scholarly journals CYP154C5 Regioselectivity in Steroid Hydroxylation Explored by Substrate and Protein Engineering

2020 ◽  
Author(s):  
Paula Bracco ◽  
Hein J. Wijma ◽  
Bastian Nicolai ◽  
Jhon Alexander Rodriguez Buitrago ◽  
Thomas Klünemann ◽  
...  
Keyword(s):  
Active Site ◽  
Md Simulation ◽  
Binding Mode ◽  
Valuable Insight ◽  
P450 Monooxygenase ◽  
Steroid Hydroxylation ◽  
Substrate Engineering ◽  
Function Relationship ◽  
Relationship Of ◽  
Insight Into

AbstractCYP154C5 from Nocardia farcinica is a P450 monooxygenase able to hydroxylate a range of steroids with high regio- and stereoselectivity at the 16α-position. Using protein and substrate engineering based on the crystal structure of CYP154C5, an altered regioselectivity of the enzyme in steroid hydroxylation could be achieved. Thus, conversion of progesterone by mutant CYP154C5 F92A resulted in formation of the corresponding 21-hydroxylated product 11-deoxycorticosterone in addition to 16α-hydroxylation. Using MD simulation, this altered regioselectivity appeared to result from an alternate binding mode of the steroid in the active site of mutant F92A. MD simulation further suggested that water entrance to the active site caused higher uncoupling in this mutant. Moreover, exclusive 15α-hydroxylation was observed for wild-type CYP154C5 in the conversion of 5α-androstan-3-one, lacking an oxy-functional group at C17. Overall, our data give valuable insight into the structure-function relationship of this cytochrome P450 monooxygenase for steroid hydroxylation.

Binding of Tetrahymena dynein to axonemes of Marsilea vestita lacking the outer dynein arm

1985 ◽  
Vol 73 (1) ◽  
pp. 299-310
Author(s):  
J.S. Hyams
Keyword(s):  
Electron Microscopy ◽  
Polyacrylamide Gel Electrophoresis ◽  
Valuable Insight ◽  
Marsilea Vestita ◽  
Thin Section Electron Microscopy ◽  
Section Electron ◽  
And Function ◽  
Relationship Of ◽  
The Relationship ◽  
Insight Into

Axonemes from the heterosporous water fern Marsilea vestita were fixed in the presence of tannic acid and examined by thin-section electron microscopy. Transverse sections revealed the normal 9+2 configuration except for the absence of the outer of the two dynein arms. Both arms were normally preserved in parallel preparations of Chlamydomonas axonemes. Isolated dynein from the ciliated protozoon Tetrahymena bound to Marsilea axonemes at the site normally occupied by the outer arm. Dynein binding was partially reversed by ATP as judged by both electron microscopy and polyacrylamide gel electrophoresis. This system should provide a valuable insight into the biochemistry and function of the inner dynein arm and the relationship of the two arms to motility in more conventionally equipped axonemes.

scholarly journals The Role of the Fibronectin IGD Motif in Stimulating Fibroblast Migration

2007 ◽  
Vol 282 (49) ◽  
pp. 35530-35535 ◽  
Author(s):  
Christopher J. Millard ◽  
Ian R. Ellis ◽  
Andrew R. Pickford ◽  
Ana M. Schor ◽  
Seth L. Schor ◽  
...  
Keyword(s):  
Fibroblast Migration ◽  
Wide Range ◽  
Migration Stimulating Factor ◽  
Function Relationship ◽  
Relationship Of ◽  
Stimulating Factor ◽  
Insight Into ◽  
Stimulation Of

The motogenic activity of migration-stimulating factor, a truncated isoform of fibronectin (FN), has been attributed to the IGD motifs present in its FN type 1 modules. The structure-function relationship of various recombinant IGD-containing FN fragments is now investigated. Their structure is assessed by solution state NMR and their motogenic ability tested on fibroblasts. Even conservative mutations in the IGD motif are inactive or have severely reduced potency, while the structure remains essentially the same. A fragment with two IGD motifs is 100 times more active than a fragment with one and up to 106 times more than synthetic tetrapeptides. The wide range of potency in different contexts is discussed in terms of cryptic FN sites and cooperativity. These results give new insight into the stimulation of fibroblast migration by IGD motifs in FN.

scholarly journals Snap-jaw morphology is specialized for high-speed power amplification in the Dracula ant, Mystrium camillae

2018 ◽  
Vol 5 (12) ◽  
pp. 181447 ◽  
Author(s):  
Fredrick J. Larabee ◽  
Adrian A. Smith ◽  
Andrew V. Suarez
Keyword(s):  
High Speed ◽  
Muscle Power ◽  
Element Analysis ◽  
Predator Prey ◽  
Mantis Shrimp ◽  
Power Amplification ◽  
Form Function ◽  
Function Relationship ◽  
Relationship Of ◽  
Insight Into

What is the limit of animal speed and what mechanisms produce the fastest movements? More than natural history trivia, the answer provides key insight into the form–function relationship of musculoskeletal movement and can determine the outcome of predator–prey interactions. The fastest known animal movements belong to arthropods, including trap-jaw ants, mantis shrimp and froghoppers, that have incorporated latches and springs into their appendage systems to overcome the limits of muscle power. In contrast to these examples of power amplification, where separate structures act as latch and spring to accelerate an appendage, some animals use a ‘snap-jaw’ mechanism that incorporates the latch and spring on the accelerating appendage itself. We examined the kinematics and functional morphology of the Dracula ant, Mystrium camillae , who use a snap-jaw mechanism to quickly slide their mandibles across each other similar to a finger snap. Kinematic analysis of high-speed video revealed that snap-jaw ant mandibles complete their strike in as little as 23 µsec and reach peak velocities of 90 m s −1 , making them the fastest known animal appendage. Finite-element analysis demonstrated that snap-jaw mandibles were less stiff than biting non-power-amplified mandibles, consistent with their use as a flexible spring. These results extend our understanding of animal speed and demonstrate how small changes in morphology can result in dramatic differences in performance.

