megasynthetases that require complex and specific interactions between multiple domains and proteins to functionally produce a metabolite. MbtH-like proteins (MLPs) are integral components of many NRPSs and interact directly with the adenylation domain of the megasynthetase...

journal_title：Biochemistry

authors： Schomer RA,Park H,Barkei JJ,Thomas MG

更新日期：2018-07-17 00:00:00

abstract：:Erwinia ligand-gated ion channel (ELIC) is a bacterial homologue of vertebrate pentameric ligand-gated ion channels (pLGICs) and has proven to be a valuable model for understanding the structure and function of this important protein family. There is nevertheless still a question about whether molecular details can be...

journal_title：Biochemistry

authors： Mosesso R,Dougherty DA,Lummis SCR

更新日期：2018-07-10 00:00:00

abstract：:S-Adenosylmethionine (SAM+) serves as the principal methylating agent in biological systems, but the thermodynamic basis of its reactivity does not seem to have been clearly established. Here, we show that methionine, methanol, and H+ combine to form S-methylmethionine (SMM+) with a temperature-independent equilibrium...

journal_title：Biochemistry

authors： Lewis CA Jr,Wolfenden R

更新日期：2018-07-03 00:00:00

abstract：:Amino acid selective isotope labeling is an important nuclear magnetic resonance technique, especially for larger proteins, providing strong bases for the unambiguous resonance assignments and information concerning the structure, dynamics, and intermolecular interactions. Amino acid selective 15N labeling suffers fro...

journal_title：Biochemistry

authors： Sugiki T,Furuita K,Fujiwara T,Kojima C

更新日期：2018-07-03 00:00:00

abstract：:Cold-shock proteins (Csps) are expressed at lower-than-optimum temperatures, and they function as RNA chaperones; however, no structural studies on psychrophilic Csps have been reported. Here, we aimed to investigate the structure and dynamics of the Csp of psychrophile Colwellia psychrerythraea 34H, ( Cp-Csp). Althou...

journal_title：Biochemistry

authors： Lee Y,Kwak C,Jeong KW,Durai P,Ryu KS,Kim EH,Cheong C,Ahn HC,Kim HJ,Kim Y

更新日期：2018-07-03 00:00:00

abstract：:Reactive metabolites of environmental chemicals and drugs can cause site specific damage to the p53 tumor suppressor gene in a major pathway for genotoxicity. We report here a high-throughput, cell-free, 96-well plate magnetic bead-enzyme system interfaced with LC-MS/MS sequencing for bioactivating test chemicals and ...

journal_title：Biochemistry

authors： Malla S,Kadimisetty K,Jiang D,Choudhary D,Rusling JF

更新日期：2018-07-03 00:00:00

abstract：:RNA binding proteins play an important role in regulating alternative pre-mRNA splicing and in turn cellular gene expression. Many of these RNA binding proteins occur as gene families with members sharing a high degree of primary structure identity and domain organization yet have tissue-specific expression patterns a...

journal_title：Biochemistry

authors： Pina JM,Reynaga JM,Truong AAM,Keppetipola NM

更新日期：2018-07-03 00:00:00

abstract：:Studying the evolution of catalytically promiscuous enzymes like those from the N-succinylamino acid racemase/ o-succinylbenzoate synthase (NSAR/OSBS) subfamily can reveal mechanisms by which new functions evolve. Some enzymes in this subfamily have only OSBS activity, while others catalyze OSBS and NSAR reactions. We...

journal_title：Biochemistry

authors： Odokonyero D,McMillan AW,Ramagopal UA,Toro R,Truong DP,Zhu M,Lopez MS,Somiari B,Herman M,Aziz A,Bonanno JB,Hull KG,Burley SK,Romo D,Almo SC,Glasner ME

更新日期：2018-07-03 00:00:00

abstract：:NahE and PhdJ are bifunctional hydratase-aldolases in bacterial catabolic pathways for naphthalene and phenanthrene, respectively. Bacterial species with these pathways can use polycyclic aromatic hydrocarbons (PAHs) as sole sources of carbon and energy. Because of the harmful properties of PAHs and their widespread d...

journal_title：Biochemistry

authors： LeVieux JA,Medellin B,Johnson WH Jr,Erwin K,Li W,Johnson IA,Zhang YJ,Whitman CP

更新日期：2018-06-26 00:00:00

abstract：:The substrate profiles for three uncharacterized enzymes (YcjM, YcjT, and YcjU) that are expressed from a cluster of 12 genes ( ycjM-W and ompG) of unknown function in Escherichia coli K-12 were determined. Through a comprehensive bioinformatic and steady-state kinetic analysis, the catalytic function of YcjT was dete...

journal_title：Biochemistry

authors： Mukherjee K,Narindoshvili T,Raushel FM

更新日期：2018-05-15 00:00:00

abstract：:An important but poorly characterized contribution to the thermodynamics of protein-DNA interactions is the loss of entropy that occurs from restricting the conformational freedom of amino acid side chains. The effect of restricting the flexibility of several side chains at a protein-DNA interface may be comparable in...

journal_title：Biochemistry

authors： Baird-Titus JM,Thapa M,Doerdelmann T,Combs KA,Rance M

更新日期：2018-05-15 00:00:00

abstract：:The relative quantitative importance of the factors that determine the fidelity of translation is largely unknown, which makes predicting the extent to which the degeneracy of the genetic code can be broken challenging. Our strategy of using orthogonal tRNA/aminoacyl tRNA synthetase pairs to precisely direct the incor...

journal_title：Biochemistry

authors： Schmitt MA,Biddle W,Fisk JD

更新日期：2018-05-15 00:00:00