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Article ; Online: Assembly and regulation of the chlorhexidine-specific efflux pump AceI.

Bolla, Jani Reddy / Howes, Anna C / Fiorentino, Francesco / Robinson, Carol V

Proceedings of the National Academy of Sciences of the United States of America

2020 Volume 117, Issue 29, Page(s) 17011–17018

Abstract: Few antibiotics are effective ... ...

Abstract	Few antibiotics are effective against
MeSH term(s)	Acinetobacter baumannii/chemistry ; Acinetobacter baumannii/enzymology ; Anti-Bacterial Agents/chemistry ; Anti-Bacterial Agents/metabolism ; Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; Chlorhexidine/chemistry ; Chlorhexidine/metabolism ; DNA-Directed RNA Polymerases/chemistry ; DNA-Directed RNA Polymerases/metabolism ; Drug Resistance, Microbial ; Hydrogen-Ion Concentration ; Mass Spectrometry ; Membrane Transport Proteins/chemistry ; Membrane Transport Proteins/metabolism ; Protein Binding ; Protein Multimerization ; Protein Subunits/chemistry ; Protein Subunits/metabolism
Chemical Substances	Anti-Bacterial Agents ; Bacterial Proteins ; Membrane Transport Proteins ; Protein Subunits ; DNA-Directed RNA Polymerases (EC 2.7.7.6) ; Chlorhexidine (R4KO0DY52L)
Language	English
Publishing date	2020-07-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2003271117
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Article ; Online: Membrane Protein-Lipid Interactions Probed Using Mass Spectrometry.

Bolla, Jani Reddy / Agasid, Mark T / Mehmood, Shahid / Robinson, Carol V

Annual review of biochemistry

2019 Volume 88, Page(s) 85–111

Abstract: Membrane proteins that exist in lipid bilayers are not isolated molecular entities. The lipid molecules that surround them play crucial roles in maintaining their full structural and functional integrity. Research directed at investigating these critical ...

Abstract	Membrane proteins that exist in lipid bilayers are not isolated molecular entities. The lipid molecules that surround them play crucial roles in maintaining their full structural and functional integrity. Research directed at investigating these critical lipid-protein interactions is developing rapidly. Advancements in both instrumentation and software, as well as in key biophysical and biochemical techniques, are accelerating the field. In this review, we provide a brief outline of structural techniques used to probe protein-lipid interactions and focus on the molecular aspects of these interactions obtained from native mass spectrometry (native MS). We highlight examples in which lipids have been shown to modulate membrane protein structure and show how native MS has emerged as a complementary technique to X-ray crystallography and cryo-electron microscopy. We conclude with a short perspective on future developments that aim to better understand protein-lipid interactions in the native environment.
MeSH term(s)	Bacteria/chemistry ; Bacteria/metabolism ; Binding Sites ; Cell Membrane/chemistry ; Cell Membrane/metabolism ; Cryoelectron Microscopy/instrumentation ; Cryoelectron Microscopy/methods ; Fungi/chemistry ; Fungi/metabolism ; Glycerophospholipids/chemistry ; Glycerophospholipids/metabolism ; Glycolipids/chemistry ; Glycolipids/metabolism ; Magnetic Resonance Spectroscopy/instrumentation ; Magnetic Resonance Spectroscopy/methods ; Mass Spectrometry/instrumentation ; Mass Spectrometry/methods ; Membrane Proteins/chemistry ; Membrane Proteins/metabolism ; Membrane Proteins/ultrastructure ; Models, Molecular ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Sphingolipids/chemistry ; Sphingolipids/metabolism ; Sterols/chemistry ; Sterols/metabolism
Chemical Substances	Glycerophospholipids ; Glycolipids ; Membrane Proteins ; Sphingolipids ; Sterols
Language	English
Publishing date	2019-03-22
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	207924-0
ISSN	1545-4509 ; 0066-4154
ISSN (online)	1545-4509
ISSN	0066-4154
DOI	10.1146/annurev-biochem-013118-111508
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Article ; Online: The Different Effects of Substrates and Nucleotides on the Complex Formation of ABC Transporters.

