journal
MENU ▼
Read by QxMD icon Read
search

Protein Science: a Publication of the Protein Society

journal
https://www.readbyqxmd.com/read/28187530/structural-and-dynamic-characterization-of-a-freestanding-acyl-carrier-protein-involved-in-the-biosynthesis-of-cyclic-lipopeptide-antibiotics
#1
Subrata Paul, Hiroaki Ishida, Leonard T Nguyen, Zhihong Liu, Hans J Vogel
Friulimicin is a cyclic lipodecapeptide antibiotic that is produced by Actinoplanes friuliensis. Like the related lipopeptide drug daptomycin, the peptide skeleton of friulimicin is synthesized by a large multienzyme Nonribosomal Peptide Synthetase (NRPS) system. The LipD protein plays a major role in the acylation reaction of friulimicin. The attachment of the fatty acid group promotes its antibiotic activity. Phylogenetic analysis reveals that LipD is most closely related to other freestanding Acyl Carrier Proteins (ACPs), for which the genes are located near to NRPS gene clusters...
February 10, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28187517/selective-cysteine-modification-of-metal-free-human-metallothionein-1a-and-its-isolated-domain-fragments-solution-structural-properties-revealed-via-esi-ms
#2
Gordon W Irvine, Melissa Santolini, Martin J Stillman
Human metallothionein 1a, a protein with two cysteine-rich metal-binding domains (α with 11 Cys and β with 9), was analyzed in its metal-free form by selective, covalent Cys modification coupled with ESI-MS techniques. The modification profiles of the isolated β- and α-fragments reacted with p-benzoquinone (Bq), N-ethylmalemide (NEM) and iodoacetamide (IAM) were compared with the full length protein using ESI-mass spectral data to follow the reaction pathway. Under denaturing conditions at low pH, the reaction profile with each modifier followed pathways that resulted in stochastic, Normal distributions of species whose maxima was equal to the mol...
February 10, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28176403/single-molecule-imaging-reveals-the-translocation-and-dna-looping-dynamics-of-hepatitis-c-virus-ns3-helicase
#3
Chang-Ting Lin, Felix Tritschler, Kyung Suk Lee, Meigang Gu, Charles M Rice, Taekjip Ha
No abstract text is available yet for this article.
February 8, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28176394/single-molecule-force-spectroscopy-reveals-the-effect-of-bip-chaperone-on-protein-folding
#4
María Paz Ramírez, Maira Rivera, Diego Quiroga-Roger, Andrés Bustamante, Marcela Vega, Mauricio Baez, Elias M Puchner, Christian A M Wilson
BiP (Immunoglobulin Binding Protein) is a member of the Hsp70 chaperones that participates in protein folding in the endoplasmic reticulum. The function of BiP relies on cycles of ATP hydrolysis driving the binding and release of its substrate proteins. It still remains unknown how BiP affects the protein folding pathway and there has been no direct demonstration showing which folding state of the substrate protein is bound by BiP, as previous work has used only peptides. Here, we employ optical tweezers for single molecule force spectroscopy experiments to investigate how BiP affects the folding mechanism of a complete protein and how this effect depends on nucleotides...
February 8, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28168866/complete-topology-inversion-can-be-part-of-normal-membrane-protein-biogenesis
#5
Nicholas B Woodall, Sarah Hadley, Ying Yin, James U Bowie
The topology of helical membrane proteins is generally defined during insertion of the transmembrane helices, yet it is now clear that it is possible for topology to change under unusual circumstances. It remains unclear, however, if topology reorientation is part of normal biogenesis. For dual topology dimer proteins such as the multidrug transporter EmrE, there may be evolutionary pressure to allow topology flipping so that the populations of both orientations can be equalized. We previously demonstrated that when EmrE is forced to insert in a distorted topology, topology flipping of the first transmembrane helix can occur during translation...
February 7, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28168800/david-davies-structural-biologist-and-mentor
#6
Brian Matthews
No abstract text is available yet for this article.
February 7, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28168783/a-novel-signal-transduction-protein-combination-of-solute-binding-and-tandem-pas-like-sensor-domains-in-one-polypeptide-chain
#7
R Wu, R Wilton, M Cuff, M Endres, G Babnigg, J N Edirisinghe, C S Henry, A Joachimiak, M Schiffer, And P R Pokkuluri
We report the structural and biochemical characterization of a novel periplasmic ligand-binding protein, Dret_0059, from Desulfohalobium retbaense DSM 5692, an organism isolated from the Salt Lake Retba in Senegal. The structure of the protein consists of a unique combination of a periplasmic solute binding protein (SBP) domain at the N-terminal and a tandem PAS-like sensor domain at the C-terminal region. SBP domains are found ubiquitously and their best known function is in solute transport across membranes...
