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Article ; Online: Cooperative Substrate Binding Controls Catalysis in Bacterial Cytochrome P450terp (CYP108A1).

Gable, Jessica A / Poulos, Thomas L / Follmer, Alec H

Journal of the American Chemical Society

2023

Abstract: Despite being one of the most well-studied aspects of cytochrome P450 chemistry, important questions remain regarding the nature and ubiquity of allosteric regulation of catalysis. The crystal structure of a bacterial P450, P450terp, in the presence of ... ...

Abstract	Despite being one of the most well-studied aspects of cytochrome P450 chemistry, important questions remain regarding the nature and ubiquity of allosteric regulation of catalysis. The crystal structure of a bacterial P450, P450terp, in the presence of substrate reveals two binding sites, one above the heme in position for regioselective hydroxylation and another in the substrate access channel. Unlike many bacterial P450s, P450terp does not exhibit an open to closed conformational change when substrate binds; instead, P450terp uses the second substrate molecule to hold the first substrate molecule in position for catalysis. Spectral titrations clearly show that substrate binding to P450terp is cooperative with a Hill coefficient of 1.4 and is supported by isothermal titration calorimetry. The importance of the allosteric site was explored by a series of mutations that weaken the second site and that help hold the first substrate in position for proper catalysis. We further measured the coupling efficiency of both the wild-type (WT) enzyme and the mutant enzymes. While the WT enzyme exhibits 97% efficiency, each of the variants showed lower catalytic efficiency. Additionally, the variants show decreased spin shifts upon binding of substrate. These results are the first clear example of positive homotropic allostery in a class 1 bacterial P450 with its natural substrate. Combined with our recent results from P450cam showing complex substrate allostery and conformational dynamics, our present study with P450terp indicates that bacterial P450s may not be as simple as once thought and share complex substrate binding properties usually associated with only mammalian P450s.
Language	English
Publishing date	2023-02-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.2c12388
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Article ; Online: Redox partner recognition and selectivity of cytochrome P450lin (CYP111A1).

Gable, Jessica A / Poulos, Thomas L / Follmer, Alec H

Journal of inorganic biochemistry

2023 Volume 244, Page(s) 112212

Abstract: The strict requirement of cytochrome P450cam for its native ferredoxin redox partner, putidaredoxin (Pdx), is not exhibited by any other known cytochrome P450 (CYP) system and the molecular details of redox partner selectivity are still not completely ... ...

Abstract	The strict requirement of cytochrome P450cam for its native ferredoxin redox partner, putidaredoxin (Pdx), is not exhibited by any other known cytochrome P450 (CYP) system and the molecular details of redox partner selectivity are still not completely understood. We therefore examined the selectivity of a related Pseudomonas cytochrome P450, P450lin, by testing its activity with non-native redox partners. We found that P450lin could utilize Arx, the native redox partner of CYP101D1, to enable turnover of its substrate, linalool, while Pdx showed limited activity. Arx exhibited a higher sequence similarity to P450lins native redox partner, linredoxin (Ldx) than Pdx, including several residues that are believed to be at the interface of the two proteins, based on the P450cam-Pdx complex structure. We therefore mutated Pdx to resemble Ldx and Arx and found that a double mutant, D38L/∆106, displayed higher activity than Arx. In addition, Pdx D38L/∆106 does not induce a low-spin shift in linalool bound P450lin but does destabilize the P450lin-oxycomplex. Together our results suggest that P450lin and its redox partners may form a similar interface to P450cam-Pdx, but the interactions that allow for productive turnover are different.
MeSH term(s)	Camphor 5-Monooxygenase/chemistry ; Oxidation-Reduction ; Acyclic Monoterpenes ; Ferredoxins/metabolism ; Cytochrome P-450 Enzyme System/metabolism ; Pseudomonas putida/metabolism
Chemical Substances	linalool (D81QY6I88E) ; Camphor 5-Monooxygenase (EC 1.14.15.1) ; Acyclic Monoterpenes ; Ferredoxins ; Cytochrome P-450 Enzyme System (9035-51-2)
Language	English
Publishing date	2023-04-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	162843-4
ISSN	1873-3344 ; 0162-0134
ISSN (online)	1873-3344
ISSN	0162-0134
DOI	10.1016/j.jinorgbio.2023.112212
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Article ; Online: Updating the Paradigm: Redox Partner Binding and Conformational Dynamics in Cytochromes P450.

