A Key Glycine in Bacterial Steroid-Degrading Acyl-CoA Dehydrogenases Allows Flavin-Ring Repositioning and Modulates Substrate Side Chain Specificity

The action of carboxypeptidase B (EC 3.4.12.3) on the benzoylglycyl dipeptides Bz-Gly-Lys(X) where X = methyl, ethyl, propyl, formyl, dimethyl, isopropyl, trimethyl, and benzyl has been investigated. All were hydrolyzed, at a rate decreasing in the order indicated, except where X = trimethyl and benzyl. Compounds where X = dimethyl, formyl, and isopropyl were hydrolyzed very slowly, and did not inhibit the hydrolysis of Bz-Gly-Lys by the enzyme. The kinetic parameters kcat and Km were determined for compounds with X = methyl and ethyl. The observed decrease in rate of hydrolysis of substrates with increasing size of X is consistent with increasing steric hindrance effects arising from the interaction of the Nε-alkyl group with residues of the protein in the cleft which accommodates the substrate side-chain, and resulting in weaker binding of the substrate.Bz-Gly-Lys(Me2) was prepared by reductive methylation of Bz-Gly-Lys. Bz-Gly-Lys(Me3) was prepared by the reaction of Bz-Gly-Lys(Me2) with diazomethane in aqueous solution. Bz-Gly-Lys(Me) and Bz-Gly-Lys(Et) were synthesized by classical coupling procedures from the appropriately protected lysine derivatives.

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Characterization of Novel Acyl Coenzyme A Dehydrogenases Involved in Bacterial Steroid Degradation

Journal of Bacteriology ◽

10.1128/jb.02420-14 ◽

2015 ◽

Vol 197 (8) ◽

pp. 1360-1367 ◽

Cited By ~ 10

Author(s):

Amanda Ruprecht ◽

Jaymie Maddox ◽

Alexander J. Stirling ◽

Nicole Visaggio ◽

Stephen Y. K. Seah

Keyword(s):

Active Site ◽

Coenzyme A ◽

Side Chain ◽

Side Chains ◽

Content Type ◽

Carbon Side Chain ◽

Acyl Coa Dehydrogenases ◽

Acyl Coenzyme A ◽

Rhodococcus Jostii

ABSTRACTThe acyl coenzyme A (acyl-CoA) dehydrogenases (ACADs) FadE34 and CasC, encoded by the cholesterol and cholate gene clusters ofMycobacterium tuberculosisandRhodococcus jostiiRHA1, respectively, were successfully purified. Both enzymes differ from previously characterized ACADs in that they contain two fused acyl-CoA dehydrogenase domains in a single polypeptide. Site-specific mutagenesis showed that only the C-terminal ACAD domain contains the catalytic glutamate base required for enzyme activity, while the N-terminal ACAD domain contains an arginine required for ionic interactions with the pyrophosphate of the flavin adenine dinucleotide (FAD) cofactor. Therefore, the two ACAD domains must associate to form a single active site. FadE34 and CasC were not active toward the 3-carbon side chain steroid metabolite 3-oxo-23,24-bisnorchol-4-en-22-oyl-CoA (4BNC-CoA) but were active toward steroid CoA esters containing 5-carbon side chains. CasC has similar specificity constants for cholyl-CoA, deoxycholyl-CoA, and 3β-hydroxy-5-cholen-24-oyl-CoA, while FadE34 has a preference for the last compound, which has a ring structure similar to that of cholesterol metabolites. Knockout of thecasCgene inR. jostiiRHA1 resulted in a reduced growth on cholate as a sole carbon source and accumulation of a 5-carbon side chain cholate metabolite. FadE34 and CasC represent unique members of ACADs with primary structures and substrate specificities that are distinct from those of previously characterized ACADs.IMPORTANCEWe report here the identification and characterization of acyl-CoA dehydrogenases (ACADs) involved in the metabolism of 5-carbon side chains of cholesterol and cholate. The two homologous enzymes FadE34 and CasC, fromM. tuberculosisandRhodococcus jostiiRHA1, respectively, contain two ACAD domains per polypeptide, and we show that these two domains interact to form a single active site. FadE34 and CasC are therefore representatives of a new class of ACADs with unique primary and quaternary structures. The bacterial steroid degradation pathway is important for the removal of steroid waste in the environment and for survival of the pathogenM. tuberculosiswithin host macrophages. FadE34 is a potential target for development of new antibiotics against tuberculosis.

