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Article: Computational Site Saturation Mutagenesis of Canonical and Non-Canonical Amino Acids to Probe Protein-Peptide Interactions.

Holden, Jeffrey K / Pavlovicz, Ryan / Gobbi, Alberto / Song, Yifan / Cunningham, Christian N

2022 Volume 9, Page(s) 848689

Abstract: Technologies for discovering peptides as potential therapeutics have rapidly advanced in recent years with significant interest from both academic and pharmaceutical labs. These advancements in turn drive the need for new computational tools to design ... ...

Abstract	Technologies for discovering peptides as potential therapeutics have rapidly advanced in recent years with significant interest from both academic and pharmaceutical labs. These advancements in turn drive the need for new computational tools to design peptides for purposes of advancing lead molecules into the clinic. Here we report the development and application of a new automated tool, AutoRotLib, for parameterizing a diverse set of non-canonical amino acids (NCAAs), N-methyl, or peptoid residues for use with the computational design program Rosetta. In addition, we developed a protocol for designing thioether-cyclized macrocycles within Rosetta, due to their common application in mRNA display using the RaPID platform. To evaluate the utility of these new computational tools, we screened a library of canonical and NCAAs on both a linear peptide and a thioether macrocycle, allowing us to quickly identify mutations that affect peptide binding and subsequently measure our results against previously published data. We anticipate
Language	English
Publishing date	2022-04-14
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2022.848689
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Article: Targeting the Hippo Pathway and Cancer through the TEAD Family of Transcription Factors.

Holden, Jeffrey K / Cunningham, Christian N

Cancers

2018 Volume 10, Issue 3

Abstract: The Hippo pathway is a critical transcriptional signaling pathway that regulates cell growth, proliferation and organ development. The transcriptional enhanced associate domain (TEAD) protein family consists of four paralogous transcription factors that ... ...

Abstract	The Hippo pathway is a critical transcriptional signaling pathway that regulates cell growth, proliferation and organ development. The transcriptional enhanced associate domain (TEAD) protein family consists of four paralogous transcription factors that function to modulate gene expression in response to the Hippo signaling pathway. Transcriptional activation of these proteins occurs upon binding to the co-activator YAP/TAZ whose entry into the nucleus is regulated by Lats1/2 kinase. In recent years, it has become apparent that the dysregulation and/or overexpression of Hippo pathway effectors is implicated in a wide range of cancers, including prostate, gastric and liver cancer. A large body of work has been dedicated to understanding the therapeutic potential of modulating the phosphorylation and localization of YAP/TAZ. However, YAP/TAZ are considered to be natively unfolded and may be intractable as drug targets. Therefore, TEAD proteins present themselves as an excellent therapeutic target for intervention of the Hippo pathway. This review summarizes the functional role of TEAD proteins in cancer and assesses the therapeutic potential of antagonizing TEAD function in vivo.
Language	English
Publishing date	2018-03-20
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers10030081
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Article ; Online: Computational Site Saturation Mutagenesis of Canonical and Non-Canonical Amino Acids to Probe Protein-Peptide Interactions

Jeffrey K. Holden / Ryan Pavlovicz / Alberto Gobbi / Yifan Song / Christian N. Cunningham

Frontiers in Molecular Biosciences, Vol

2022 Volume 9

Abstract	Technologies for discovering peptides as potential therapeutics have rapidly advanced in recent years with significant interest from both academic and pharmaceutical labs. These advancements in turn drive the need for new computational tools to design peptides for purposes of advancing lead molecules into the clinic. Here we report the development and application of a new automated tool, AutoRotLib, for parameterizing a diverse set of non-canonical amino acids (NCAAs), N-methyl, or peptoid residues for use with the computational design program Rosetta. In addition, we developed a protocol for designing thioether-cyclized macrocycles within Rosetta, due to their common application in mRNA display using the RaPID platform. To evaluate the utility of these new computational tools, we screened a library of canonical and NCAAs on both a linear peptide and a thioether macrocycle, allowing us to quickly identify mutations that affect peptide binding and subsequently measure our results against previously published data. We anticipate in silico screening of peptides against a diverse chemical space will be a fundamental component for peptide design and optimization, as more amino acids can be explored in a single in silico screen than an in vitro screen. As such, these tools will enable maturation of peptide affinity for protein targets of interest and optimization of peptide pharmacokinetics for therapeutic applications.
Keywords	noncanonical ; peptide ; macrocycle ; design ; rosetta ; Biology (General) ; QH301-705.5
Subject code	540
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
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Article ; Online: Incorporating NOE-Derived Distances in Conformer Generation of Cyclic Peptides with Distance Geometry.