Poulos, Thomas L / Follmer, Alec H

Accounts of chemical research

2021 Volume 55, Issue 3, Page(s) 373–380

Abstract: This Account summarizes recent findings centered on the role that redox partner binding, allostery, and conformational dynamics plays in cytochrome P450 proton coupled electron transfer. P450s are one of Nature's largest enzyme families and it is not ... ...

Abstract	This Account summarizes recent findings centered on the role that redox partner binding, allostery, and conformational dynamics plays in cytochrome P450 proton coupled electron transfer. P450s are one of Nature's largest enzyme families and it is not uncommon to find a P450 wherever substrate oxidation is required in the formation of essential molecules critical to the life of the organism or in xenobiotic detoxification. P450s can operate on a remarkably large range of substrates from the very small to the very large, yet the overall P450 three-dimensional structure is conserved. Given this conservation of structure, it is generally assumed that the basic catalytic mechanism is conserved. In nearly all P450s, the O
MeSH term(s)	Binding Sites ; Camphor 5-Monooxygenase/chemistry ; Catalytic Domain ; Cytochrome P-450 Enzyme System/metabolism ; Ferredoxins/chemistry ; Humans ; Molecular Dynamics Simulation ; Oxidation-Reduction ; Protein Conformation
Chemical Substances	Ferredoxins ; Cytochrome P-450 Enzyme System (9035-51-2) ; Camphor 5-Monooxygenase (EC 1.14.15.1)
Language	English
Publishing date	2021-12-29
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	1483291-4
ISSN	1520-4898 ; 0001-4842
ISSN (online)	1520-4898
ISSN	0001-4842
DOI	10.1021/acs.accounts.1c00632
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Article ; Online: Computational analysis of the tryptophan cation radical energetics in peroxidase Compound I.

Poulos, Thomas L / Kim, Jenny S / Murarka, Vidhi C

Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry

2022 Volume 27, Issue 2, Page(s) 229–237

Abstract: Three well-characterized heme peroxidases (cytochrome c peroxidase = CCP, ascorbate peroxidase = APX, and Leishmania major peroxidase = LMP) all have a Trp residue tucked under the heme stacked against the proximal His heme ligand. The reaction of ... ...

Abstract	Three well-characterized heme peroxidases (cytochrome c peroxidase = CCP, ascorbate peroxidase = APX, and Leishmania major peroxidase = LMP) all have a Trp residue tucked under the heme stacked against the proximal His heme ligand. The reaction of peroxidases with H
MeSH term(s)	Cations ; Cytochrome-c Peroxidase/chemistry ; Electron Spin Resonance Spectroscopy ; Heme/metabolism ; Hydrogen Peroxide/chemistry ; Oxidation-Reduction ; Peroxidase/metabolism ; Peroxidases/chemistry ; Tryptophan/metabolism
Chemical Substances	Cations ; Heme (42VZT0U6YR) ; Tryptophan (8DUH1N11BX) ; Hydrogen Peroxide (BBX060AN9V) ; Peroxidases (EC 1.11.1.-) ; Cytochrome-c Peroxidase (EC 1.11.1.5) ; Peroxidase (EC 1.11.1.7)
Language	English
Publishing date	2022-01-21
Publishing country	Germany
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1464026-0
ISSN	1432-1327 ; 0949-8257
ISSN (online)	1432-1327
ISSN	0949-8257
DOI	10.1007/s00775-022-01925-8
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Article ; Online: Structural Insights on the Conversion of Cytochrome P450 to P420.

Gable, Jessica A / Tripathi, Sarvind / Poulos, Thomas L

ACS omega

2022 Volume 7, Issue 22, Page(s) 18481–18485

Abstract: A characteristic feature of cytochromes P450* is that the complex formed between the ferrous heme iron and carbon monoxide generates an intense absorption band at 450 nm. This unique feature of P450s is due to the proximal thiolate Cys ligand coordinated ...