Fiorentino, Francesco / Bolla, Jani Reddy / Mehmood, Shahid / Robinson, Carol V

Structure (London, England : 1993)

2019 Volume 27, Issue 4, Page(s) 651–659.e3

Abstract: The molybdate importer (ModBC-A of Archaeoglobus fulgidus) and the vitamin ... ...

Abstract	The molybdate importer (ModBC-A of Archaeoglobus fulgidus) and the vitamin B
MeSH term(s)	ATP-Binding Cassette Transporters/chemistry ; ATP-Binding Cassette Transporters/genetics ; ATP-Binding Cassette Transporters/metabolism ; Adenosine Triphosphate/chemistry ; Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Archaeoglobus fulgidus/genetics ; Archaeoglobus fulgidus/metabolism ; Binding Sites ; Cloning, Molecular ; Crystallography, X-Ray ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Escherichia coli Proteins/chemistry ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Gene Expression ; Genetic Vectors/chemistry ; Genetic Vectors/metabolism ; Ion Transport ; Models, Molecular ; Molybdenum/chemistry ; Molybdenum/metabolism ; Periplasmic Binding Proteins/chemistry ; Periplasmic Binding Proteins/genetics ; Periplasmic Binding Proteins/metabolism ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Protein Multimerization ; Recombinant Proteins/chemistry ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Species Specificity ; Substrate Specificity
Chemical Substances	ATP-Binding Cassette Transporters ; BtuC peptide, E coli ; BtuD peptide, E coli ; Escherichia coli Proteins ; Periplasmic Binding Proteins ; Recombinant Proteins ; btuF protein, E coli ; molybdate (14259-85-9) ; Molybdenum (81AH48963U) ; Adenosine Triphosphate (8L70Q75FXE)
Language	English
Publishing date	2019-02-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1213087-4
ISSN	1878-4186 ; 0969-2126
ISSN (online)	1878-4186
ISSN	0969-2126
DOI	10.1016/j.str.2019.01.010
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Article ; Online: A 'Build and Retrieve' methodology to simultaneously solve cryo-EM structures of membrane proteins.

Su, Chih-Chia / Lyu, Meinan / Morgan, Christopher E / Bolla, Jani Reddy / Robinson, Carol V / Yu, Edward W

Nature methods

2021 Volume 18, Issue 1, Page(s) 69–75

Abstract: Single-particle cryo-electron microscopy (cryo-EM) has become a powerful technique in the field of structural biology. However, the inability to reliably produce pure, homogeneous membrane protein samples hampers the progress of their structural ... ...

Abstract	Single-particle cryo-electron microscopy (cryo-EM) has become a powerful technique in the field of structural biology. However, the inability to reliably produce pure, homogeneous membrane protein samples hampers the progress of their structural determination. Here, we develop a bottom-up iterative method, Build and Retrieve (BaR), that enables the identification and determination of cryo-EM structures of a variety of inner and outer membrane proteins, including membrane protein complexes of different sizes and dimensions, from a heterogeneous, impure protein sample. We also use the BaR methodology to elucidate structural information from Escherichia coli K12 crude membrane and raw lysate. The findings demonstrate that it is possible to solve high-resolution structures of a number of relatively small (<100 kDa) and less abundant (<10%) unidentified membrane proteins within a single, heterogeneous sample. Importantly, these results highlight the potential of cryo-EM for systems structural proteomics.
MeSH term(s)	Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; Burkholderia pseudomallei/metabolism ; Cell Membrane/chemistry ; Cell Membrane/metabolism ; Cryoelectron Microscopy/methods ; Escherichia coli/metabolism ; Humans ; Membrane Proteins/chemistry ; Membrane Proteins/metabolism ; Models, Molecular ; Molecular Structure ; Protein Conformation
Chemical Substances	Bacterial Proteins ; Membrane Proteins
Language	English
Publishing date	2021-01-06
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2169522-2
ISSN	1548-7105 ; 1548-7091
ISSN (online)	1548-7105
ISSN	1548-7091
DOI	10.1038/s41592-020-01021-2
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Article ; Online: Direct observation of the influence of cardiolipin and antibiotics on lipid II binding to MurJ.

