Understanding the thermostability and activity of Bacillus subtilis lipase mutants: insights from molecular dynamics simulations

Construction of highly active and stable recombinant nattokinase by engineered bacteria and computational design

Nattokinase (NK) is an enzyme that has been recognized as a new potential thrombolytic drug due to its strong thrombolytic activity. However, it is difficult to maintain the enzyme activity of NK during high temperature environment of industrial production. In this study, we constructed six NK mutants with potential for higher thermostability using a rational protein engineering strategy integrating free energy-based methods and molecular dynamics (MD) simulation. Then, wild-type NK and NK mutants were expressed in Escherichia coli (E. coli), and their thermostability and thrombolytic activity were tested. The results showed that, compared with wild-type NK, the mutants Y256P, Q206L and E156F all had improved thermostability. The optimal mutant Y256P showed a higher melting temperature (Tm) of 77.4 °C, an increase of 4 °C in maximum heat-resistant temperature and an increase of 51.8 % in activity at 37 °C compared with wild-type NK. Moreover, we also explored the mechanism of the increased thermostability of these mutants by analysing the MD trajectories under different simulation temperatures.

Characterization and rational engineering of an alkaline-tolerant azoreductase derived from Roseibium sp. H3510 for enhanced decolorization of azo dyes

rAzoR2326, an azoreductase derived from Roseibium sp. H3510, functions as an FMN-dependent homodimer utilizing NADH as cofactor. It demonstrated maximum activity at 45 °C and retained moderate activity above 50 °C, exhibiting stability from pH 7-10. Evolution and structure guided rational design of wild-type rAzoR2326 (WT) efficiently yielded 6 single-point mutants with improved thermostability and activity from a 22-variant library. Further combinatorial mutation led to mutant M20 with substantially enhanced thermostability (15-fold longer half-life at 50 °C) and activity (3.24-fold higher kcat/Km). M20 exhibited superior catalytic properties for decolorizing Allura Red compared to WT. Specifically, its decolorization capacity at pH 10.0 was 4.26-fold higher than WT. Additionally, M20 demonstrated remarkable thermostability, retaining 76.83 % decolorization activity for Allura Red after 120 min at 50 °C, whereas WT nearly lost all catalytic activity under the same conditions. Molecular dynamics simulations revealed the structural changes in M20, such as improved hydrogen bonding and a new C-H···π interaction, led to a more compact and rigid enzyme structure. This resulted in a more stable FMN-binding pocket and substrate tunnel, thereby improving the catalytic stability and activity of M20. Given its enhanced dye decolorization ability and alkaline tolerance, M20 shows promise as a biocatalyst for treating azo dye effluents.

In-silico assessment of novel peptidomimetics inhibitor targeting STAT3 and STAT4 N-terminal domain dimerization: A comprehensive study using molecular docking, molecular dynamics simulation, and binding free energy analysis

Dysregulation in Janus kinase-Signal Transducer and Activation of Transcription (JAK-STAT) pathway is closely linked to various cancer types. The N-terminal domain (NTD) of STAT proteins, upon dimerization, assumes a multifaceted role with remarkable adaptability in mediating interactions between proteins. Consequently, the strategic targeting of the N-terminal domain of STATs has emerged as a promising tactic for disrupting dimerization and impeding the translocation of STAT proteins. In this study, we have deployed an integrated in-silico methodology to rationally design Peptidomimetic foldamers as inhibitors of the N-terminal domains of STAT3 and STAT4, with the objective of disrupting protein dimerization. Consequently, we have judiciously designed a series of peptidomimetics that encompass β3-amino acids, bearing side chains that mimic the residues within interface II of the dimeric structures of the NTDs. Employing molecular docking techniques; we have assessed the binding affinity of these designed peptidomimetics toward both the NTDs. Furthermore, we have conducted an evaluation of the stability and conformational alterations within the docked complexes over an extensive Molecular Dynamics, subsequently computing the binding free energy utilizing MM/PBSA calculations. Our findings unequivocally demonstrate that the peptidomimetic foldamers we have devised (Peptide-A, Peptide-B, and Peptide-C) exhibit a propensity to bind to and impede the dimerization process of the NTDs of both STAT3 and STAT4. These outcomes serve to underscore the potential of these meticulously designed peptidomimetics as potential candidates meriting further exploration in the realm of cancer prevention and management.

