scholarly journals Off-pathway 3D-structure provides protection against spontaneous Asn/Asp isomerization: shielding proteins Achilles heel

2020 ◽  
Vol 53 ◽  
Author(s):  
András Láng ◽  
Imre Jákli ◽  
Kata Nóra Enyedi ◽  
Gábor Mező ◽  
Dóra K. Menyhárd ◽  
...  
Keyword(s):  
Protective Factor ◽  
Structural Integrity ◽  
3D Structure ◽  
Nucleophilic Attack ◽  
Structural Element ◽  
Backbone Conformation ◽  
Peptide Models ◽  
Geometric Descriptors ◽  
Restricted Mobility ◽  
Methylene Group

Abstract Spontaneous deamidation prompted backbone isomerization of Asn/Asp residues resulting in – most cases – the insertion of an extra methylene group into the backbone poses a threat to the structural integrity of proteins. Here we present a systematical analysis of how temperature, pH, presence of charged residues, but most importantly backbone conformation and dynamics affect isomerization rates as determined by nuclear magnetic resonance in the case of designed peptide-models. We demonstrate that restricted mobility (such as being part of a secondary structural element) may safeguard against isomerization, but this protective factor is most effective in the case of off-pathway folds which can slow the reaction by several magnitudes compared to their on-pathway counterparts. We show that the geometric descriptors of the initial nucleophilic attack of the isomerization can be used to classify local conformation and contribute to the design of stable protein drugs, antibodies or the assessment of the severity of mutations.

Peptide models. IX. A complete conformational set of For-Ala-Ala-NH2 from ab inito computations

1994 ◽  
Vol 72 (10) ◽  
pp. 2050-2070 ◽  
Author(s):  
András Perczel ◽  
Michael A. McAllister ◽  
Pál Császár ◽  
Imre G. Csizmadia
Keyword(s):  
Ab Initio ◽  
Minimum Energy ◽  
3D Structure ◽  
Geometry Optimization ◽  
Relative Energy ◽  
Field Methods ◽  
Peptide Bonds ◽  
Assignment Method ◽  
Peptide Models ◽  
Structure Assignment

This paper reports the complete set of minimum energy (i.e. stable) conformations of For-Ala-Ala-NH2 (containing three peptide bonds), computed by ab initio geometry optimization. A more confident structure and relative energy comparison of the 49 different relaxed geometries was possible using the HF/3-21G method as compared to empirical (force field) methods. The analysis of the different conformers resulted in a useful structure database, incorporating 30 different β-turns, which will have some relevance to the description of peptide folding. Spectroscopic (e.g. NMR) consequences of the reported ab initio calculations are also discussed, and a 3D-structure assignment method for proteins is provided.

scholarly journals The zinc-binding motif in tankyrases is required for the structural integrity and proper function of the catalytic domain

2021 ◽  
Author(s):  
Sven T Sowa ◽  
Lari Lehtiö
Keyword(s):  
Structural Integrity ◽  
Catalytic Domain ◽  
Zinc Binding ◽  
Structural Defects ◽  
Proper Function ◽  
Binding Motif ◽  
Acceptor Site ◽  
Structural Element ◽  
Zinc Binding Motif

Tankyrases are ADP-ribosylating enzymes that regulate many physiological processes in the cell and they are therefore possible drug targets for cancer and fibrotic diseases. The catalytic ADP-ribosyl-transferase domain of tankyrases contains a unique zinc-binding motif of unknown function. Recently, this motif was suggested to be involved in the catalytic activity of tankyrases. In this work, we set out to study the effect of the zinc-binding motif on activity, stability and structure of human tankyrases. We generated mutants of human TNKS1 and TNKS2 abolishing the zinc-binding capabilities and characterized the proteins biochemically and biophysically in vitro. We further generated a crystal structure of TNKS2, in which the zinc ion was oxidatively removed. Our work shows that the zinc-binding motif in tankyrases is a crucial structural element which is particularly important for the structural integrity of the acceptor site. While mutation of the motif rendered TNKS1 inactive likely due to introduction of major structural defects, the TNKS2 mutant remained active and displayed a different activity profile compared to the wild type.

High-resolution NMR structure of a Zn2+-containing form of the bacteriophage T5l-alanyl-d-glutamate peptidase

RSC Advances ◽  
2015 ◽  
Vol 5 (51) ◽  
pp. 41041-41049 ◽  
Author(s):  
Dmitry A. Prokhorov ◽  
Galina V. Mikoulinskaia ◽  
Nikolai V. Molochkov ◽  
Vladimir N. Uversky ◽  
Victor P. Kutyshenko
Keyword(s):  
Nmr Spectroscopy ◽  
High Resolution ◽  
Solution Structure ◽  
Structural Integrity ◽  
3D Structure ◽  
Nmr Structure ◽  
Structure Solution ◽  
High Resolution Nmr ◽  
Bacteriophage T5