Abstract	A characteristic feature of cytochromes P450* is that the complex formed between the ferrous heme iron and carbon monoxide generates an intense absorption band at 450 nm. This unique feature of P450s is due to the proximal thiolate Cys ligand coordinated to the heme iron. Various harsh treatments shift this band to 420 nm, thereby giving P420 which is most often associated with an inactive form of the enzyme. Various explanations have been put forward to explain the P450-to-P420 change ranging from protonation of the Cys heme ligand, displacement of the Cys ligand, or replacement of the Cys ligand with His. There are two crystal structures of the well-studied cytochrome P450cam that have a high fraction of P420. In one, P450cam is cross-linked to its redox partner, putidaredoxin (Pdx), and the second is P450cam crystallized in the absence of substrate. In both of these structures, a significant part of the substrate pocket is disordered and the poor quality of the electron density for the substrate indicates substantial disorder. However, in both structures there is no detectable change in the Cys-iron ligation or surrounding structure. These results indicate that the P450-to-P420 switch is due primarily to an opening and disordering around the substrate binding pocket and not ligand displacement or ligand swapping. Since it remains a possibility that ligand swapping could be responsible for P420 in some cases, we mutated to Gln the 3 His residues (352, 355, and 361) close enough to the proximal side of the heme that could possibly serve as heme ligands. The triple variant forms P420 which indicates that swapping Cys for His is not a requirement for the P450-to-P420 switch.
Language	English
Publishing date	2022-05-27
Publishing country	United States
Document type	Journal Article
ISSN	2470-1343
ISSN (online)	2470-1343
DOI	10.1021/acsomega.2c00960
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Article ; Online: Crystallographic and Computational Insights into Isoform-Selective Dynamics in Nitric Oxide Synthase.

Li, Huiying / Hardy, Christine D / Reidl, Cory T / Jing, Qing / Xue, Fengtian / Cinelli, Maris / Silverman, Richard B / Poulos, Thomas L

Biochemistry

2024 Volume 63, Issue 6, Page(s) 788–796

Abstract: In our efforts to develop inhibitors selective for neuronal nitric oxide synthase (nNOS) over endothelial nitric oxide synthase (eNOS), we found that nNOS can undergo conformational changes in response to inhibitor binding that does not readily occur in ... ...

Abstract	In our efforts to develop inhibitors selective for neuronal nitric oxide synthase (nNOS) over endothelial nitric oxide synthase (eNOS), we found that nNOS can undergo conformational changes in response to inhibitor binding that does not readily occur in eNOS. One change involves movement of a conserved tyrosine, which hydrogen bonds to one of the heme propionates, but in the presence of an inhibitor, changes conformation, enabling part of the inhibitor to hydrogen bond with the heme propionate. This movement does not occur as readily in eNOS and may account for the reason why these inhibitors bind more tightly to nNOS. A second structural change occurs upon the binding of a second inhibitor molecule to nNOS, displacing the pterin cofactor. Binding of this second site inhibitor requires structural changes at the dimer interface, which also occurs more readily in nNOS than in eNOS. Here, we used a combination of crystallography, mutagenesis, and computational methods to better understand the structural basis for these differences in NOS inhibitor binding. Computational results show that a conserved tyrosine near the primary inhibitor binding site is anchored more tightly in eNOS than in nNOS, allowing for less flexibility of this residue. We also find that the inefficiency of eNOS to bind a second inhibitor molecule is likely due to the tighter dimer interface in eNOS compared with nNOS. This study provides a better understanding of how subtle structural differences in NOS isoforms can result in substantial dynamic differences that can be exploited in the development of isoform-selective inhibitors.
MeSH term(s)	Nitric Oxide Synthase/metabolism ; Nitric Oxide Synthase Type III/genetics ; Nitric Oxide Synthase Type III/chemistry ; Nitric Oxide Synthase Type I ; Protein Isoforms/chemistry ; Crystallography, X-Ray ; Enzyme Inhibitors/pharmacology ; Heme/chemistry ; Tyrosine ; Nitric Oxide
Chemical Substances	Nitric Oxide Synthase (EC 1.14.13.39) ; Nitric Oxide Synthase Type III (EC 1.14.13.39) ; Nitric Oxide Synthase Type I (EC 1.14.13.39) ; Protein Isoforms ; Enzyme Inhibitors ; Heme (42VZT0U6YR) ; Tyrosine (42HK56048U) ; Nitric Oxide (31C4KY9ESH)
Language	English
Publishing date	2024-02-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/acs.biochem.3c00601
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Article ; Online: Biosynthesis of a new skyllamycin in