Design, synthesis and antimicrobial activity of novel quinoline derivatives: an in silico and in vitro study

A series of new quinoline derivatives has been designed, synthesized and evaluated as antibacterial and antifungal agents functioning as peptide deformylase enzyme (PDF) inhibitors and fungal cell wall disruptors on the basis of computational and experimental methods. The molecular docking and ADMET assessment aided in the synthesis of quinoline derivatives starting from 6-amino-4-methyl-1H-quinoline-2-one substituted with different types of sulfonyl/benzoyl/propargyl moieties. These newly synthesized compounds were evaluated for their in vitro antibacterial and antifungal activity. Antibacterial screening of all compounds showed excellent MIC value (MIC, 50 - 3.12 µg/mL) against bacterial strains, viz. Bacillus cerus, Staphylococcus, Pseudomonas and Escherichia coli. Compounds 2 and 6 showed better activity. Fractional inhibitory concentration (FIC) values of compounds were lowered by 1/2 to 1/128 of the original MIC values when a combinatorial screening with reference drugs was performed. Further, antifungal screening against fungal strains, viz. A. flavus, A. niger, F. oxysporum and C. albicans also showed that all compounds were potentially active and compound 6 being the most potent. Further, the cytotoxicity experiments revealed that compound 6 was the least toxic molecule. The molecular dynamics (MD) simulation investigations elucidated the conformational stability of compound 6-PDF complex with flexible binding pocket residues. The highest number of stable hydrogen bonds with the PDF residues during the entire simulation time illustrated strong binding affinity of compound 6 with PDF.Communicated by Ramaswamy H. Sarma.

Thermodynamics of a hyperthermostable carboxylesterase from Anoxybacillus geothermalis D9

Hyperthermostable enzymes are highly desirable biocatalysts due to their exceptional stability at extreme temperatures. Recently, a hyperthermostable carboxylesterase EstD9 from Anoxybacillus geothermalis D9 was biochemically characterized. The enzyme exhibited remarkable stability at high temperature. In this study, we attempted to probe the conformational adaptability of EstD9 under extreme conditions via in silico approaches. Circular dichroism revealed that EstD9 generated new β-sheets at 80 °C, making the core of the hydrolase fold more stable. Interestingly, the profiles of molecular dynamics simulation showed the lowest scores of radius of gyration and solvent accessible surface area (SASA) at 80 °C. Three loops were responsible for protecting the catalytic site, which resided at the interface between the large and cap domains. To further investigate the structural adaptation in extreme conditions, the intramolecular interactions of the native structure were investigated. EstD9 revealed 18 hydrogen bond networks, 7 salt bridges, and 9 hydrophobic clusters, which is higher than the previously reported thermostable Est30. Collectively, the analysis indicates that intramolecular interactions and structural dynamics play distinct roles in preserving the overall EstD9 structure at elevated temperatures. This work is relevant to both fundamental and applied research involving protein engineering of industrial thermostable enzymes.

Lipase A from Bacillus subtilis: Substrate Binding, Conformational Dynamics, and Signatures of a Lid

Protein-ligand binding studies are crucial for understanding the molecular basis of biological processes and for further advancing industrial biocatalysis and drug discovery. Using computational modeling and molecular dynamics simulations, we investigated the binding of a butyrate ester substrate to the lipase A (LipA) enzyme of Bacillus subtilis. Besides obtaining a close agreement of the binding free energy with the experimental value, the study reveals a remarkable reorganization of the catalytic triad upon substrate binding, leading to increased essential hydrogen bond populations. The investigation shows the distortion of the oxyanion hole in both the substrate-bound and unbound states of LipA and highlights the strengthening of the same in the tetrahedral intermediate complex. Principal component analysis of the unbound ensemble reveals the dominant motion in LipA to be the movement of Loop-1 (Tyr129-Arg142) between two states that cover and uncover the active site, mirroring that of a lid prevalent in several lipases. This lid-like motion of Loop-1 is also supported by its tendency to spontaneously open up at an oil-water interface. Overall, this study provides valuable insights into the impact of substrate binding on the structure, flexibility, and conformational dynamics of the LipA enzyme.