The 3D-structure solution structure of the Zn2+-containing form of the bacteriophage T5 EndoT5-Zn2+is determined by the high-resolution NMR spectroscopy. The structural integrity of the entire molecule is controlled by the Zn2+binding.

scholarly journals Cyanide Hydratase Modification Using Computational Design and Docking Analysis for Improved Binding Affinity in Cyanide Detoxification

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1799
Author(s):  
Narges Malmir ◽  
Najaf Allahyari Fard ◽  
Yamkela Mgwatyu ◽  
Lukhanyo Mekuto
Keyword(s):  
Trichoderma Harzianum ◽  
Homology Modelling ◽  
3D Structure ◽  
Design Procedure ◽  
Computational Design ◽  
Ligand Docking ◽  
Nucleophilic Attack ◽  
Total Charge ◽  
Ligand Complex ◽  
Cyanide Hydratase

Cyanide is a hazardous and detrimental chemical that causes the inactivation of the respiration system through the inactivation of cytochrome c oxidase. Because of the limitation in the number of cyanide-degrading enzymes, there is a great demand to design and introduce new enzymes with better functionality. This study developed an integrated method of protein-homology-modelling and ligand-docking protein-design approaches that reconstructs a better active site from cyanide hydratase (CHT) structure. Designing a mutant CHT (mCHT) can improve the CHT performance. A computational design procedure that focuses on mutation for constructing a new model of cyanide hydratase with better activity was used. In fact, this study predicted the three-dimensional (3D) structure of CHT for subsequent analysis. Inducing mutation on CHT of Trichoderma harzianum was performed and molecular docking was used to compare protein interaction with cyanide as a ligand in both CHT and mCHT. By combining multiple designed mutations, a significant improvement in docking for CHT was obtained. The results demonstrate computational capabilities for enhancing and accelerating enzyme activity. The result of sequence alignment and homology modeling show that catalytic triad (Cys-Glu-Lys) was conserved in CHT of Trichoderma harzianum. By inducing mutation in CHT structure, MolDock score enhanced from −18.1752 to −23.8575, thus the nucleophilic attack can occur rapidly by adding Cys in the catalytic cavity and the total charge of protein in pH 6.5 is increased from −6.0004 to −5.0004. Also, molecular dynamic simulation shows a stable protein-ligand complex model. These changes would help in the cyanide degradation process by mCHT.

scholarly journals QUANTUM-CHEMICAL STUDY OF INTERACTION 1,2-ETHANEDITHIOL WITH 1,3-DICHLOROBUTENE-2 IN THE SYSTEM HYDRASINEHYDRATEKOH

2018 ◽  
Vol 1 (12) ◽  
pp. 121-127
Author(s):  
Elena Chirkina
Keyword(s):  
Carbon Atom ◽  
Quantum Chemical ◽  
Quantum Chemical Study ◽  
Chemical Study ◽  
Nucleophilic Attack ◽  
Central Carbon ◽  
Chemical Studies ◽  
Quantum Chemical Studies ◽  
Methylene Group ◽  
Mechanism Of The Reaction

According to the results of quantum-chemical studies in the framework of the theory of functional density of the electron density using the B3LYP / 6-311 ++ G (d, p) method, a theoretical mechanism of the reaction of 1,3-dichlorobutene-2 with 1,2-ethanedithiol in the hydrazine hydrateKOH system has been proposed. It has been shown that this interaction proceeds sequentially in several stages, including the nucleophilic substitution of the chlorine atom of the sp3 hybridized carbon atom to the sulfur atom with the formation of a monosubstitution product (SN2 mechanism), which under the action of alkali undergoes deprotonation of the methylene group to form an allyl carbanion . The resulting carbanion, due to the migration of hydrogen and the removal of chlorine, is converted into an allene derivative, which as a result of the intramolecular nucleophilic attack of the free thiolate group on the central carbon atom of the allene fragment closes into the final dithian cycle.

scholarly journals Modelling Long-Term Bridge Deterioration at Structural Member Level Using Artificial Intelligence Techniques

2011 ◽  
Vol 99-100 ◽  
pp. 444-453 ◽  
Author(s):  
Jae Ho Lee ◽  
Hong Guan ◽  
Yew Chaye Loo ◽  
Michael Blumenstein ◽  
Xin Ping Wang
Keyword(s):  
Neural Network ◽  
Artificial Intelligence ◽  
Asset Management ◽  
Structural Integrity ◽  
Actual Condition ◽  
Bridge Management ◽  
Structural Element ◽  
Deterioration Model ◽  
Historical Condition

