Works Published in 2007
Displaying works 1 - 20 of 40 in total
Sorted by most recent date added to the index first, which may not be the same as publication date order.
2007 journal article
Characterization of Helicobacter pyloriγ-Glutamyltranspeptidase Reveals the Molecular Basis for Substrate Specificity and a Critical Role for the Tyrosine 433-Containing Loop in Catalysis†,‡
Biochemistry, 46(46), 13407–13414.
MeSH headings : Binding Sites; Catalysis; Crystallography, X-Ray; Glutamic Acid / chemistry; Glutamic Acid / metabolism; Helicobacter pylori / enzymology; Hydrolysis; Kinetics; Ligands; Models, Molecular; Protein Structure, Tertiary; Substrate Specificity; Tyrosine / chemistry; Tyrosine / genetics; gamma-Glutamyltransferase / chemistry; gamma-Glutamyltransferase / genetics; gamma-Glutamyltransferase / metabolism
TL;DR:
Results provide evidence that access to this buried site may occur through conformational changes in the Tyr 433-containing loop, as disruption of the intricate hydrogen-bond network responsible for optimal placement of Tyr 433 significantly diminishes catalytic activity.
(via Semantic Scholar)
Source: Crossref
Added: October 29, 2020
2007 journal article
Characterization of Human UDP-Glucose Dehydrogenase Reveals Critical Catalytic Roles for Lysine 220 and Aspartate 280†
Biochemistry, 46(2), 369–378.
MeSH headings : Amino Acid Substitution; Aspartic Acid / chemistry; Catalytic Domain / genetics; Dimerization; Humans; In Vitro Techniques; Kinetics; Lysine / chemistry; Models, Molecular; Mutagenesis, Site-Directed; Protein Structure, Quaternary; Recombinant Proteins / chemistry; Recombinant Proteins / genetics; Recombinant Proteins / metabolism; Uridine Diphosphate Glucose Dehydrogenase / chemistry; Uridine Diphosphate Glucose Dehydrogenase / genetics; Uridine Diphosphate Glucose Dehydrogenase / metabolism
TL;DR:
Three putative active site residues were identified and gel filtration of this substrate-binding mutant also determined it was a dimer, indicating that hexameric quaternary structure is not critical for catalysis.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2007 journal article
Structural Basis for Induced Fit Mechanisms in DNA Recognition by the Pdx1 Homeodomain†,‡
Biochemistry, 46(11), 2948–2957.
MeSH headings : Amino Acid Sequence; Animals; Base Sequence; Cricetinae; Crystallization; Crystallography, X-Ray; DNA / metabolism; Homeodomain Proteins / genetics; Homeodomain Proteins / metabolism; Mesocricetus; Models, Molecular; Molecular Sequence Data; Nucleic Acid Conformation; Protein Conformation; Sequence Alignment; Trans-Activators / genetics; Trans-Activators / metabolism
TL;DR:
It is demonstrated that the homeodomain reproduces the binding specificity of the full-length protein and an induced fit model is proposed that depends on the DNA conformation and provides a mechanism for nonlocal contributions to binding specificity.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Sources: Crossref, ORCID
Added: February 10, 2020
2007 journal article
Dynamic analysis of unwinding yarn from cylindrical packages, part III: The three-region model revisited
Textile Research Journal, 77.
Source: NC State University Libraries
Added: August 6, 2018
2007 journal article
NMR assignment of the N-terminal repeat domain of Bacillus subtilis ClpC
BIOMOLECULAR NMR ASSIGNMENTS, 1(2), 163–165.
author keywords: ClpC; Bacillus subtilis; N-domain; genetic competence; HSP100/AAA+
MeSH headings : Amino Acid Sequence; Bacterial Proteins / chemistry; Connexins / chemistry; Heat-Shock Proteins / chemistry; Magnetic Resonance Spectroscopy / methods; Protein Structure, Tertiary; Repetitive Sequences, Amino Acid
TL;DR:
The backbone and side-chain assignments of the N-terminal repeat domain (residues 1–145) of ClpC from Bacillus subtilis are presented.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2007 journal article
Anti-inflammatory properties of Lactobacillus gasseri expressing manganese superoxide dismutase using the interleukin 10-deficient mouse model of colitis
AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY, 293(4), G729–G738.