Computer-Aided Lipase Engineering for Improving Their Stability and Activity in the Food Industry: State of the Art

As some of the most widely used biocatalysts, lipases have exhibited extreme advantages in many processes, such as esterification, amidation, and transesterification reactions, which causes them to be widely used in food industrial production. However, natural lipases have drawbacks in terms of organic solvent resistance, thermostability, selectivity, etc., which limits some of their applications in the field of foods. In this systematic review, the application of lipases in various food processes was summarized. Moreover, the general structure of lipases is discussed in-depth, and the engineering strategies that can be used in lipase engineering are also summarized. The protocols of some classical methods are compared and discussed, which can provide some information about how to choose methods of lipase engineering. Thermostability engineering and solvent tolerance engineering are highlighted in this review, and the basic principles for improving thermostability and solvent tolerance are summarized. In the future, comput er-aided technology should be more emphasized in the investigation of the mechanisms of reactions catalyzed by lipases and guide the engineering of lipases. The engineering of lipase tunnels to improve the diffusion of substrates is also a promising prospect for further enhanced lipase activity and selectivity.

Application of molecular dynamics simulation in the field of food enzymes: improving the thermal-stability and catalytic ability

Enzymes can produce high-quality food with low pollution, high function, high acceptability, and medical aid. However, most enzymes, in their native form, do not meet the industrial requirements. Sequence-based and structure-based methods are the two main strategies used for enzyme modification. Molecular Dynamics (MD) simulation is a sufficiently comprehensive technology, from a molecular perspective, which has been widely used for structure information analysis and enzyme modification. In this review, we summarize the progress and development of MD simulation, particularly for software, force fields, and a standard procedure. Subsequently, we review the application of MD simulation in various food enzymes for thermostability and catalytic improvement was reviewed in depth. Finally, the limitations and prospects of MD simulation in food enzyme modification research are discussed. This review highlights the significance of MD simulation and its prospects in food enzyme modification.

Structural dynamics and mechanistic action guided engineering of lipolytic enzymes

Lipases have been established as important biocatalysts in several industrial applications, owing to their diverse substrate specificity. The availability of data on three-dimensional crystal structures for various lipases offers an opportunity for modulating their structural and functional aspects to design and engineer better versions of lipases. With the aim of investigating the structural components governing the extremophilic behavior of lipases, structural analysis of microbial lipases was performed using advanced bioinformatics and molecular dynamics simulation approaches. In sequences and functionally distinct alkaliphilic and thermophilic lipases were investigated for their functional properties to understand the distinguishing features of their structures. The alkaliphilic lipase from Bacillus subtilis (LipA) showed conformational changes in the loop region Ala132-Met137, subsequently, the active site residue His156 shows two conformations, toward the active site nucleophilic residues Ser77 and away from the Ser77. Interestingly, the active site of LipA is more solvent-exposed and can be correlated with the adoption of an open conformation which might extend and expose the active site region to solvents during the catalysis process. Furthermore, the MD simulation of thermophilic lipase from marine Streptomyces (MAS1) revealed the role of N- and C-terminal regions with disulfide bridges and identified a metal ion binding site that facilitates the enzyme stability. The novel thermo-alkaliphilic lipase can be designed to integrate the stability features of MAS1 into the alkaliphilic LipA. These structural-level intrinsic characteristics can be used for lipase engineering to amend the lipase activity and stability as per the requirements of the industrial processes.

Structural features, temperature adaptation and industrial applications of microbial lipases from psychrophilic, mesophilic and thermophilic origins

Microbial lipases are very prominent biocatalysts because of their ability to catalyze a wide variety of reactions in aqueous and non-aqueous media. Here microbial lipases from different origins (psychrophiles, mesophiles, and thermophiles) have been reviewed. This review emphasizes an update of structural diversity in temperature adaptation and industrial applications, of psychrophilic, mesophilic, and thermophilic lipases. The microbial origins of lipases are logically dynamic, proficient, and also have an extensive range of industrial uses with the manufacturing of altered molecules. It is therefore of interest to understand the molecular mechanisms of adaptation to temperature in occurring lipases. However, lipases from extremophiles (psychrophiles, and thermophiles) are widely used to design biotransformation reactions with higher yields, fewer byproducts, or useful side products and have been predicted to catalyze those reactions also, which otherwise are not possible with the mesophilic lipases. Lipases as a multipurpose biological catalyst have given a favorable vision in meeting the needs of several industries such as biodiesel, foods, and drinks, leather, textile, detergents, pharmaceuticals, and medicals.