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Electroluminescent properties of side-chain naphthalimide-derivated polymers

Journal de Chimie Physique ◽

10.1051/jcp:1998281 ◽

1998 ◽

Vol 95 (6) ◽

pp. 1351-1354 ◽

Cited By ~ 1

Author(s):

C.-M. Bouché ◽

P. Le Barny ◽

H. Facoetti ◽

F. Soyer ◽

P. Robin

Keyword(s):

Side Chain

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New 6-Bromotryptamine Derivatives from Marine Bacterium Pseudoalteromonas rubra QD1 - 2 and the Impact of Side Chain Length on Their Cytotoxicity

Planta Medica ◽

10.1055/s-0033-1348634 ◽

2013 ◽

Vol 79 (10) ◽

Author(s):

S He ◽

L Ding ◽

X Yan

Keyword(s):

Chain Length ◽

Marine Bacterium ◽

Side Chain ◽

Side Chain Length ◽

The Impact ◽

Pseudoalteromonas Rubra

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Evidence for Impaired Hepatic Vitamin K1 Metabolism in Patients Treated with N-Methyl-Thiotetrazole Cephalosporins

Thrombosis and Haemostasis ◽

10.1055/s-0038-1661101 ◽

1984 ◽

Vol 51 (03) ◽

pp. 358-361 ◽

Cited By ~ 78

Author(s):

H Bechtold ◽

K Andrassy ◽

E Jähnchen ◽

J Koderisch ◽

H Koderisch ◽

...

Keyword(s):

Protein C ◽

Oral Intake ◽

Bleeding Complications ◽

Side Chain ◽

Acute Administration ◽

Vitamin K1 ◽

New Class ◽

Parenteral Alimentation ◽

Hepatocellular Regeneration ◽

Echis Carinatus

SummaryIn 8 patients on no oral intake and with parenteral alimentation, administration of cephalosporins with N-methyl-thiotetrazole side chain (moxalactam, cefamandole), was associated with prolongation of prothrombin time, appearance in the circulation of descarboxy-prothrombin (counter immunoelectrophoresis and echis carinatus assay) and diminution of protein C. Acute administration of 10 mg vitamin Ki was followed by the transient appearance of vitamin K1 2,3-epoxide, indicating an impaired hepatocellular regeneration of vitamin K1 from the epoxide. Impaired hepatic vitamin K1 metabolism, tentatively ascribed to the N-methyl-thiotetrazole group, is one (but possibly not the only) cause of bleeding complications and depression of vitamin K1dependent procoagulants in patients treated with the new class of cephalosporins.

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METABOLISM OF 17α-HYDROXYPROGESTERONE-4-14C-17α-CAPROATE BY HOMOGENATES OF RAT LIVER AND HUMAN PLACENTA

Acta Endocrinologica ◽

10.1530/acta.0.0360511 ◽

1961 ◽

Vol 36 (4) ◽

pp. 511-519 ◽

Cited By ~ 6

Author(s):

Margaret Wiener ◽

Charles I. Lupa ◽

E. Jürgen Plotz

Keyword(s):

Rat Liver ◽

Human Placenta ◽

Steric Hindrance ◽

Placental Tissue ◽

Caproic Acid ◽

Major Product ◽

Side Chain ◽

Anaerobic Conditions ◽

Prolonged Action ◽

Long Acting

ABSTRACT 17α-hydroxyprogesterone-4-14C-17α-caproate (HPC), a long-acting progestational agent, was incubated with homogenates of rat liver and human placenta. The rat liver was found to reduce Ring A of HPC under anaerobic conditions to form allopregnane-3β,17α-diol-20-one-17α-caproate and pregnane-3β,17α-diol-20-one-17α-caproate, the allopregnane isomer being the major product. The caproic acid ester was neither removed nor altered during the incubation. Placental tissue did not attack HPC under conditions where the 20-ketone of progesterone was reduced. It is postulated that this absence of attack on the side chain is due to steric hindrance from the caproate ester, and that this may account for the prolonged action of HPC.

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P450 side-chain cleavage enzyme autoantibodies in canine Addison's disease

Endocrine Abstracts ◽

10.1530/endoabs.31.p329 ◽

2013 ◽

pp. 1-1

Author(s):

Alisdair Boag ◽

Kerry McLaughlin ◽

Mike Christie ◽

Peter Graham ◽

Harriet Syme ◽

...