Song, Yuhao / Amaya, Jose A / Murarka, Vidhi C / Mendez, Hugo / Hogan, Mark / Muldoon, Jimmy / Evans, Paul / Ortin, Yannick / Kelly, Steven L / Lamb, David C / Poulos, Thomas L / Caffrey, Patrick

Organic & biomolecular chemistry

2024 Volume 22, Issue 14, Page(s) 2835–2843

Abstract: Activation of a silent gene cluster ... ...

Abstract	Activation of a silent gene cluster in
MeSH term(s)	Cytochrome P-450 Enzyme System/chemistry ; Depsipeptides ; Peptides, Cyclic/chemistry ; Streptomyces
Chemical Substances	skyllamycins ; Cytochrome P-450 Enzyme System (9035-51-2) ; Depsipeptides ; Peptides, Cyclic
Language	English
Publishing date	2024-04-03
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2097583-1
ISSN	1477-0539 ; 1477-0520
ISSN (online)	1477-0539
ISSN	1477-0520
DOI	10.1039/d4ob00178h
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Article ; Online: Heme enzyme structure and function.

Poulos, Thomas L

Chemical reviews

2014 Volume 114, Issue 7, Page(s) 3919–3962

MeSH term(s)	Biocatalysis ; Catalytic Domain ; Chloride Peroxidase/chemistry ; Chloride Peroxidase/metabolism ; Cytochrome P-450 Enzyme System/chemistry ; Cytochrome P-450 Enzyme System/metabolism ; Enzymes/chemistry ; Enzymes/metabolism ; Heme/chemistry ; Heme Oxygenase (Decyclizing)/chemistry ; Heme Oxygenase (Decyclizing)/metabolism ; Indoleamine-Pyrrole 2,3,-Dioxygenase/chemistry ; Indoleamine-Pyrrole 2,3,-Dioxygenase/metabolism ; Nitric Oxide Synthase/chemistry ; Nitric Oxide Synthase/metabolism ; Peroxidases/chemistry ; Peroxidases/metabolism ; Protoporphyrins/chemistry ; Tryptophan Oxygenase/chemistry ; Tryptophan Oxygenase/metabolism
Chemical Substances	Enzymes ; Indoleamine-Pyrrole 2,3,-Dioxygenase ; Protoporphyrins ; Heme (42VZT0U6YR) ; Cytochrome P-450 Enzyme System (9035-51-2) ; Peroxidases (EC 1.11.1.-) ; Chloride Peroxidase (EC 1.11.1.10) ; Tryptophan Oxygenase (EC 1.13.11.11) ; Nitric Oxide Synthase (EC 1.14.13.39) ; Heme Oxygenase (Decyclizing) (EC 1.14.14.18)
Language	English
Publishing date	2014-01-08
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	207949-5
ISSN	1520-6890 ; 0009-2665
ISSN (online)	1520-6890
ISSN	0009-2665
DOI	10.1021/cr400415k
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Article ; Online: Effect of redox partner binding on CYP101D1 conformational dynamics.

Batabyal, Dipanwita / Poulos, Thomas L

Journal of inorganic biochemistry

2018 Volume 183, Page(s) 179–183

Abstract: We have compared the thermodynamics of substrate and redox partner binding of P450cam to its close homologue, CYP101D1, using isothermal titration calorimetry (ITC). CYP101D1 binds camphor about 10-fold more weakly than P450cam which is consistent with ... ...