Structural insights into conformational stability and binding of thiazolo-[2,3-b] quinazolinone derivatives with EGFR-TKD and in-vitro study

Heterocyclic molecules are well-known drugs against various diseases including cancer. Many tyrosine kinase inhibitors including erlotinib, osimertinib, and sunitinib were developed and approved but caused adverse effects among treated patients. Which prevents them from being used as cancer therapeutics. In this study, we strategically developed heterocyclic thiazolo-[2,3-b]quinazolinone derivatives by an organic synthesis approach. These synthesized molecules were assessed against the epidermal growth factor receptor tyrosine kinase domain (EGFR-TKD) by in silico methods. Molecular docking simulations unravel derivative 17 showed better binding energy scores and followed Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) properties. The binding affinity displayed by synthetic congener and reference molecule erlotinib was found to be -8.26 ± 0.0033 kcal/mol and -7.54 ± 0.1411 kcal/mol with the kinase domain. Further, molecular dynamic simulations were conducted thrice to validate the molecular docking study and achieved significant results. Both synthetic derivative and reference molecule attained stability in the active site of the TKD. The synthetic congener and erlotinib showed free energy binding (ΔGbind) -102.975 ± 3.714 kJ/mol and -130.378 ± 0.355 kJ/mol computed by Molecular Mechanics Poison Boltzmann Surface Area (MM-PBSA) method. In addition, the motions of each sampled system including the Apo complex were determined by the principal component analysis and Gibbs energy landscape analysis. The in-vitro apoptosis study was performed using MCF-7 and H-1299 cancer cell lines. However, thiazolo-[2,3-]-quinazoline derivative 17 showed fair anti-proliferative activity against MCF-7 and H-1299. Further, the in-vivo study is necessary to determine the effectivity of the potent anti-proliferative, non-toxic molecule against TKD.

Interdisciplinary in silico studies to understand in-depth molecular level mechanism of drug resistance involving NS3-4A protease of HCV

Hepatitis C virus (HCV) causes hepatitis, a life-threatening disease responsible for liver cirrhosis. Urgent measures have been taken to develop therapeutics against this deadly pathogen. NS3/4A protease is an extremely important target. A series of inhibitors have been developed against this viral protease including Faldaprevir. Unfortunately, the error-prone viral RNA polymerase causes the emergence of resistance, thereby causing reduced effectiveness of those peptidomimetic inhibitors. Among the drug resistant variants, three single amino acid residues (R155, A156 and D168) are notable for their presence in clinical isolates and also their effectivity against most of the known inhibitors in clinical development. Therefore, it is crucial to understand the mechanistic role of those drug resistant variants while designing potent novel inhibitors. In this communication, we have deeply analyzed through using in silico studies to understand the molecular mechanism of alteration of inhibitor binding between wild type and its R155K, A156V and D168V variants. Principal component analysis was carried to identify the backbone fluctuations of important residues in HCV NS3/4A responsible for the inhibitor binding and maintaining drug resistance. Free energy landscape as a function of the principal components has been used to identify the stability and conformation of the key residues that regulate inhibitor binding and their impact in developing drug resistance. Our findings are consistent with the trend of experimental results. The observations are also true in case of other Faldaprevir-like peptidomimetic inhibitors. Understanding this binding mechanism would be significant for the development of novel inhibitors with less susceptibility towards drug resistance.

