journal
MENU ▼
Read by QxMD icon Read
search

Biochemistry

journal
https://www.readbyqxmd.com/read/28102671/structural-analysis-of-glycosylated-intact-hiv-1-gp120-b12-antibody-complex-using-hydroxyl-radical-protein-footprinting
#1
Xiaoyan Li, Oliver C Grant, Keigo Ito, Aaron Wallace, Shixia Wang, Peng Zhao, Lance Wells, Shan Lu, Robert J Woods, Joshua S Sharp
Glycoprotein gp120 is a surface antigen and virulence factor of the human immunodeficiency virus-1 (HIV-1). Broadly neutralizing antibodies (bNAbs) that are reactive to gp120 from a variety of HIV isolates offer hope for the development of broadly effective immunogens for vaccination purposes, if the interactions between gp120 and bNAbs can be understood. From a structural perspective, gp120 is a particularly difficult system due to its size, the presence of multiple flexible regions, and the large amount of glycosylation, all of which are important in gp120-bNAb interactions...
January 19, 2017: Biochemistry
https://www.readbyqxmd.com/read/28102665/cosolute-and-crowding-effects-on-a-side-by-side-protein-dimer
#2
Alex J Guseman, Gary J Pielak
The effects of small (~102 Da) and larger (>103 Da) cosolutes on protein stability are broadly understood: excluding volume stabilizes proteins, and chemical interactions are stabilizing when repulsive, but destabilizing when attractive. Proteins, however, rarely work alone. Here, we investigate the effects of small and larger cosolutes on the equilibrium stability of the simplest defined protein-protein interactions, the side-by-side homodimer formed by the A34F variant of the 56-residue B1 domain of protein G...
January 19, 2017: Biochemistry
https://www.readbyqxmd.com/read/28102071/temperature-induced-misfolding-in-prion-protein-evidences-of-multiple-partially-disordered-states-stabilized-by-non-native-hydrogen-bonds
#3
Neharika G Chamachi, Suman Chakrabarty
The structural basis of misfolding pathways of a cellular Prion (PrP(C)) into the toxic scrapie form (PrP(SC)) and identification of possible intermediates (e.g. PrP(*)) still eludes us. In this work, we have used a cumulative ~65µs of Replica Exchange Molecular Dynamics simulation data to construct the conformational free energy landscapes and capture the structural and thermodynamic characteristics associated with various stages of the thermal denaturation process in human Prion protein. The temperature dependent free energy surfaces consist of multiple metastable states stabilized by non-native contacts and hydrogen bonds, thus rendering the protein prone towards misfolding...
January 19, 2017: Biochemistry
https://www.readbyqxmd.com/read/28098985/hmgb1-stimulates-activity-of-polymerase-%C3%AE-on-nucleosome-substrates
#4
Angela Balliano, Fanfan Hao, Catherine Njeri, Lata Balakrishnan, Jeffrey J Hayes
The process of base excision repair (BER) recognizes and repairs small lesions or inappropriate bases on DNA through either a short-patch or long-patch pathway. The enzymes involved in BER have been well-characterized on DNA substrates, and, somewhat surprisingly, many of these enzymes, including several DNA glycosylases, AP endonuclease (APE), FEN1 endonuclease, and DNA ligases, have been shown to have activity on DNA substrates within nucleosomes. DNA polymerase β (Pol β), however, exhibits drastically reduced or no activity on nucleosomal DNA...
January 18, 2017: Biochemistry
https://www.readbyqxmd.com/read/28098450/the-serum-amyloid-p-component-sap-interactome-in-human-plasma-containing-physiological-calcium-levels
#5
Ebbe Toftgaard Poulsen, Kata Wolff Pedersen, Anna Maria Marzeda, Jan Johannes Enghild
The pentraxin serum amyloid p component (SAP) is secreted by the liver and found in plasma at a concentration of approximately 30 mg/L. SAP is a 25 kDa homo-pentamer known to bind both protein and non-protein ligands, all in a calcium-dependent manner. The function of SAP is unclear, but likely involves the humoral innate immune system spanning the complement system, inflammation, and coagulation. Also, SAP is known to binding to the generic structure of amyloid deposits and possibly to protect these against proteolysis...