Wang, Shuzhe / Krummenacher, Kajo / Landrum, Gregory A / Sellers, Benjamin D / Di Lello, Paola / Robinson, Sarah J / Martin, Bryan / Holden, Jeffrey K / Tom, Jeffrey Y K / Murthy, Anastasia C / Popovych, Nataliya / Riniker, Sereina

Journal of chemical information and modeling

2022 Volume 62, Issue 3, Page(s) 472–485

Abstract: Nuclear magnetic resonance (NMR) data from NOESY (nuclear Overhauser enhancement spectroscopy) and ROESY (rotating frame Overhauser enhancement spectroscopy) experiments can easily be combined with distance geometry (DG) based conformer generators by ... ...

Abstract	Nuclear magnetic resonance (NMR) data from NOESY (nuclear Overhauser enhancement spectroscopy) and ROESY (rotating frame Overhauser enhancement spectroscopy) experiments can easily be combined with distance geometry (DG) based conformer generators by modifying the molecular distance bounds matrix. In this work, we extend the modern DG based conformer generator ETKDG, which has been shown to reproduce experimental crystal structures from small molecules to large macrocycles well, to include NOE-derived interproton distances. In noeETKDG, the experimentally derived interproton distances are incorporated into the distance bounds matrix as loose upper (or lower) bounds to generate large conformer sets. Various subselection techniques can subsequently be applied to yield a conformer bundle that best reproduces the NOE data. The approach is benchmarked using a set of 24 (mostly) cyclic peptides for which NOE-derived distances as well as reference solution structures obtained by other software are available. With respect to other packages currently available, the advantages of noeETKDG are its speed and that no prior force-field parametrization is required, which is especially useful for peptides with unnatural amino acids. The resulting conformer bundles can be further processed with the use of structural refinement techniques to improve the modeling of the intramolecular nonbonded interactions. The noeETKDG code is released as a fully open-source software package available at www.github.com/rinikerlab/customETKDG.
MeSH term(s)	Magnetic Resonance Imaging ; Magnetic Resonance Spectroscopy/methods ; Models, Molecular ; Peptides ; Peptides, Cyclic ; Protein Conformation
Chemical Substances	Peptides ; Peptides, Cyclic
Language	English
Publishing date	2022-01-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.1c01165
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Article ; Online: Functional screening in human HSPCs identifies optimized protein-based enhancers of Homology Directed Repair.

Perez-Bermejo, Juan A / Efagene, Oghene / Matern, William M / Holden, Jeffrey K / Kabir, Shaheen / Chew, Glen M / Andreoletti, Gaia / Catton, Eniola / Ennis, Craig L / Garcia, Angelica / Gerstenberg, Trevor L / Hill, Kaisle A / Jain, Aayami / Krassovsky, Kristina / Lalisan, Cassandra D / Lord, Daniel / Quejarro, B Joy / Sales-Lee, Jade / Shah, Meet /

Silva, Brian J / Skowronski, Jason / Strukov, Yuri G / Thomas, Joshua / Veraz, Michael / Vijay, Twaritha / Wallace, Kirby A / Yuan, Yue / Grogan, Jane L / Wienert, Beeke / Lahiri, Premanjali / Treusch, Sebastian / Dever, Daniel P / Soros, Vanessa B / Partridge, James R / Seim, Kristen L

Nature communications

2024 Volume 15, Issue 1, Page(s) 2625

Abstract: Homology Directed Repair (HDR) enables precise genome editing, but the implementation of HDR-based therapies is hindered by limited efficiency in comparison to methods that exploit alternative DNA repair routes, such as Non-Homologous End Joining (NHEJ). ...

Abstract	Homology Directed Repair (HDR) enables precise genome editing, but the implementation of HDR-based therapies is hindered by limited efficiency in comparison to methods that exploit alternative DNA repair routes, such as Non-Homologous End Joining (NHEJ). In this study, we develop a functional, pooled screening platform to identify protein-based reagents that improve HDR in human hematopoietic stem and progenitor cells (HSPCs). We leverage this screening platform to explore sequence diversity at the binding interface of the NHEJ inhibitor i53 and its target, 53BP1, identifying optimized variants that enable new intermolecular bonds and robustly increase HDR. We show that these variants specifically reduce insertion-deletion outcomes without increasing off-target editing, synergize with a DNAPK inhibitor molecule, and can be applied at manufacturing scale to increase the fraction of cells bearing repaired alleles. This screening platform can enable the discovery of future gene editing reagents that improve HDR outcomes.
MeSH term(s)	Humans ; CRISPR-Cas Systems ; Recombinational DNA Repair ; Gene Editing/methods ; DNA Repair ; DNA End-Joining Repair
Language	English
Publishing date	2024-03-23
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-46816-5
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Article ; Online: Allosteric inhibition of HTRA1 activity by a conformational lock mechanism to treat age-related macular degeneration.