Deciphering the thermotolerance of chitinase O from Chitiniphilus shinanonensis by in vitro and in silico studies

Biochemical and biophysical studies revealed that chitinase O from Chitiniphilus shinanonensis (CsChiO) exhibits considerable thermotolerance, possibly due to the formation of a stable structural conformation. CsChiO is an exochitinase with a temperature optimum of 70 °C. The secondary structures of CsChiO and its catalytic domain (Cat-CsChiO) are only marginally affected upon heating up to 90 °C, as revealed by circular dichroism (CD) spectroscopy. Differential scanning calorimetric (DSC) studies revealed that CsChiO exhibits two endothermic transitions at ca. 51 °C (T_m1) and 59 °C (T_m2), whereas Cat-CsChiO shows a single endothermic transition at 52 °C. Together, the CD and DSC analyses suggested that the catalytic domain of CsChiO undergoes a thermotropic transition at ~52 °C from native state to another stable structural conformation. Results from molecular dynamic simulations corroborated that Cat-CsChiO adopts a stable structural conformation above 50 °C by partial unfolding. Thermotolerant CsChiO would be useful for the conversion of chitin, which is highly abundant, to biologically active COS. This study unveiled the adaptability of enzymes/proteins in nature to perform biological functions at elevated temperatures.

Exploring binding stability of hydroxy-3-(4-hydroxyphenyl)-5-(4-nitrophenyl)-5,5a,7,8,9,9a-hexahydrothiazolo[2,3-b] quinazolin-6-one with T790M/L858R EGFR-TKD

Cancer causes innumerable deaths every year globally. Breast cancer and non-small cell lung carcinoma are the most prevalent worldwide. EGFR-TKD is a neoplastic survival therapeutic target in a wide array of carcinoma cells. Various non-specific tyrosine kinase inhibitors lead to hyperphosphorylation and overexpression of EGFR-TKD and further mutations recognise deletion of exon 19. In this work, we study the binding affinity, binding stability, and strength of hydroxy-3-(4-hydroxyphenyl)-5-(4-nitrophenyl)-5,5a,7,8,9,9a-hexahydrothiazolo[2,3-b] quinazolin-6-one with TMLR mutated EGFR-TKD (T790M/L858R). The collective motions, residual mobility, and flexibility of TMLR mutated EGFR-TKD bound with reference and title molecule were calculated by principal component analysis. The meta-state conformations of both the simulated complexes were determined by Gibb's energy landscape analysis. The binding affinity exhibited by thiazolo-[2,3-b] quinazolinone and the reference molecule was found to be -7.95 ± 0.088 Kcal/mol and -9.13 ± 0.018 kcal/mol with TMLR mutated EGFR-TKD. The alignment of both the docked complexes was done by blosum40 matrix. Similar spatial orientations were exhibited by the synthesised ligand in the binding pocket of TMLR mutated EGFR-TKD, corresponding to the reference ligand. The ligand stability was computed for 100 ns. In addition, the radius of gyration, solvent accessible surface area, hydrogen bonds formed was calculated. The average ΔGbind of thiazolo-[2,3-b] quinazolinone was -41.212 ± 0.834 kJ/mol and for reference ligand -71.938 ± 0.367 kJ/mol, calculated by MM-PBSA. ADMET analysis concludes thiazolo-[2,3-b] quinazolinone derivative is safe. Further research work is encouraged to determine the efficacy of thiazolo-[2,3-b] quinazolinone against in vivo models.Communicated by Ramaswamy H. Sarma.

Insights of conformational dynamics on catalytic activity in the computational stability design of Bacillus subtilis LipA

In protein engineering, the contributions of individual mutations to designed combinatorial mutants are unpredictable. Screening designed mutations that affect enzyme catalytic activity enables evolutions towards efficient activities. Here, Bacillus subtilis LipA (BSLA) was selected as a model protein for thermostabilization designs, and the circular dichroism measurements showed six combinatorial designs with improved stability (from 5.81 °C to 13.61 °C). Based on molecular dynamic simulations, the conformational dynamics of the mutants revealed that mutations alter the populations of conformational states and the increased ensembles of inactive conformations might lead to a reduction in activity. We further demonstrated that the mutations responsible for the reduced enzyme catalytic activity involved a short dynamic correlation path to disturbing the equilibrium conformation of active sites. By removing N82V, which had a close dynamic correlation to the active sites in mutant D3, the redesigned mutant RD3 had an increased activity of 57.6%. By combining computational simulation with experimental verification, this work established that essential sites to counteract the activity-stability trade-off in multipoint combinatorial mutants could be computationally predicted and thus provide a possible strategy by which to indirectly or directly guide protein design.