Efficient use of public funds for structural integrity of bridge networks requires an effective bridge asset management technology. To achieve this, a reliable deterioration model is essential in any Bridge Management System (BMS). The deterioration rate is calculated based on historical condition ratings obtained from the structural element-level bridge inspections. Although most bridge authorities have previously conducted inspection and maintenance tasks, these past inspection records are incompatible with what are required by a typical BMS as input. Such incompatibility is a major cause for the deficiency of the current BMS outcomes. Artificial Intelligence (AI)-based bridge deterioration model has recently been developed to minimise uncertainties in predicting deterioration of structural bridge members (e.g. beams, piers etc). This model contains two components: (1) using Neural Network-based Backward Prediction Model (BPM) to generate unavailable historical condition ratings; and (2) using Time Delay Neural Network (TDNN) to perform long-term performance prediction of bridge structural members. However new problems have emerged in the process of TDNN prediction. This is because the BPM-generated condition ratings are used together with the actual condition ratings. The incompatibility between the two sets of data produces unreliable prediction outcomes during the TDNN process. This research is thus to develop a new process based on the existing method, thereby overcoming the abovementioned problems. To achieve this, the actual overall condition ratings are replaced by the BPM forward predicted condition ratings. Consequently, the outcome of this study can improve accuracy of long-term bridge deterioration prediction.

scholarly journals Development and characterization of a 3D multicell microtissue culture model of airway smooth muscle

2013 ◽  
Vol 304 (1) ◽  
pp. L4-L16 ◽  
Author(s):  
Adrian R. West ◽  
Nishat Zaman ◽  
Darren J. Cole ◽  
Matthew J. Walker ◽  
Wesley R. Legant ◽  
...  
Keyword(s):  
Smooth Muscle ◽  
Airway Smooth Muscle ◽  
Structural Integrity ◽  
Force Measurement ◽  
Ex Vivo ◽  
3D Structure ◽  
3D Culture ◽  
Rapid Screening ◽  
Tension Development ◽  
Culture Model

Airway smooth muscle (ASM) cellular and molecular biology is typically studied with single-cell cultures grown on flat 2D substrates. However, cells in vivo exist as part of complex 3D structures, and it is well established in other cell types that altering substrate geometry exerts potent effects on phenotype and function. These factors may be especially relevant to asthma, a disease characterized by structural remodeling of the airway wall, and highlights a need for more physiologically relevant models of ASM function. We utilized a tissue engineering platform known as microfabricated tissue gauges to develop a 3D culture model of ASM featuring arrays of ∼0.4 mm long, ∼350 cell “microtissues” capable of simultaneous contractile force measurement and cell-level microscopy. ASM-only microtissues generated baseline tension, exhibited strong cellular organization, and developed actin stress fibers, but lost structural integrity and dissociated from the cantilevers within 3 days. Addition of 3T3-fibroblasts dramatically improved survival times without affecting tension development or morphology. ASM-3T3 microtissues contracted similarly to ex vivo ASM, exhibiting reproducible responses to a range of contractile and relaxant agents. Compared with 2D cultures, microtissues demonstrated identical responses to acetylcholine and KCl, but not histamine, forskolin, or cytochalasin D, suggesting that contractility is regulated by substrate geometry. Microtissues represent a novel model for studying ASM, incorporating a physiological 3D structure, realistic mechanical environment, coculture of multiple cells types, and comparable contractile properties to existing models. This new model allows for rapid screening of biochemical and mechanical factors to provide insight into ASM dysfunction in asthma.

scholarly journals Shifts in Backbone Conformation of Acetylcholinesterases upon Binding of Covalent Inhibitors, Reversible Ligands and Substrates

Crystals ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1557
Author(s):  
Zoran Radić
Keyword(s):  
Conformational Changes ◽  
Dynamic Properties ◽  
Catalytic Reactions ◽  
Structural Element ◽  
X Ray ◽  
Ache Inhibitors ◽  
Allosteric Interaction ◽  
Backbone Conformation ◽  
Covalent Inhibitors ◽  
Planar Geometries

The influence of ligand binding to human, mouse and Torpedo californica acetylcholinesterase (EC 3.1.1.7; AChE) backbone structures is analyzed in a pairwise fashion by comparison with X-ray structures of unliganded AChEs. Both complexes with reversible ligands (substrates and inhibitors) as well as covalently interacting ligands leading to the formation of covalent AChE conjugates of tetrahedral and of trigonal-planar geometries are considered. The acyl pocket loop (AP loop) in the AChE backbone is recognized as the conformationally most adaptive, but not necessarily sterically exclusive, structural element. Conformational changes of the centrally located AP loop coincide with shifts in C-terminal α-helical positions, revealing interacting components for a potential allosteric interaction within the AChE backbone. The stabilizing power of the aromatic choline binding site, with the potential to attract and pull fitting entities covalently tethered to the active Ser, is recognized. Consequently, the pull can promote catalytic reactions or relieve steric pressure within the impacted space of the AChE active center gorge. These dynamic properties of the AChE backbone inferred from the analysis of static X-ray structures contribute towards a better understanding of the molecular template important in the structure-based design of therapeutically active molecules, including AChE inhibitors as well as reactivators of conjugated, inactive AChE.

Sign in / Sign up

Export Citation Format

Share Document