author keywords: probiotic; Lactobacilli; oxidative stress; inflammatory bowel disease
MeSH headings : Animals; Anti-Inflammatory Agents / therapeutic use; Colitis / drug therapy; Colitis / pathology; Colon / pathology; Cyclooxygenase 2 / metabolism; Disease Models, Animal; Immunohistochemistry; Interleukin-10 / deficiency; Lactobacillus / enzymology; Mice; Peroxidase / metabolism; Probiotics / therapeutic use; Specific Pathogen-Free Organisms; Superoxide Dismutase / biosynthesis; Superoxide Dismutase / therapeutic use
TL;DR:
This study demonstrates that L. gasseri producing MnSOD has significant anti-inflammatory activity that reduces the severity of colitis in the IL-10-deficient mouse.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2007 journal article
Abh and AbrB control of Bacillus subtilis antimicrobial gene expression
JOURNAL OF BACTERIOLOGY, 189(21), 7720–7732.
MeSH headings : Bacillus subtilis / genetics; Bacillus subtilis / growth & development; Bacterial Proteins / genetics; Bacterial Proteins / metabolism; Base Sequence; Binding Sites; DNA-Binding Proteins / genetics; DNA-Binding Proteins / metabolism; Gene Expression Regulation, Bacterial; Genes, Bacterial; Kinetics; Molecular Sequence Data; Mutation; Plasmids; Transcription Factors / genetics; Transcription Factors / metabolism
TL;DR:
Abh is part of the complex interconnected regulatory system that controls gene expression during the transition from active growth to stationary phase and is subject to a degree of AbrB-affording negative regulation.
(via Semantic Scholar)
jb.asm.org (publisher PDF)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Source: Web Of Science
Added: August 6, 2018
2007 journal article
Trranscript profiling of a conifer pathosystem: response of Pinus sylvestris root tissues to pathogen (Heterobasidion annosum) invasion
TREE PHYSIOLOGY, 27(10), 1441–1458.
author keywords: antimicrobial peptide; microarray; peroxidase; phenylopropanoid pathway; pine; plant defence
MeSH headings : Fungi / physiology; Gene Expression Profiling; Gene Expression Regulation, Plant; Oligonucleotide Array Sequence Analysis; Pinus sylvestris / metabolism; Plant Diseases / microbiology; Plant Proteins / genetics; Plant Proteins / metabolism; Plant Roots / metabolism; Plant Roots / microbiology; Plant Roots / ultrastructure; Seedlings
TL;DR:
The similarity of the expression profiling pattern observed in this pathosystem to those documented in crop pathology suggests that angiosperms and gymnosperms use similar genetic programs in responding to invasive growth by microbial pathogens.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018
2007 journal article
Peptide binding proclivities of calcium loaded calbindin-D28k
FEBS LETTERS, 581(24), 4778–4782.
author keywords: calbindin-D28k; NMR; chemical shift; peptides; modeling
MeSH headings : Animals; Calbindin 1; Calbindins; Calcium / metabolism; Circular Dichroism; Models, Molecular; Nuclear Magnetic Resonance, Biomolecular; Peptides / metabolism; Protein Binding; Protein Structure, Tertiary; Rats; S100 Calcium Binding Protein G / metabolism; Titrimetry
TL;DR:
It is shown that calbindin‐D28k undergoes significant conformational changes upon binding calcium, whereas only minor changes occur when binding target peptides in its Ca2+‐loaded state.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2007 journal article
Infection of cells by Sindbis virus at low temperature
Virology, 362(2), 461–467.
MeSH headings : Animals; Cell Fusion; Cell Line; Cricetinae; Endocytosis; Microscopy, Immunoelectron; Neutral Red / metabolism; Sindbis Virus / physiology; Temperature; Time Factors; Viral Plaque Assay; Virus Internalization
TL;DR:
The ability of Sind Bis virus to infect Baby Hamster Kidney cells at temperatures which block endocytosis is examined and it is found that under these conditions Sindbis virus infects cells in a temperature- and time-dependent fashion.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: NC State University Libraries
Added: August 6, 2018
2007 journal article
High-frequency reversion of geminivirus replication protein mutants during infection
JOURNAL OF VIROLOGY, 81(20), 11005–11015.