February 7, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28168761/functional-clues-from-the-crystal-structure-of-an-orphan-periplasmic-ligand-binding-protein-from-treponema-pallidum
#8
Chad A Brautigam, Ranjit K Deka, Wei Z Liu, Diana R Tomchick, Michael V Norgard
The spirochete Treponema pallidum is the causative agent of syphilis, a sexually transmitted infection of major global importance. Other closely related subspecies of Treponema also are the etiological agents of the endemic treponematoses, such as yaws, pinta, and bejel. The inability of T. pallidum and its close relatives to be cultured in vitro has prompted efforts to characterize T. pallidum's proteins structurally and biophysically, particularly those potentially relevant to treponemal membrane biology, with the goal of possibly revealing the functions of those proteins...
February 7, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28168758/crystal-structure-of-tbc1d15-gtpase-activating-protein-gap-domain-and-its-activity-on-rab-gtpases
#9
Yan-Na Chen, Xin Gu, X Edward Zhou, Weidong Wang, Dandan Cheng, Yinghua Ge, Fei Ye, H Eric Xu, Zhengbing Lv
TBC1D15 belongs to the TBC (Tre-2/Bub2/Cdc16) domain family and functions as a GTPase-activating protein (GAP) for Rab GTPases. So far, the structure of TBC1D15 or the TBC1D15·Rab complex has not been determined, thus, its catalytic mechanism on Rab GTPases is still unclear. In this study, we solved the crystal structures of the Shark and Sus TBC1D15 GAP domains, to 2.8 Å and 2.5 Å resolution, respectively. Shark-TBC1D15 and Sus-TBC1D15 belong to the same subfamily of TBC domain-containing proteins, and their GAP-domain structures are highly similar...
February 7, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28168755/palbociclib-can-overcome-mutations-in-cyclin-dependent-kinase-6-that-break-hydrogen-bonds-between-the-drug-and-the-protein
#10
Stella Hernandez Maganhi, Patrizia Jensen, Ignez Caracelli, Julio Zukerman Schpector, Stefan Fröhling, Ran Friedman
Inhibition of cyclin dependent kinases (CDKs) 4 and 6 prevent cells from entering the synthesis phase of the cell cycle. CDK4 and 6 are therefore important drug targets in various cancers. The selective CDK4/6 inhibitor palbociclib is approved for the treatment of breast cancer and has shown activity in a cellular model of mixed lineage leukaemia (MLL)-rearranged acute myeloid leukaemia (AML). We studied the interactions of palbociclib and CDK6 using molecular dynamics simulations. Analysis of the simulations suggested several interactions that stabilised the drug in its binding site and that were not observed in the crystal structure of the protein-drug complex...
February 7, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28160335/targeting-human-set1-mll-family-of-proteins
#11
REVIEW
Masoud Vedadi, Levi Blazer, Mohammad S Eram, Dalia Barsyte-Lovejoy, Cheryl H Arrowsmith, Taraneh Hajian
The SET1 family of proteins, and in particular MLL1, are essential regulators of transcription and key mediators of normal development and disease. Here, we summarize the detailed characterization of the methyltransferase activity of SET1 complexes and the role of the key subunits, WDR5, RbBP5, ASH2L and DPY30. We present new data on full kinetic characterization of human MLL1, MLL3, SET1A and SET1B trimeric, tetrameric and pentameric complexes to elaborate on substrate specificities and compare our findings with what has been reported before...
February 4, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28152563/structural-thermodynamic-and-phosphatidylinositol-3-phosphate-binding-properties-of-phafin2
#12
Tuo-Xian Tang, Ami Jo, Jingren Deng, Jeffrey F Ellena, Iulia M Lazar, Richey M Davis, Daniel G S Capelluto
Phafin2 is a phosphatidylinositol 3-phosphate- (PtdIns(3)P) binding protein involved in the regulation of endosomal cargo trafficking and lysosomal induction of autophagy. Binding of Phafin2 to PtdIns(3)P is mediated by both its PH and FYVE domains. However, there are no studies on the structural basis, conformational stability, and lipid interactions of Phafin2 to better understand how this protein participates in signaling at the surface of endomembrane compartments. Here, we show that human Phafin2 is a moderately elongated monomer of ∼28 kDa with an intensity-average hydrodynamic diameter of ∼ 7 nm...
February 2, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28142214/epitope-mapping-of-borrelia-burgdorferi-ospc-protein-in-homodimeric-fold
#13
Adam Norek, Lubomír Janda
In current work, we used recombinant OspC protein derived from B. afzelii strain BRZ31 in the native homodimeric fold for mice immunisation and following selection process to produce three mouse monoclonal antibodies able to bind to variable parts of up to five different OspC proteins. Applying the combination of mass spectrometry assisted epitope mapping and affinity based theoretical prediction we have localised regions responsible for antigen-antibody interactions and approximate epitopes' amino acid composition...
January 31, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28142198/incorporating-an-allosteric-regulatory-site-in-an-antibody-through-backbone-design
#14
Olga Khersonsky, Sarel J Fleishman
Allosteric regulation underlies living cells' ability to sense changes in nutrient and signaling-molecule concentrations, but the ability to computationally design allosteric regulation into non-allosteric proteins has been elusive. Allosteric-site design is complicated by the requirement to encode the relative stabilities of active and inactive conformations of the same protein in the presence and absence of both ligand and effector. To address this challenge, we used Rosetta to design the backbone of the flexible heavy-chain complementarity-determining region 3 (HCDR3), and used geometric matching and sequence optimization to place a Zn(2+) -coordination site in a fluorescein-binding antibody...