Gerhardy, Stefan / Ultsch, Mark / Tang, Wanjian / Green, Evan / Holden, Jeffrey K / Li, Wei / Estevez, Alberto / Arthur, Chris / Tom, Irene / Rohou, Alexis / Kirchhofer, Daniel

Nature communications

2022 Volume 13, Issue 1, Page(s) 5222

Abstract: The trimeric serine protease HTRA1 is a genetic risk factor associated with geographic atrophy (GA), a currently untreatable form of age-related macular degeneration. Here, we describe the allosteric inhibition mechanism of HTRA1 by a clinical Fab ... ...

Abstract	The trimeric serine protease HTRA1 is a genetic risk factor associated with geographic atrophy (GA), a currently untreatable form of age-related macular degeneration. Here, we describe the allosteric inhibition mechanism of HTRA1 by a clinical Fab fragment, currently being evaluated for GA treatment. Using cryo-EM, X-ray crystallography and biochemical assays we identify the exposed LoopA of HTRA1 as the sole Fab epitope, which is approximately 30 Å away from the active site. The cryo-EM structure of the HTRA1:Fab complex in combination with molecular dynamics simulations revealed that Fab binding to LoopA locks HTRA1 in a non-competent conformational state, incapable of supporting catalysis. Moreover, grafting the HTRA1-LoopA epitope onto HTRA2 and HTRA3 transferred the allosteric inhibition mechanism. This suggests a conserved conformational lock mechanism across the HTRA family and a critical role of LoopA for catalysis, which was supported by the reduced activity of HTRA1-3 upon LoopA deletion or perturbation. This study reveals the long-range inhibition mechanism of the clinical Fab and identifies an essential function of the exposed LoopA for activity of HTRA family proteases.
MeSH term(s)	Crystallography, X-Ray ; Epitopes ; High-Temperature Requirement A Serine Peptidase 1/genetics ; High-Temperature Requirement A Serine Peptidase 1/metabolism ; Humans ; Immunoglobulin Fab Fragments/pharmacology ; Macular Degeneration/drug therapy ; Macular Degeneration/genetics ; Macular Degeneration/metabolism ; Serine Endopeptidases/genetics ; Serine Endopeptidases/metabolism
Chemical Substances	Epitopes ; Immunoglobulin Fab Fragments ; HTRA3 protein, human (EC 3.4.21.-) ; High-Temperature Requirement A Serine Peptidase 1 (EC 3.4.21.-) ; HTRA1 protein, human (EC 3.4.21.-) ; Serine Endopeptidases (EC 3.4.21.-)
Language	English
Publishing date	2022-09-05
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-32760-9
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Article ; Online: Optimizing Clinical Reasoning Assessments With Analytic and Holistic Ratings: Examining the Validity, Reliability, and Cost of a Simplified Patient Note Scoring Procedure.

Cheung, Jeffrey J H / Park, Yoon Soo / Aufderheide, Kassidee / Holden, Jaime / Yudkowsky, Rachel

Academic medicine : journal of the Association of American Medical Colleges

2022 Volume 97, Issue 11S, Page(s) S15–S21

Abstract: Purpose: Post-standardized patient (SP) encounter patient notes used to assess students' clinical reasoning represent a significant time burden for faculty who traditionally score them. To reduce this burden, the authors previously reported a complex ... ...