January 18, 2017: Biochemistry
https://www.readbyqxmd.com/read/28098447/the-stories-tryptophans-tell-exploring-protein-dynamics-of-heptosyltransferase-i-from-escherichia-coli
#6
Joy M Cote, Carlos Andres Ramirez-Mondragon, Zarek S Siegel, Daniel Joseph Czyzyk, Jiali Gao, Yuk Yin Sham, Ishita Mukerji, Erika A Taylor
Heptosyltransferase I (HepI) catalyzes the addition of a single L-glycero-β-D-manno-heptose sugar (heptose) onto the membrane incorporated Kdo2-Lipid A as part of the biosynthesis of the core region of lipopolysaccharide (LPS). Gram-negative bacteria with gene knockouts of HepI have reduced virulence with enhanced susceptibility to hydrophobic antibiotics, making design of inhibitors against HepI of interest. Previous studies have shown that HepI protein dynamics are partially rate limiting, and therefore disruption of protein dynamics might provide a new strategy for inhibiting HepI...
January 18, 2017: Biochemistry
https://www.readbyqxmd.com/read/28032976/dynamics-of-lysine-as-a-heme-axial-ligand-nmr-analysis-of-the-chlamydomonas-reinhardtii-hemoglobin-thb1
#7
Matthew R Preimesberger, Ananya Majumdar, Juliette T J Lecomte
Nitrate metabolism in Chlamydomonas reinhardtii involves THB1, a monomeric hemoglobin thought to function as a nitric oxide dioxygenase (NOD). NOD activity requires dioxygen and nitric oxide binding followed by a one-electron oxidation of the heme iron and nitrate release. Unlike pentacoordinate flavohemoglobins, which are efficient NODs, THB1 uses two iron axial ligands: the conserved proximal histidine and a distal lysine (Lys53). As a ligand in both the oxidized (ferric) and reduced (ferrous) states, Lys53 is expected to lower the reorganization energy associated with electron transfer and therefore facilitate reduction of the ferric enzyme...
January 18, 2017: Biochemistry
https://www.readbyqxmd.com/read/28029780/a-transition-metal-binding-trimeric-%C3%AE-%C3%AE-crystallin-from-methane-producing-thermophilic-archaea-methanosaeta-thermophila
#8
Shanti Swaroop Srivastava, Aditya Anand Jamkhindikar, Rajeev Raman, Maroor K Jobby, Swathi Chadalawada, Rajan Sankaranarayanan, Yogendra Sharma
βγ-Crystallins are important constituents of the vertebrate eye lens, whereas in microbes, they are prevalent as Ca(2+)-binding proteins. In archaea, βγ-crystallins are conspicuously confined to two methanogens, viz., Methanosaeta and Methanosarcina. One of these, i.e., M-crystallin from Methanosarcina acetivorans, has been shown to be a typical Ca(2+)-binding βγ-crystallin. Here, with the aid of a high-resolution crystal structure and isothermal titration calorimetry, we report that "Methallin", a βγ-crystallin from Methanosaeta thermophila, is a trimeric, transition metal-binding protein...
January 18, 2017: Biochemistry
https://www.readbyqxmd.com/read/28092444/engineering-of-the-bacillus-circulans-%C3%AE-galactosidase-product-specificity
#9
Huifang Yin, Tjaard Pijning, Xiangfeng Meng, Lubbert Dijkhuizen, Sander Sebastiaan van Leeuwen
Microbial β-galactosidase enzymes are widely used as biocatalysts in industry to produce prebiotic galactooligosaccharides (GOS) from lactose. GOS mixtures are used as beneficial additives in infant formula to mimic the prebiotic effects of human milk oligosaccharides (hMOS). The structural variety in GOS mixtures is significantly lower than in hMOS. Since this structural complexity is considered as the basis for the multiple biological functions of hMOS, it is important to broaden the variety of GOS structures...
January 16, 2017: Biochemistry
https://www.readbyqxmd.com/read/28092443/kinetics-and-structure-of-a-cold-adapted-hetero-octameric-atp-phosphoribosyltransferase
#10
Rozanne Stroek, Ying Ge, Paul D Talbot, Mateusz K Glok, Klaudia E Bernas, Catherine M Thomson, Eoin R Gould, Magnus S Alphey, Huanting Liu, Gordon J Florence, James H Naismith, Rafael Guimaraes da Silva
ATP-phosphoribosyltransferase (ATPPRT) catalyses the first step in histidine biosynthesis, the condensation of ATP and 5-phospho-α-D-ribosyl-1-pyrophosphate to generate N(1)-(5-phospho-β-D-ribosyl)-ATP and inorganic pyrophosphate. The enzyme is allosterically inhibited by histidine. Two forms of ATPPRT, encoded by the hisG gene, exist in nature, depending on the species. The long form, HisGL, is a single polypeptide chain with catalytic and regulatory domains. The short form, HisGS, lacks a regulatory domain, and cannot bind histidine...