Keyword(s):

Addison’S Disease ◽

Side Chain ◽

Addison's Disease ◽

Side Chain Cleavage ◽

Chain Cleavage ◽

Cleavage Enzyme

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Influence of Flexible Side-Chains on the Breathing Phase Transition of Pillared Layer MOFs: A Force Field Investigation

10.26434/chemrxiv.11720679.v1 ◽

2020 ◽

Author(s):

Julian Keupp ◽

Johannes P. Dürholt ◽

Rochus Schmid

Keyword(s):

First Principles ◽

Good Accuracy ◽

Field Investigation ◽

Square Lattice ◽

Side Chain ◽

Second Step ◽

Side Chains ◽

Dynamics Simulations ◽

Complex Phenomena ◽

Closed Pore

The prototypical pillared layer MOFs, formed by a square lattice of paddle- wheel units and connected by dinitrogen pillars, can undergo a breathing phase transition by a “wine-rack” type motion of the square lattice. We studied this not yet fully understood behavior using an accurate first principles parameterized force field (MOF-FF) for larger nanocrystallites on the example of Zn 2 (bdc) 2 (dabco) [bdc: benzenedicarboxylate, dabco: (1,4-diazabicyclo[2.2.2]octane)] and found clear indi- cations for an interface between a closed and an open pore phase traveling through the system during the phase transformation [Adv. Theory Simul. 2019, 2, 11]. In conventional simulations in small supercells this mechanism is prevented by periodic boundary conditions (PBC), enforcing a synchronous transformation of the entire crystal. Here, we extend this investigation to pillared layer MOFs with flexible side-chains, attached to the linker. Such functionalized (fu-)MOFs are experimen- tally known to have different properties with the side-chains acting as fixed guest molecules. First, in order to extend the parameterization for such flexible groups, 1a new parametrization strategy for MOF-FF had to be developed, using a multi- structure force based fit method. The resulting parametrization for a library of fu-MOFs is then validated with respect to a set of reference systems and shows very good accuracy. In the second step, a series of fu-MOFs with increasing side-chain length is studied with respect to the influence of the side-chains on the breathing behavior. For small supercells in PBC a systematic trend of the closed pore volume with the chain length is observed. However, for a nanocrystallite model a distinct interface between a closed and an open pore phase is visible only for the short chain length, whereas for longer chains the interface broadens and a nearly concerted trans- formation is observed. Only by molecular dynamics simulations using accurate force fields such complex phenomena can be studied on a molecular level.

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Modeling the Effects of O-sulfonation on the CID of Serine

10.26434/chemrxiv.11783628.v2 ◽

2020 ◽

Author(s):

Kenneth Lucas ◽

George Barnes

Keyword(s):

Sulfo Group ◽

High Energy ◽

Empirical Method ◽

Side Chain ◽

Energy Structure ◽

Direct Dynamics ◽

Theoretical Mass ◽

Intermolecular Proton Transfer ◽

Dynamics Simulations ◽

Semi Empirical

We present the results of direct dynamics simulations and DFT calculations aimed at elucidating the effect of \textit{O}-sulfonation on the collision induced dissociation for serine. Towards this end, direct dynamics simulations of both serine and sulfoserine were performed at multiple collision energies and theoretical mass spectra obtained. Comparisons to experimental results are favorable for both systems. Peaks related to the sulfo group are identified and the reaction dynamics explored. In particular, three significant peaks (m\z 106, 88, and 81) seen in the theoretical mass spectrum directly related to the sulfo group are analyzed as well as major peaks shared by both systems. Our analysis shows that the m\z 106 peaks result from intramolecular rearrangements, intermolecular proton transfer among complexes composed of initial fragmentation products, and at high energy side-chain fragmentation. The \mz 88 peak was found to contain multiple constitutional isomers, including a previously unconsidered, low energy structure. It was also seen that the RM1 semi empirical method was not able to obtain all of the major peaks seen in experiment for sulfoserine. In contrast, PM6 did obtain all major experimental peaks.

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Polypeptides Folding: Rules for the Calculation of the Backbone Dihedral Angles φ starting from the Amino Acid Sequence

10.26434/chemrxiv.12000132 ◽

2020 ◽

Author(s):

Michele Larocca

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Theoretical Approach ◽

Polypeptide Chain ◽

Hydrophobic Effect ◽

Side Chain ◽

Dihedral Angles ◽

Mechanical Forces ◽

Specific Chemical

Protein folding is strictly related to the determination of the backbone dihedral angles and depends on the information contained in the amino acid sequence as well as on the hydrophobic effect. To date, the type of information embedded in the amino acid sequence has not yet been revealed. The present study deals with these problematics and aims to furnish a possible explanation of the information contained in the amino acid sequence, showing and reporting rules to calculate the backbone dihedral angles φ. The study is based on the development of mechanical forces once specific chemical interactions are established among the side chain of the residues in a polypeptide chain. It aims to furnish a theoretical approach to predict backbone dihedral angles which, in the future, may be applied to computational developments focused on the prediction of polypeptide structures.

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