Bolla, Jani Reddy / Sauer, Joshua B / Wu, Di / Mehmood, Shahid / Allison, Timothy M / Robinson, Carol V

Nature chemistry

2018 Volume 10, Issue 3, Page(s) 363–371

Abstract: Translocation of lipid II across the cytoplasmic membrane is essential in peptidoglycan biogenesis. Although most steps are understood, identifying the lipid II flippase has yielded conflicting results, and the lipid II binding properties of two ... ...

Abstract	Translocation of lipid II across the cytoplasmic membrane is essential in peptidoglycan biogenesis. Although most steps are understood, identifying the lipid II flippase has yielded conflicting results, and the lipid II binding properties of two candidate flippases-MurJ and FtsW-remain largely unknown. Here we apply native mass spectrometry to both proteins and characterize lipid II binding. We observed lower levels of lipid II binding to FtsW compared to MurJ, consistent with MurJ having a higher affinity. Site-directed mutagenesis of MurJ suggests that mutations at A29 and D269 attenuate lipid II binding to MurJ, whereas chemical modification of A29 eliminates binding. The antibiotic ramoplanin dissociates lipid II from MurJ, whereas vancomycin binds to form a stable complex with MurJ:lipid II. Furthermore, we reveal cardiolipins associate with MurJ but not FtsW, and exogenous cardiolipins reduce lipid II binding to MurJ. These observations provide insights into determinants of lipid II binding to MurJ and suggest roles for endogenous lipids in regulating substrate binding.
MeSH term(s)	Anti-Bacterial Agents/chemistry ; Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; Binding Sites ; Cardiolipins/chemistry ; Cardiolipins/metabolism ; Depsipeptides/chemistry ; Escherichia coli Proteins/chemistry ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Mass Spectrometry ; Membrane Proteins/chemistry ; Membrane Proteins/metabolism ; Mutagenesis, Site-Directed ; Phospholipid Transfer Proteins/chemistry ; Phospholipid Transfer Proteins/genetics ; Phospholipid Transfer Proteins/metabolism ; Uridine Diphosphate N-Acetylmuramic Acid/analogs & derivatives ; Uridine Diphosphate N-Acetylmuramic Acid/chemistry
Chemical Substances	Anti-Bacterial Agents ; Bacterial Proteins ; Cardiolipins ; Depsipeptides ; Escherichia coli Proteins ; Membrane Proteins ; MurJ protein, E coli ; Phospholipid Transfer Proteins ; Uridine Diphosphate N-Acetylmuramic Acid ; muramyl-NAc-(pentapeptide)pyrophosphoryl-undecaprenol ; ramoplanin (0WX9996O2G) ; FtsW protein, Bacteria (125724-13-2)
Language	English
Publishing date	2018-01-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2464596-5
ISSN	1755-4349 ; 1755-4330
ISSN (online)	1755-4349
ISSN	1755-4330
DOI	10.1038/nchem.2919
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Article ; Online: The structure of nontypeable Haemophilus influenzae SapA in a closed conformation reveals a constricted ligand-binding cavity and a novel RNA binding motif.

Lukacik, Petra / Owen, C David / Harris, Gemma / Bolla, Jani Reddy / Picaud, Sarah / Alibay, Irfan / Nettleship, Joanne E / Bird, Louise E / Owens, Raymond J / Biggin, Philip C / Filippakopoulos, Panagis / Robinson, Carol V / Walsh, Martin A

PloS one

2021 Volume 16, Issue 10, Page(s) e0256070

Abstract: Nontypeable Haemophilus influenzae (NTHi) is a significant pathogen in respiratory disease and otitis media. Important for NTHi survival, colonization and persistence in vivo is the Sap (sensitivity to antimicrobial peptides) ABC transporter system. ... ...