January 16, 2017: Biochemistry
https://www.readbyqxmd.com/read/28085267/cyclotide-structure-and-function-the-role-of-membrane-binding-and-permeation
#11
Sónia Troeira Henriques, David J Craik
There is a growing interest in the use of peptides as therapeutic drugs and, in particular, in the potential of cyclotides - a family of cyclic peptides with remarkable stability and amenability to sequence engineering- as scaffolds in drug design. As well as having an ultra-stable structure, many natural cyclotides have intrinsic biological activities with potential pharmaceutical or agricultural applications. Some cyclotides also have the ability cross membrane barriers and to enter into cells; in particular, cyclotides belonging to the Möbius and bracelet subfamilies have been found to harbor lipid-binding domains, which allow for the specific recognition of phosphatidylethanolamine (PE)-phospholipids in biological membranes...
January 13, 2017: Biochemistry
https://www.readbyqxmd.com/read/28045507/linear-free-energy-relationship-analysis-of-transition-state-mimicry-by-3-deoxy-d-arabino-heptulosonate-7-phosphate-dahp-oxime-a-dahp-synthase-inhibitor-and-phosphate-mimic
#12
Naresh Balachandran, Frederick To, Paul J Berti
3-Deoxy-d-arabino-heptulosonate-7-phosphate (DAHP) synthase catalyzes an aldol-like reaction of phosphoenolpyruvate (PEP) with erythrose 4-phosphate (E4P) to form DAHP in the first step of the shikimate biosynthetic pathway. DAHP oxime, in which an oxime replaces the ketone, is a potent inhibitor, with Ki = 1.5 μM. Linear free energy relationship (LFER) analysis of DAHP oxime inhibition using DAHP synthase mutants revealed an excellent correlation between transition state stabilization and inhibition. The equations of LFER analysis were rederived to formalize the possibility of proportional, rather than equal, changes in the free energies of transition state stabilization and inhibitor binding, in accord with the fact that the majority of LFER analyses in the literature demonstrate nonunity slopes...
January 13, 2017: Biochemistry
https://www.readbyqxmd.com/read/28035815/binding-site-configurations-probe-the-structure-and-dynamics-of-the-zinc-finger-of-nemo-nf-%C3%AE%C2%BAb-essential-modulator
#13
Ryan C Godwin, Ryan L Melvin, William H Gmeiner, Freddie R Salsbury
Zinc-finger proteins are regulators of critical signaling pathways for various cellular functions, including apoptosis and oncogenesis. Here, we investigate how binding site protonation states and zinc coordination influence protein structure, dynamics, and ultimately function, as these pivotal regulatory proteins are increasingly important for protein engineering and therapeutic discovery. To better understand the thermodynamics and dynamics of the zinc finger of NEMO (NF-κB essential modulator), as well as the role of zinc, we present results of 20 μs molecular dynamics trajectories, 5 μs for each of four active site configurations...
January 13, 2017: Biochemistry
https://www.readbyqxmd.com/read/28080034/the-mechanism-of-the-flavoprotein-6-hydroxy-l-nicotine-oxidase-ph-and-solvent-isotope-effects-and-identification-of-key-active-site-residues
#14
Paul F Fitzpatrick, Fatemeh Chadegani, Shengnan Zhang, Vi Dougherty
The flavoenzyme L-6-hydroxynicotine oxidase (LHNO) is a member of the monoamine oxidase family that catalyzes the oxidation of (S)-6-hydroxynicotine to 6-hydroxypseudooxynicotine during microbial catabolism of nicotine. While the enzyme has long been understood to catalyze oxidation of carbon-carbon bond, it has recently been shown to catalyze oxidation of a carbon-nitrogen bond (Fitzpatrick et al., Biochemistry 55, 697-703). The effects of pH and mutagenesis of active site residues have now been utilized to study the mechanism and the roles of active site residues...
January 12, 2017: Biochemistry
https://www.readbyqxmd.com/read/28029774/the-structure-of-murine-n-1-acetylspermine-oxidase-reveals-molecular-details-of-vertebrate-polyamine-catabolism
#15
Tove Sjögren, Carola M Wassvik, Arjan Snijder, Anna Aagaard, Taichi Kumanomidou, Louise Barlind, Tim P Kaminski, Akiko Kashima, Takehiro Yokota, Ola Fjellström
N(1)-Acetylspermine oxidase (APAO) catalyzes the conversion of N(1)-acetylspermine or N(1)-acetylspermidine to spermidine or putrescine, respectively, with concomitant formation of N-acetyl-3-aminopropanal and hydrogen peroxide. Here we present the structure of murine APAO in its oxidized holo form and in complex with substrate. The structures provide a basis for understanding molecular details of substrate interaction in vertebrate APAO, highlighting a key role for an asparagine residue in coordinating the N(1)-acetyl group of the substrate...