Critical assessment of structure-based approaches to improve protein resistance in aqueous ionic liquids by enzyme-wide saturation mutagenesis

Ionic liquids (IL) and aqueous ionic liquids (aIL) are attractive (co-)solvents for green industrial processes involving biocatalysts, but often reduce enzyme activity. Experimental and computational methods are applied to predict favorable substitution sites and, most often, subsequent site-directed surface charge modifications are introduced to enhance enzyme resistance towards aIL. However, almost no studies evaluate the prediction precision with random mutagenesis or the application of simple data-driven filtering processes. Here, we systematically and rigorously evaluated the performance of 22 previously described structure-based approaches to increase enzyme resistance to aIL based on an experimental complete site-saturation mutagenesis library of Bacillus subtilis Lipase A (BsLipA) screened against four aIL. We show that, surprisingly, most of the approaches yield low gain-in-precision (GiP) values, particularly for predicting relevant positions: 14 approaches perform worse than random mutagenesis. Encouragingly, exploiting experimental information on the thermostability of BsLipA or structural weak spots of BsLipA predicted by rigidity theory yields GiP = 3.03 and 2.39 for relevant variants and GiP = 1.61 and 1.41 for relevant positions. Combining five simple-to-compute physicochemical and evolutionary properties substantially increases the precision of predicting relevant variants and positions, yielding GiP = 3.35 and 1.29. Finally, combining these properties with predictions of structural weak spots identified by rigidity theory additionally improves GiP for relevant variants up to 4-fold to ∼10 and sustains or increases GiP for relevant positions, resulting in a prediction precision of ∼90% compared to ∼9% in random mutagenesis. This combination should be applicable to other enzyme systems for guiding protein engineering approaches towards improved aIL resistance.

Targeting N-Terminal Human Maltase-Glucoamylase to Unravel Possible Inhibitors Using Molecular Docking, Molecular Dynamics Simulations, and Adaptive Steered Molecular Dynamics Simulations

There are multiple drugs for the treatment of type 2 diabetes, including traditional sulfonylureas biguanides, glinides, thiazolidinediones, α-glucosidase inhibitors, glucagon-like peptide-1 (GLP-1) receptor agonists, dipeptidyl peptidase IV (DPP-4) inhibitors, and sodium-glucose cotransporter 2 (SGLT2) inhibitors. α-Glucosidase inhibitors have been used to control postprandial glucose levels caused by type 2 diabetes since 1990. α-Glucosidases are rather crucial in the human metabolic system and are principally found in families 13 and 31. Maltase-glucoamylase (MGAM) belongs to glycoside hydrolase family 31. The main function of MGAM is to digest terminal starch products left after the enzymatic action of α-amylase; hence, MGAM becomes an efficient drug target for insulin resistance. In order to explore the conformational changes in the active pocket and unbinding pathway for NtMGAM, molecular dynamics (MD) simulations and adaptive steered molecular dynamics (ASMD) simulations were performed for two NtMGAM-inhibitor [de-O-sulfonated kotalanol (DSK) and acarbose] complexes. MD simulations indicated that DSK bound to NtMGAM may influence two domains (inserted loop 1 and inserted loop 2) by interfering with the spiralization of residue 497–499. The flexibility of inserted loop 1 and inserted loop 2 can influence the volume of the active pocket of NtMGAM, which can affect the binding progress for DSK to NtMGAM. ASMD simulations showed that compared to acarbose, DSK escaped from NtMGAM easily with lower energy. Asp542 is an important residue on the bottleneck of the active pocket of NtMGAM and could generate hydrogen bonds with DSK continuously. Our theoretical results may provide some useful clues for designing new α-glucosidase inhibitors to treat type 2 diabetes.

Temperature-resistant and solvent-tolerant lipases as industrial biocatalysts: Biotechnological approaches and applications

The development of new biocatalytic systems to replace the chemical catalysts, with suitable characteristics in terms of efficiency, stability under high temperature reactions and in the presence of organic solvents, reusability, and eco-friendliness is considered a very important step to move towards the green processes. From this basis, the use of lipase as a catalyst is highly desired for many industrial applications because it offers the reactions in which could be used, stability in harsh conditions, reusability and a greener process. Therefore, the introduction of temperature-resistant and solvent-tolerant lipases have become essential and ideal for industrial applications. Temperature-resistant and solvent-tolerant lipases have been involved in many large-scale applications including biodiesel, detergent, food, pharmaceutical, organic synthesis, biosensing, pulp and paper, textile, animal feed, cosmetics, and leather industry. So, the present review provides a comprehensive overview of the industrial use of lipase. Moreover, special interest in biotechnological and biochemical techniques for enhancing temperature-resistance and solvent-tolerance of lipases to be suitable for the industrial uses.