Abstract	Purpose: Post-standardized patient (SP) encounter patient notes used to assess students' clinical reasoning represent a significant time burden for faculty who traditionally score them. To reduce this burden, the authors previously reported a complex faculty-developed scoring method to assess patient notes rated by nonclinicians. The current study explored whether a simplified scoring procedure for nonclinician raters could further optimize patient note assessments by reducing time, cost, and creating additional opportunities for formative feedback. Method: Ten nonclinician raters scored patient notes of 141 students across 5 SP cases by identifying case-specific patient note checklist items. The authors identified the bottom quintile of students using the proportion of correct items identified in the note (percent-scores) and case-specific faculty-generated scoring formulas (formula-scores). Five faculty raters scored a subset of notes from low, borderline, and high-performing students (n = 30 students) using a global rating scale. The authors performed analyses to gather validity evidence for percent-scores (i.e., relationship to other variables), investigate its reliability (i.e., generalizability study), and evaluate its costs (i.e., faculty time). Results: Nonclinician percent- and formula-scores were highly correlated ( r = .88) and identified similar lists of low-performing students. Both methods demonstrated good agreement for pass-fail determinations with each other (Kappa = .68) and with faculty global ratings (Kappa percent =.61; Kappa formula =.66). The G-coefficient of percent-scores was .52, with 38% of variability attributed to checklist items nested in cases. Using percent-scores saved an estimated $746 per SP case (including 6 hours of faculty time) in development costs over formula-scores. Conclusions: Nonclinician percent-scores reliably identified low-performing students without the need for complex faculty-developed scoring formulas. Combining nonclinician analytic and faculty holistic ratings can reduce the time and cost of patient note scoring and afford faculty more time to coach at-risk students and provide targeted assessment input for high-stakes summative exams.
MeSH term(s)	Humans ; Educational Measurement/methods ; Clinical Reasoning ; Clinical Competence ; Reproducibility of Results ; Problem Solving
Language	English
Publishing date	2022-08-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	96192-9
ISSN	1938-808X ; 1040-2446
ISSN (online)	1938-808X
ISSN	1040-2446
DOI	10.1097/ACM.0000000000004908
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Article ; Online: Birang Daruganora: a protocol for a qualitative study to elicit Aboriginal and Torres Strait Islander community views about cultural needs and experiences for a new Australian health facility.

Carrigan, Ann / Austin, Elizabeth E / Clay-Williams, Robyn / Hibbert, Peter D / Maka, Katherine / Holden, Narelle / Grigg, Shai / Loy, Graeme / Braithwaite, Jeffrey

BMJ open

2023 Volume 13, Issue 4, Page(s) e069951

Abstract: Introduction: To address challenges regarding the delivery of healthcare, governments and health services are focusing on the implementation of models that are flexible, person-centred, cost-effective and integrate hospital services more closely with ... ...

Abstract	Introduction: To address challenges regarding the delivery of healthcare, governments and health services are focusing on the implementation of models that are flexible, person-centred, cost-effective and integrate hospital services more closely with primary healthcare and social services. Such models increasingly embed consumer codesign, multidisciplinary teams and leverage digital technologies, such as telehealth, attempting to deliver care more seamlessly and to continually improve services. This paper provides a study protocol to describe a method to explore Aboriginal and/or Torres Strait Islander consumer and healthcare provider needs and expectations for the design and development of a new healthcare facility in Australia. Methods and analysis: A qualitative study of consumer members' and health providers' needs and expectations. Data collection includes a short consumer-specific and provider-specific, demographic questionnaire and culturally appropriate facilitator-coordinated consultation workshops. Data will be analysed thematically (qualitatively). Ethics and dissemination: The results will be actively disseminated through peer-reviewed journals, conference presentations, reports to stakeholders and community meetings. This study was reviewed and approved by a health service-based Ethics Committee in New South Wales, Australia and the Aboriginal Health and Medical Research Committee.
MeSH term(s)	Humans ; Australia ; Australian Aboriginal and Torres Strait Islander Peoples ; Health Facilities ; Health Services, Indigenous ; Surveys and Questionnaires ; Community Participation ; Qualitative Research ; Needs Assessment ; Culturally Competent Care ; Social Determinants of Health ; Health Services Needs and Demand ; Delivery of Health Care
Language	English
Publishing date	2023-04-06
Publishing country	England
Document type	Clinical Trial Protocol ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2599832-8
ISSN	2044-6055 ; 2044-6055
ISSN (online)	2044-6055
ISSN	2044-6055
DOI	10.1136/bmjopen-2022-069951
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Article ; Online: Elucidating nitric oxide synthase domain interactions by molecular dynamics.

Hollingsworth, Scott A / Holden, Jeffrey K / Li, Huiying / Poulos, Thomas L

Protein science : a publication of the Protein Society

2016 Volume 25, Issue 2, Page(s) 374–382

Abstract: Nitric oxide synthase (NOS) is a multidomain enzyme that catalyzes the production of nitric oxide (NO) by oxidizing L-Arg to NO and L-citrulline. NO production requires multiple interdomain electron transfer steps between the flavin mononucleotide (FMN) ... ...