Abstract	Nontypeable Haemophilus influenzae (NTHi) is a significant pathogen in respiratory disease and otitis media. Important for NTHi survival, colonization and persistence in vivo is the Sap (sensitivity to antimicrobial peptides) ABC transporter system. Current models propose a direct role for Sap in heme and antimicrobial peptide (AMP) transport. Here, the crystal structure of SapA, the periplasmic component of Sap, in a closed, ligand bound conformation, is presented. Phylogenetic and cavity volume analysis predicts that the small, hydrophobic SapA central ligand binding cavity is most likely occupied by a hydrophobic di- or tri- peptide. The cavity is of insufficient volume to accommodate heme or folded AMPs. Crystal structures of SapA have identified surface interactions with heme and dsRNA. Heme binds SapA weakly (Kd 282 μM) through a surface exposed histidine, while the dsRNA is coordinated via residues which constitute part of a conserved motif (estimated Kd 4.4 μM). The RNA affinity falls within the range observed for characterized RNA/protein complexes. Overall, we describe in molecular-detail the interactions of SapA with heme and dsRNA and propose a role for SapA in the transport of di- or tri-peptides.
MeSH term(s)	ATP-Binding Cassette Transporters/genetics ; ATP-Binding Cassette Transporters/metabolism ; Anti-Bacterial Agents/pharmacology ; Carrier Proteins/genetics ; Carrier Proteins/metabolism ; Crystallography, X-Ray ; Drug Resistance, Multiple, Bacterial/genetics ; Haemophilus Infections/microbiology ; Haemophilus Infections/pathology ; Haemophilus influenzae/drug effects ; Haemophilus influenzae/genetics ; Haemophilus influenzae/metabolism ; Heme/metabolism ; Otitis Media/microbiology ; Otitis Media/pathology ; Protein Conformation ; Protein Transport/physiology ; RNA, Double-Stranded/genetics ; RNA, Double-Stranded/metabolism ; RNA-Binding Motifs/genetics ; Virulence Factors/metabolism
Chemical Substances	ATP-Binding Cassette Transporters ; Anti-Bacterial Agents ; Carrier Proteins ; RNA, Double-Stranded ; Virulence Factors ; Heme (42VZT0U6YR)
Language	English
Publishing date	2021-10-15
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0256070
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Article ; Online: Crystallization of membrane proteins by vapor diffusion.

Delmar, Jared A / Bolla, Jani Reddy / Su, Chih-Chia / Yu, Edward W

Methods in enzymology

2015 Volume 557, Page(s) 363–392

Abstract: X-ray crystallography remains the most robust method to determine protein structure at the atomic level. However, the bottlenecks of protein expression and purification often discourage further study. In this chapter, we address the most common problems ... ...

Abstract	X-ray crystallography remains the most robust method to determine protein structure at the atomic level. However, the bottlenecks of protein expression and purification often discourage further study. In this chapter, we address the most common problems encountered at these stages. Based on our experiences in expressing and purifying antimicrobial efflux proteins, we explain how a pure and homogenous protein sample can be successfully crystallized by the vapor diffusion method. We present our current protocols and methodologies for this technique. Case studies show step-by-step how we have overcome problems related to expression and diffraction, eventually producing high-quality membrane protein crystals for structural determinations. It is our hope that a rational approach can be made of the often anecdotal process of membrane protein crystallization.
MeSH term(s)	Animals ; Bacteria/chemistry ; Bacteria/genetics ; Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Bacterial Proteins/isolation & purification ; Crystallography, X-Ray/methods ; Detergents/chemistry ; Diffusion ; Gene Expression ; Humans ; Membrane Proteins/chemistry ; Membrane Proteins/genetics ; Membrane Proteins/isolation & purification ; Models, Molecular ; Volatilization
Chemical Substances	Bacterial Proteins ; Detergents ; Membrane Proteins
Language	English
Publishing date	2015
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ISSN	1557-7988 ; 0076-6879
ISSN (online)	1557-7988
ISSN	0076-6879
DOI	10.1016/bs.mie.2014.12.018
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Article ; Online: The antibiotic darobactin mimics a β-strand to inhibit outer membrane insertase.