Abstract	We have compared the thermodynamics of substrate and redox partner binding of P450cam to its close homologue, CYP101D1, using isothermal titration calorimetry (ITC). CYP101D1 binds camphor about 10-fold more weakly than P450cam which is consistent with the inability of camphor to cause a complete low- to high-spin shift in CYP101D1. Even so molecular dynamics simulations show that camphor is very stable in the CYP101D1 active site similar to P450cam. ITC data on the binding of the CYP101D1 ferredoxin redox partner (abbreviated Arx) shows that the substrate-bound closed state of CYP101D1 binds Arx more tightly than the substrate-free open form. This is just the opposite to P450cam where Pdx (ferredoxin redox partner of P450cam) favors binding to the P450cam open state. In addition, CYP101D1-Arx binding has a large negative ΔS while the P450cam-Pdx has a much smaller ΔS indicating that interactions at the docking interface are different. The most obvious difference is that PDX
MeSH term(s)	Calorimetry ; Camphor 5-Monooxygenase/chemistry ; Camphor 5-Monooxygenase/metabolism ; Ferredoxins/metabolism ; Molecular Dynamics Simulation ; Oxidation-Reduction ; Protein Binding ; Protein Conformation
Chemical Substances	Ferredoxins ; Camphor 5-Monooxygenase (EC 1.14.15.1)
Language	English
Publishing date	2018-03-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	162843-4
ISSN	1873-3344 ; 0162-0134
ISSN (online)	1873-3344
ISSN	0162-0134
DOI	10.1016/j.jinorgbio.2018.02.013
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Article ; Online: Testing the N-Terminal Velcro Model of CooA Carbon Monoxide Activation.

Tripathi, Sarvind / Poulos, Thomas L

Biochemistry

2018 Volume 57, Issue 21, Page(s) 3059–3064

Abstract: CooAs are dimeric bacterial CO-sensing transcription factors that activate a series of enzymes responsible for CO oxidation. The crystal structure of Rhodospirillum rubrum (rrCooA) shows that the N-terminal Pro from monomer A of the dimer coordinates the ...

Abstract	CooAs are dimeric bacterial CO-sensing transcription factors that activate a series of enzymes responsible for CO oxidation. The crystal structure of Rhodospirillum rubrum (rrCooA) shows that the N-terminal Pro from monomer A of the dimer coordinates the heme of monomer B that locks rrCooA in the "off" state. When CO binds, it is postulated that the Pro is replaced with CO, resulting in a very large reorientation of the DNA binding domains required for specific binding to DNA. Crystal structures of the closely related CooA from Carboxydothermus hydrogenoformans (chCooA) are available, and in one of these, the CO-bound on-state indicates that the N-terminal region that is displaced when CO binds provides contacts between the heme and DNA binding domains that hold the DNA binding domain in position for DNA binding. This has been termed the N-terminal velcro model of CooA activation. The study presented here tests this hypothesis by generating a disulfide mutant that covalently locks chCooA in the on-state. A simple fluorescence assay was used to measure DNA binding, and the S-S mutant was found to be in the on-state even without CO. We also determined the high-resolution crystal structure of the apo-heme domain, and the resulting structure is very similar to the holo-heme-bound structure. This result shows that the heme binding motif forms a stable structure without heme or the DNA binding domain.
MeSH term(s)	Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; Carbon Monoxide/metabolism ; DNA/chemistry ; DNA-Binding Proteins/chemistry ; Heme/chemistry ; Hemeproteins/chemistry ; Hemeproteins/metabolism ; Models, Molecular ; Oxidation-Reduction ; Protein Binding ; Protein Conformation ; Rhodospirillum rubrum/enzymology ; Rhodospirillum rubrum/metabolism ; Trans-Activators/chemistry ; Trans-Activators/metabolism
Chemical Substances	Bacterial Proteins ; CooA protein, Rhodospirillum rubrum ; DNA-Binding Proteins ; Hemeproteins ; Trans-Activators ; Heme (42VZT0U6YR) ; Carbon Monoxide (7U1EE4V452) ; DNA (9007-49-2)
Language	English
Publishing date	2018-05-11
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/acs.biochem.8b00359
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