January 12, 2017: Biochemistry
https://www.readbyqxmd.com/read/28005340/probing-the-flexibility-of-the-catalytic-nucleophile-in-the-lyase-catalytic-pocket-of-human-dna-polymerase-%C3%AE-with-unnatural-lysine-analogues
#16
Sasha M Daskalova, Chandrabali Bhattacharya, Larisa M Dedkova, Sidney M Hecht
DNA polymerase β (Pol β) is a key enzyme in mammalian base excision repair (BER), contributing stepwise 5'-deoxyribose phosphate (dRP) lyase and "gap-filling" DNA polymerase activities. The lyase reaction is believed to occur via a β-elimination reaction following the formation of a Schiff base between the dRP group at the pre-incised apurinic/apyrimidinic site and the ε-amino group of Lys72. To probe the steric constraints on the formation and subsequent resolution of the putative Schiff base intermediate within the lyase catalytic pocket, Lys72 was replaced with each of several nonproteinogenic lysine analogues...
January 12, 2017: Biochemistry
https://www.readbyqxmd.com/read/28076679/molecular-dynamics-simulations-for-deciphering-structural-basis-of-recognition-of-pre-let-7-mirnas-by-lin28
#17
Chhaya Sharma, Debasisa Mohanty
LIN28 protein inhibits biogenesis of miRNAs belonging to let-7 family by binding to precursor forms of miRNAs. Over expression of LIN28 and low levels of let-7 miRNAs are associated with several forms of cancer cells. We have performed multiple explicit solvent molecular dynamics simulations ranging from 200 to 500 ns in length on different isoforms of preE-let7 in complex with LIN28 and also in isolation to identify structural features and key specificity determining residues (SDR) important for inhibitory role of LIN28...
January 11, 2017: Biochemistry
https://www.readbyqxmd.com/read/28074650/revisiting-the-val-ile-mutation-in-mammalian-and-bacterial-no-synthases-a-spectroscopic-and-kinetic-study
#18
Marine Weisslocker-Schaetzel, Mehdi Lembrouk, Jerome Santolini, Pierre Dorlet
Nitric oxide (NO) is produced in mammals by the nitric oxide synthase (NOS) isoforms at a catalytic site comprising a heme associated with a biopterin cofactor. Through genome sequencing, proteins with high homology to the oxygenase domain of NOSs have been identified, in particular in bacteria. The active site is highly conserved except for a valine residue in the distal pocket that is replaced by an isoleucine in bacteria. This switch was previously reported to influence the kinetics of the reaction. We have used the V346I mutant of the mouse inducible NOS (iNOS) as well as the I224V mutant of the NOS from Bacillus subtilis (bsNOS) to study their spectroscopic signatures in solution and look for potential structural differences compared to their respective wild types...
January 11, 2017: Biochemistry
https://www.readbyqxmd.com/read/28074648/mispacking-and-the-fitness-landscape-of-the-green-fluorescent-protein-chromophore-milieu
#19
Shounak Banerjee, Christian D Schenkelberg, Thomas B Jordan, Julia M Reimertz, Emily E Crone, Donna E Crone, Christopher Bystroff
The auto-catalytic maturation of the chromophore in green fluorescent protein (GFP) was thought to require the precise positioning of the side chains surrounding it in the core of the protein, many of which are strongly conserved among homologous fluorescent proteins. In this study, we screened for green fluorescence in an exhaustive set of point mutations of seven residues that make up the chromophore microenvironment, excluding R96 and E222 because mutations of these positions have been previously characterized...
January 11, 2017: Biochemistry
https://www.readbyqxmd.com/read/28074646/differences-in-protein-concentration-dependence-for-nucleation-and-elongation-in-light-chain-amyloid-formation
#20
Luis Miguel Blancas-Mejía, Pinaki Misra, Marina Ramirez-Alvarado
Light chain (AL) amyloidosis is a lethal disease characterized by the deposition of the immunoglobulin light chain into amyloid fibrils, resulting in organ dysfunction and failure. Amyloid fibrils have the ability to self-propagate recruiting soluble protein into the fibril by a nucleation-polymerization mechanism, characteristic of auto-catalytic reactions. Experimental data suggest the existence of a critical concentration to initiate fibril formation. As such, the initial concentration of soluble amyloidogenic protein is expected to have a profound effect on the rate of fibril formation...
January 11, 2017: Biochemistry
journal
journal
23359
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"