Kaur, Hundeep / Jakob, Roman P / Marzinek, Jan K / Green, Robert / Imai, Yu / Bolla, Jani Reddy / Agustoni, Elia / Robinson, Carol V / Bond, Peter J / Lewis, Kim / Maier, Timm / Hiller, Sebastian

Nature

2021 Volume 593, Issue 7857, Page(s) 125–129

Abstract: Antibiotics that target Gram-negative bacteria in new ways are needed to resolve the antimicrobial resistance ... ...

Abstract	Antibiotics that target Gram-negative bacteria in new ways are needed to resolve the antimicrobial resistance crisis
MeSH term(s)	Anti-Bacterial Agents/chemistry ; Anti-Bacterial Agents/pharmacology ; Bacterial Outer Membrane Proteins/antagonists & inhibitors ; Bacterial Outer Membrane Proteins/chemistry ; Bacterial Outer Membrane Proteins/metabolism ; Binding Sites ; Cryoelectron Microscopy ; Crystallography, X-Ray ; Drug Design ; Escherichia coli/cytology ; Escherichia coli/drug effects ; Escherichia coli/enzymology ; Escherichia coli Proteins/antagonists & inhibitors ; Escherichia coli Proteins/chemistry ; Escherichia coli Proteins/metabolism ; Mass Spectrometry ; Molecular Dynamics Simulation ; Phenylpropionates/chemistry ; Phenylpropionates/pharmacology ; Protein Structure, Secondary
Chemical Substances	Anti-Bacterial Agents ; Bacterial Outer Membrane Proteins ; BamA protein, E coli ; Escherichia coli Proteins ; Phenylpropionates ; darobactin
Language	English
Publishing date	2021-04-14
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-021-03455-w
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Article: Biomolecular membrane protein crystallization.

Bolla, Jani Reddy / Su, Chih-Chia / Yu, Edward W

Philosophical magazine (Abingdon, England)

2013 Volume 92, Issue 19-21, Page(s) 2648–2661

Abstract: Integral membrane proteins comprise approximately 30% of the sequenced genomes, and there is an immediate need for their high-resolution structural information. Currently, the most reliable approach to obtain these structures is x-ray crystallography. ... ...

Abstract	Integral membrane proteins comprise approximately 30% of the sequenced genomes, and there is an immediate need for their high-resolution structural information. Currently, the most reliable approach to obtain these structures is x-ray crystallography. However, obtaining crystals of membrane proteins that diffract to high resolution appears to be quite challenging, and remains a major obstacle in structural determination. This brief review summarizes a variety of methodologies for use in crystallizing these membrane proteins. Hopefully, by introducing the available methods, techniques, and providing a general understanding of membrane proteins, a rational decision can be made about now to crystallize these complex materials.
Language	English
Publishing date	2013-07-12
Publishing country	England
Document type	Journal Article
ZDB-ID	3441-1
ISSN	1478-6435 ; 0031-8086
ISSN	1478-6435 ; 0031-8086
DOI	10.1080/14786435.2012.670734
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Article ; Online: MmpL3 is a lipid transporter that binds trehalose monomycolate and phosphatidylethanolamine.

Su, Chih-Chia / Klenotic, Philip A / Bolla, Jani Reddy / Purdy, Georgiana E / Robinson, Carol V / Yu, Edward W

Proceedings of the National Academy of Sciences of the United States of America

2019 Volume 116, Issue 23, Page(s) 11241–11246

Abstract: The cell envelope ... ...

Abstract	The cell envelope of
MeSH term(s)	Bacterial Proteins/metabolism ; Biological Transport/physiology ; Cell Membrane/metabolism ; Cell Wall/metabolism ; Cord Factors/metabolism ; Membrane Transport Proteins/metabolism ; Mycobacterium smegmatis/metabolism ; Mycolic Acids/metabolism ; Phosphatidylethanolamines/metabolism
Chemical Substances	Bacterial Proteins ; Cord Factors ; Membrane Transport Proteins ; Mycolic Acids ; Phosphatidylethanolamines ; trehalose monomycolate ; phosphatidylethanolamine (39382-08-6)
Language	English
Publishing date	2019-05-21
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	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1901346116
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