Structure–function relationship of terpenoid glycosyltransferases from plants

2021 ◽  
Author(s):  
Elisabeth Kurze ◽  
Matthias Wüst ◽  
Jieren Liao ◽  
Kate McGraphery ◽  
Thomas Hoffmann ◽  
...  
Keyword(s):  
Enzymatic Activity ◽  
Structure Function ◽  
Active Site ◽  
Substrate Preference ◽  
Uridine Diphosphate ◽  
Hydrophobic Pocket ◽  
Structure Function Relationship ◽  
Spatial Size ◽  
Function Relationship ◽  
Relationship Of

The spatial size of the catalytic centre and a large hydrophobic pocket in the active site affect the enzymatic activity and substrate preference of uridine diphosphate–sugar-dependent terpenoid glycosyltransferases in plants.

scholarly journals Advances in Molecular Dynamics Simulations and Enhanced Sampling Methods for the Study of Protein Systems

2020 ◽  
Vol 21 (17) ◽  
pp. 6339
Author(s):  
Raudah Lazim ◽  
Donghyuk Suh ◽  
Sun Choi
Keyword(s):  
Molecular Dynamics ◽  
Md Simulation ◽  
Enhanced Sampling ◽  
Structure Based Drug Design ◽  
Simulation Tools ◽  
Computer Calculations ◽  
Function Relationship ◽  
Dynamics Simulations ◽  
Relationship Of

Molecular dynamics (MD) simulation is a rigorous theoretical tool that when used efficiently could provide reliable answers to questions pertaining to the structure-function relationship of proteins. Data collated from protein dynamics can be translated into useful statistics that can be exploited to sieve thermodynamics and kinetics crucial for the elucidation of mechanisms responsible for the modulation of biological processes such as protein-ligand binding and protein-protein association. Continuous modernization of simulation tools enables accurate prediction and characterization of the aforementioned mechanisms and these qualities are highly beneficial for the expedition of drug development when effectively applied to structure-based drug design (SBDD). In this review, current all-atom MD simulation methods, with focus on enhanced sampling techniques, utilized to examine protein structure, dynamics, and functions are discussed. This review will pivot around computer calculations of protein-ligand and protein-protein systems with applications to SBDD. In addition, we will also be highlighting limitations faced by current simulation tools as well as the improvements that have been made to ameliorate their efficiency.

Insight into the Binding Mode between HIV-1 Integrase and Pyrimidone Analogue Inhibitors with MD Simulation and 3D-QSAR

2013 ◽  
Vol 9 (3) ◽  
pp. 420-433 ◽  
Author(s):  
Songyao Ma ◽  
Wei Ye ◽  
Dingjue Ji ◽  
Hai-Feng Chen
Keyword(s):  
Md Simulation ◽  
3D Qsar ◽  
Binding Mode ◽  
Insight Into ◽  
Hiv 1

scholarly journals Identification of SARS-CoV2 Main Protease Coldspots Suitable for Drug Targeting

2020 ◽  
Author(s):  
Navaneethakrishnan Krishnamoorthy ◽  
Khalid Fakhro
Keyword(s):  
Active Site ◽  
Missense Mutations ◽  
The Novel ◽  
X Ray ◽  
X Ray Crystallography ◽  
Main Protease ◽  
New Perspective ◽  
Function Relationship ◽  
Novel Coronavirus ◽  
Relationship Of

Abstract Most attempts to target the novel coronavirus SARS-CoV2 are focusing on the main protease (Mpro) 1,2. We already have access to high resolution 3D-structures of the SARS-CoV2 Mpro, which were developed with inhibitors as co-crystals using X-ray crystallography 3-9. However, >19,000 missense mutations in the Mpro have already been reported 10. The mutations encompassing 282 amino acid positions and these “hotspots” might change the Mpro structure and activity, potentially rendering novel antivirals and vaccines ineffective. Here we identified 24 mutational “coldspots” that have resisted mutation since the virus was first detected. We compared the structure-function relationship of these coldspots with several SARS-CoV2 Mpro X-ray crystal structures. We found that three coldspot residues (Leu141, Phe185 and Gln192) help to form the active site, while six (Gly2, Arg4, Tyr126, Lys137, Leu141 and Leu286) contribute to dimer formation that is required for Mpro activity. Importantly, seven coldpots are conserved among other coronaviruses and available on the surface of the active site and at the dimer interface for targeting. The identification and short list of these coldspots offers a new perspective to target the SARS-CoV2 Mpro while avoiding mutation-based drug resistance.

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