January 31, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28127814/transport-capabilities-of-environmental-pseudomonads-for-sulfur-compounds
#15
Sarah Zerbs, Peter J Korajczyk, Philippe H Noirot, Frank R Collart
Sulfur is an essential element in plant rhizospheres and microbial activity plays a key role in increasing the biological availability of sulfur in soil environments. To better understand the mechanisms facilitating the exchange of sulfur-containing molecules in soil, we profiled the binding specificities of eight previously uncharacterized ABC transporter solute-binding proteins from plant-associated Pseudomonads. A high-throughput screening procedure indicated eighteen significant organosulfur binding ligands, with at least one high-quality screening hit for each protein target...
January 27, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28127810/crystallographic-and-mutational-analyses-of-cystathionine-%C3%AE-synthase-in-the-h2-s-synthetic-gene-cluster-in-lactobacillus-plantarum
#16
Yasuyuki Matoba, Tomoki Yoshida, Hisae Izuhara-Kihara, Masafumi Noda, Masanori Sugiyama
Cystathionine β-synthase (CBS) catalyzes the formation of L-cystathionine from L-serine and L-homocysteine. The resulting L-cystathionine is decomposed into L-cysteine, ammonia, and α-ketobutylic acid by cystathionine γ-lyase (CGL). This reverse transsulfuration pathway, which is catalyzed by both enzymes, mainly occurs in eukaryotic cells. The eukaryotic CBS and CGL have recently been recognized as major physiological enzymes for the generation of hydrogen sulfide (H2 S). In some bacteria, including the plant-derived lactic acid bacterium Lactobacillus plantarum, the CBS- and CGL-encoding genes form a cluster in their genomes...
January 27, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28120389/modulating-the-wnt-signaling-pathway-with-small-molecules
#17
REVIEW
Freddi Huan Tran, Jie J Zheng
Wnt signaling is a critical component during embryonic development and also plays an important role in regulating adult tissue homeostasis. Abnormal activation of Wnt signaling has been implicated in many cancers, while reduced activity of Wnt signaling leads to poor wound healing and structural formations. Thus, extensive efforts have been focused on developing small molecules that have potential to either inhibit or activate the pathway, hoping these molecules can offer leads for novel approaches in treating different human diseases...
January 25, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28097776/molecular-mechanisms-underlying-deoxy-adp-pi-activation-of-pre-powerstroke-myosin
#18
Sarah G Nowakowski, Michael Regnier, Valerie Daggett
Myosin activation is a viable approach to treat systolic heart failure. We previously demonstrated that striated muscle myosin is a promiscuous ATPase that can use most nucleoside triphosphates as energy substrates for contraction. When 2-deoxy ATP (dATP) is used, it acts as a myosin activator, enhancing cross-bridge binding and cycling. In vivo, we have demonstrated that elevated dATP levels increase basal cardiac function and rescues function of infarcted rodent and pig hearts. Here we investigate the molecular mechanism underlying this physiological effect...
January 18, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28097774/structural-and-functional-insights-into-thermally-stable-cytochrome-c-from-a-thermophile
#19
Sotaro Fujii, Hiroya Oki, Kazuki Kawahara, Daisuke Yamane, Masaru Yamanaka, Takahiro Maruno, Yuji Kobayashi, Misa Masanari, Satoshi Wakai, Hirofumi Nishihara, Tadayasu Ohkubo, Yoshihiro Sambongi
Thermophilic Hydrogenophilus thermoluteolus cytochrome c' (PHCP) exhibits higher thermal stability than a mesophilic counterpart, Allochromatium vinosum cytochrome c' (AVCP), which has a homo-dimeric structure and ligand-binding ability. To understand the thermal stability mechanism and ligand-binding ability of the thermally stable PHCP protein, the crystal structure of PHCP was first determined. It formed a homo-dimeric structure, the main chain root mean square deviation (rmsd) value between PHCP and AVCP being 0...
January 18, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28097769/high-resolution-crystal-structures-of-human-kynurenine-aminotransferase-i-bound-to-plp-cofactor-and-in-complex-with-aminooxyacetate
#20
Naveed A Nadvi, Noeris K Salam, Joohong Park, Fady N Akladios, Vimal Kapoor, Charles A Collyer, Mark D Gorrell, And W Bret Church
In this study we report two high-resolution structures of the pyridoxal 5' phosphate (PLP)-dependent enzyme kynurenine aminotransferase-I (KAT-I). One is the native structure with the cofactor in the PLP form bound to Lys247 with the highest resolution yet available for KAT-I at 1.28 Å resolution, and the other with the general PLP-dependent aminotransferase inhibitor, aminooxyacetate (AOAA) covalently bound to the cofactor at 1.54 Å. Only small conformational differences are observed in the vicinity of the aldimine (oxime) linkage with which the PLP forms the Schiff base with Lys247 in the 1...
January 18, 2017: Protein Science: a Publication of the Protein Society
journal
journal
31107
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"