MeSH headings : Arabidopsis / virology; Geminiviridae / genetics; Geminiviridae / physiology; Mosaic Viruses; Mutation, Missense; Plant Diseases / virology; Plant Viruses / genetics; Plant Viruses / physiology; Viral Proteins / genetics; Viral Proteins / metabolism; Viral Proteins / physiology; Virus Replication / genetics
TL;DR:
There is strong selection for reversion of the TGMV L148V and CaLCuV L145A mutations but that the nature of the selected revertants is influenced by both the viral background and host components.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
3. Good Health and Well-being
(OpenAlex)
13. Climate Action
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2007 journal article
Conformational energy and structure in canonical and noncanonical forms of tRNA determined by temperature analysis of the rate of s(4)U8-C13 photocrosslinking
RNA, 13(11), 2000–2011.
author keywords: RNA tertiary structure; photocrosslinking rates; activation energy; conformational energy; T-1 excited state lifetimes
MeSH headings : Base Composition; Base Sequence; Buffers; Cytosine / chemistry; Molecular Sequence Data; Nucleic Acid Conformation; RNA, Bacterial; RNA, Transfer / chemistry; RNA, Transfer, Met / chemistry; RNA, Transfer, Phe / chemistry; RNA, Transfer, Val / chemistry; Temperature; Thermodynamics; Uracil / chemistry
TL;DR:
Measurements of the temperature dependence of the rate constants for photocrosslinking between the s(4)U8 and C13 have been used to investigate the tRNA conformational energy and structure in Escherichia coli tRNA(Val), tRNA (Phe), and t RNA(fMet) under different conditions.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
7. Affordable and Clean Energy
(OpenAlex)
Source: Web Of Science
Added: August 6, 2018
2007 journal article
E-coli glutamyl-tRNA synthetase is inhibited by anticodon stem-loop domains and a minihelix
RNA BIOLOGY, 4(2), 85–92.
author keywords: designed inhibitors; RNA fragments; competitive inhibitors; identity elements; modified RNA; translation
MeSH headings : Anticodon / chemistry; Base Sequence; Binding Sites; Enzyme Inhibitors / chemistry; Escherichia coli / enzymology; Escherichia coli Proteins / antagonists & inhibitors; Escherichia coli Proteins / metabolism; Glutamate-tRNA Ligase / antagonists & inhibitors; Glutamate-tRNA Ligase / metabolism; Molecular Sequence Data; Nucleic Acid Conformation; RNA, Transfer / chemistry; Thermodynamics; Transfer RNA Aminoacylation; Uridine / analogs & derivatives; Uridine / chemistry
TL;DR:
The modified ASLGlu-s2U34, though having a higher affinity for ERS, may be released more readily and thus, not be as good an inhibitor as the unmodified ASL, but the RNA constructs are effective tools to study RNA-protein interaction.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2007 journal article
X-ray crystal structural analysis of the binding site in the ferric and oxyferrous forms of the recombinant heme dehaloperoxidase cloned from Amphitrite ornata
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 63, 1094–1101.
MeSH headings : Animals; Binding Sites; Crystallography, X-Ray / methods; Cysteine / chemistry; Escherichia coli / metabolism; Heme / chemistry; Hemoglobins / chemistry; Hydrogen Bonding; Models, Chemical; Models, Molecular; Molecular Conformation; Peroxidases / chemistry; Polychaeta / metabolism; Protein Conformation; Recombinant Proteins / chemistry; Serine / chemistry
TL;DR:
Hydrogen-bonding interaction between His55 and the bound diatomic oxygen molecule provides new insight into the catalytic activation of H(2)O(2), which is essential for peroxidase activity.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2007 journal article
Transformation efficiency of RasQ61 mutants linked to structural features of the switch regions in the presence of Raf
STRUCTURE, 15(12), 1618–1629.
MeSH headings : Catalysis; Crystallography, X-Ray; Guanosine Triphosphate / metabolism; Hydrolysis; Models, Molecular; Mutation; Protein Conformation; raf Kinases / metabolism; ras Proteins / chemistry; ras Proteins / genetics
TL;DR:
The results suggest that Y32 and a water molecule bridging it to the gamma-phosphate in the wild-type structure play a role in GTP hydrolysis in lieu of the Arg finger in the absence of GAP.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
6. Clean Water and Sanitation
(OpenAlex)
Source: Web Of Science
Added: August 6, 2018
2007 journal article
Tandem mass spectrometry acquisition approaches to enhance identification of protein-protein interactions using low-energy collision-induced dissociative chemical crosslinking reagents
RAPID COMMUNICATIONS IN MASS SPECTROMETRY, 21(21), 3395–3408.