Abstract	Nitric oxide synthase (NOS) is a multidomain enzyme that catalyzes the production of nitric oxide (NO) by oxidizing L-Arg to NO and L-citrulline. NO production requires multiple interdomain electron transfer steps between the flavin mononucleotide (FMN) and heme domain. Specifically, NADPH-derived electrons are transferred to the heme-containing oxygenase domain via the flavin adenine dinucleotide (FAD) and FMN containing reductase domains. While crystal structures are available for both the reductase and oxygenase domains of NOS, to date there is no atomic level structural information on domain interactions required for the final FMN-to-heme electron transfer step. Here, we evaluate a model of this final electron transfer step for the heme-FMN-calmodulin NOS complex based on the recent biophysical studies using a 105-ns molecular dynamics trajectory. The resulting equilibrated complex structure is very stable and provides a detailed prediction of interdomain contacts required for stabilizing the NOS output state. The resulting equilibrated complex model agrees well with previous experimental work and provides a detailed working model of the final NOS electron transfer step required for NO biosynthesis.
MeSH term(s)	Calmodulin/metabolism ; Electron Transport ; Flavin Mononucleotide/metabolism ; Heme/metabolism ; Humans ; Molecular Dynamics Simulation ; NADP/metabolism ; Nitric Oxide/metabolism ; Nitric Oxide Synthase Type II/chemistry ; Nitric Oxide Synthase Type II/metabolism ; Oxidation-Reduction ; Protein Interaction Domains and Motifs
Chemical Substances	Calmodulin ; Nitric Oxide (31C4KY9ESH) ; Heme (42VZT0U6YR) ; NADP (53-59-8) ; Flavin Mononucleotide (7N464URE7E) ; NOS2 protein, human (EC 1.14.13.39) ; Nitric Oxide Synthase Type II (EC 1.14.13.39)
Language	English
Publishing date	2016-02
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1106283-6
ISSN	1469-896X ; 0961-8368
ISSN (online)	1469-896X
ISSN	0961-8368
DOI	10.1002/pro.2824
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Article ; Online: Identification of redox partners and development of a novel chimeric bacterial nitric oxide synthase for structure activity analyses.

Holden, Jeffrey K / Lim, Nathan / Poulos, Thomas L

The Journal of biological chemistry

2014 Volume 289, Issue 42, Page(s) 29437–29445

Abstract: Production of nitric oxide (NO) by nitric oxide synthase (NOS) requires electrons to reduce the heme iron for substrate oxidation. Both FAD and FMN flavin groups mediate the transfer of NADPH derived electrons to NOS. Unlike mammalian NOS that contain ... ...

Abstract	Production of nitric oxide (NO) by nitric oxide synthase (NOS) requires electrons to reduce the heme iron for substrate oxidation. Both FAD and FMN flavin groups mediate the transfer of NADPH derived electrons to NOS. Unlike mammalian NOS that contain both FAD and FMN binding domains within a single polypeptide chain, bacterial NOS is only composed of an oxygenase domain and must rely on separate redox partners for electron transfer and subsequent activity. Here, we report on the native redox partners for Bacillus subtilis NOS (bsNOS) and a novel chimera that promotes bsNOS activity. By identifying and characterizing native redox partners, we were also able to establish a robust enzyme assay for measuring bsNOS activity and inhibition. This assay was used to evaluate a series of established NOS inhibitors. Using the new assay for screening small molecules led to the identification of several potent inhibitors for which bsNOS-inhibitor crystal structures were determined. In addition to characterizing potent bsNOS inhibitors, substrate binding was also analyzed using isothermal titration calorimetry giving the first detailed thermodynamic analysis of substrate binding to NOS.
MeSH term(s)	Amino Acid Sequence ; Animals ; Anti-Bacterial Agents/chemistry ; Bacillus subtilis/enzymology ; Bacterial Proteins/genetics ; Calorimetry ; Cloning, Molecular ; Cytochromes c/metabolism ; Electrons ; Escherichia coli/metabolism ; Ferredoxin-NADP Reductase/genetics ; Flavodoxin/genetics ; Humans ; Imidazoles/chemistry ; Inhibitory Concentration 50 ; Microbial Sensitivity Tests ; Molecular Sequence Data ; NADH, NADPH Oxidoreductases/metabolism ; NADP/metabolism ; Nitric Oxide/metabolism ; Nitric Oxide Synthase/metabolism ; Nitrites/metabolism ; Oxidation-Reduction ; Rats
Chemical Substances	Anti-Bacterial Agents ; Bacterial Proteins ; Flavodoxin ; Imidazoles ; Nitrites ; Nitric Oxide (31C4KY9ESH) ; NADP (53-59-8) ; imidazole (7GBN705NH1) ; Cytochromes c (9007-43-6) ; Nitric Oxide Synthase (EC 1.14.13.39) ; Ferredoxin-NADP Reductase (EC 1.18.1.2) ; NADH, NADPH Oxidoreductases (EC 1.6.-) ; flavodoxin NADPH oxidoreductase (EC 1.6.-)
Language	English
Publishing date	2014-09-06
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.M114.595165
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