MeSH headings : Amino Acid Sequence; Bacillus subtilis / chemistry; Bacillus subtilis / metabolism; Bacterial Proteins / chemistry; Cross-Linking Reagents / chemistry; DNA-Binding Proteins / chemistry; Molecular Sequence Data; Peptide Mapping; Peptides / chemistry; Protein Conformation; Spectrometry, Mass, Electrospray Ionization; Tandem Mass Spectrometry / methods; Transcription Factors / chemistry
TL;DR:
The ability to segregate intrapeptide and interpeptide crosslinks using ITCID represents the first step towards high-throughput analysis of protein-protein cross links using the CID-CXL reagents.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
7. Affordable and Clean Energy
(OpenAlex)
Source: Web Of Science
Added: August 6, 2018
2007 journal article
Location and role of free cysteinyl residues in the Sindbis virus E1 and E2 glycoproteins
JOURNAL OF VIROLOGY, 81(12), 6231–6240.
MeSH headings : Amino Acid Sequence; Animals; Capsid / chemistry; Cell Line; Chromatography, Liquid; Cricetinae; Cysteine / chemistry; Disulfides / chemistry; Iodoacetamide / pharmacology; Mass Spectrometry; Membrane Glycoproteins / chemistry; Molecular Sequence Data; Mutation; Protein Conformation; Viral Envelope Proteins / chemistry
TL;DR:
Native virus particles alkylated with iodoacetamide demonstrated a 4-log decrease in viral infectivity, which suggests that the modification of free cysteinyl residues results in the loss of infectivity by destabilizing the virus particle or that a rearrangement of disulfide bonds, which is required forinfectivity, is blocked by the modification.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2007 review
In vitro reconstitution and affinity purification of catalytically active archaeal box C/D sRNP complexes
[Review of ]. RNA modification, 425, 263–282.
MeSH headings : Chromatography, Affinity / methods; Chromatography, Ion Exchange / methods; Methanococcaceae; Ribonucleoproteins, Small Nuclear / isolation & purification
TL;DR:
A novel affinity purification scheme that uses differentially tagged core proteins and a sequential three-step affinity selection protocol that yields fully assembled and catalytically active box C/D RNPs.
(via Semantic Scholar)
Source: NC State University Libraries
Added: August 6, 2018
2007 journal article
Rapid folding and unfolding of Apaf-1 CARD
JOURNAL OF MOLECULAR BIOLOGY, 369(1), 290–304.
author keywords: caspase recruitment domain; protein folding; folding kinetics; parallel folding channels; sequential mixing stopped-flow
MeSH headings : Apoptotic Protease-Activating Factor 1 / chemistry; Apoptotic Protease-Activating Factor 1 / metabolism; Crystallography, X-Ray; Fluorescence; Kinetics; Models, Biological; Protein Denaturation; Protein Folding; Protein Structure, Secondary; Protein Structure, Tertiary; Thermodynamics
TL;DR:
Examination of the equilibrium and kinetic folding of the CARD of Apaf-1 (apoptotic protease activating factor 1), which consists of 97 amino acid residues, at pH 6 and pH 8 showed that the native ensemble is formed rapidly upon refolding, in contrast to other CARDs in which folding appears to be dominated by formation of kinetic traps.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2007 journal article
Predominantly buried residues in the response regulator Spo0F influence specific sensor kinase recognition
FEBS LETTERS, 581(7), 1425–1429.
author keywords: sporulation; kinases; Spo0F mutants
MeSH headings : Alanine / chemistry; Alanine / genetics; Amino Acid Sequence; Amino Acid Substitution; Bacillus subtilis / metabolism; Bacillus subtilis / physiology; Bacterial Proteins / chemistry; Bacterial Proteins / genetics; Bacterial Proteins / metabolism; Histidine Kinase; Nuclear Magnetic Resonance, Biomolecular; Protein Conformation; Protein Interaction Mapping; Protein Kinases / chemistry; Protein Kinases / metabolism; Protein Structure, Secondary; Spores, Bacterial
TL;DR:
How buried residues and intra‐protein communication networks contribute to precise molecular recognition by ensuring that the correct surface is presented is discussed.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
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