Surface charged amino acid-based strategy for rational engineering of kinetic stability and specific activity of enzymes: Linking experiments with computational modeling

A rational workflow for engineering kinetically stable enzymes with good specific activity by surface charged amino acids engineering was proposed based on systematically analyzing the results of mutating 44 negatively charged surface amino acids of a thermophilic β-mannanase (ManAK). Computational data, combined with experimental results indicated that percentage side-chain solvent accessibility (PSSA), changes in Gibbs free energy of unfolding (∆∆G_mut) and root-mean-square fluctuations (RMSF) could be suitable for screening kinetically stable mutants. A combinational standard (∆∆G_mut < -0.5 kJ/mol and RMSF >0.68 Å) resulted a decrease in the proportion of destabilizing mutants to 12.5%. The perturbations of substrate affinity and specific activity caused by mutation were weakened as the shortest distance from C_α of mutated site to C_α of catalytic sites (Ds_Cα-Cα) increased. Results indicated that hotspot zones contributing to the local stability and integrity of catalytic motif at elevated temperatures might be widely distributed across spatial structure of the protein, while the mutation perturbation on enzyme specific activity demonstrated a gradually weakening trend from the catalytic core to the protein surface. These findings further our understanding of the structural-functional relationships of protein and highlight a deduced workflow to engineering industrially useful enzymes.

Improving the kinetic stability of a hyperthermostable β-mannanase by a rationally combined strategy

Feasible and easily accessible methods for the rational design of enzyme engineering strategies remain to be established. Thus, a new rationally combined strategy based on disulfide bond engineering and HotSpot Wizard 3.0 was proposed and experimentally demonstrated to be effective using a hyperthermostable β-mannanase. Ten of 42 mutants showed prominent enhancement of kinetic stability with 26.4%-39.9% increases in t_1/2 (75 °C) compared with the parent enzyme ManAKH. The best mutant, D273-V308, showed apparent increases in both optimal temperature (5 °C) and T₅₀ (6.8 °C), as well as advanced catalytic efficiency. The low rate of inactive mutants and the high rate of positive mutants indicated that newly introduced screening factors (distance from catalytic residues, Gibbs free energy term, molecular simulation, and visual inspections) greatly enhance the design of thermostable β-mannanase. Moreover, these findings further advance the industrial application of β-mannanase (ManAK) in food and food-related applications.

Examination of the Role of Mg2+ in the Mechanism of Nucleotide Binding to the Monomeric YME1L AAA+ Domain

The first line of defense in the mitochondrial quality control network involves the stress response from a family of ATP-dependent proteases. We have reported that a solubilized version of the mitochondrial inner membrane ATP-dependent protease YME1L displays nucleotide binding kinetics that are sensitive to the reactive oxygen species hydrogen peroxide under a limiting ATP concentration. Our observations were consistent with an altered YME1L conformational ensemble leading to increased nucleotide binding site accessibility under oxidative stress conditions. To examine this hypothesis further, we report here the results of a comprehensive study of the thermodynamic and kinetic properties underlying the binding of nucleoside di- and triphosphate to the isolated YME1L AAA+ domain (YME1L-AAA+). A combination of fluorescence titrations, molecular dynamics, and stopped-flow fluorescence experiments have demonstrated similarity between nucleotide binding behaviors for YME1L under oxidative conditions and the isolated AAA+ domain. Our data demonstrate that YME1L-AAA+ binds ATP and ADP with affinities equal to ∼30 and 5 μM, respectively, in the absence of Mg2+. We note a negative heterotropic linkage effect between Mg2+ and ATP that arises as the MgCl2 concentration is increased such that the affinity of YME1L-AAA+ for ATP decreases to ∼60 μM in the presence of 10 mM MgCl2. Molecular dynamics methods allow for structural rationalization by revealing condition-dependent conformational populations for YME1L-AAA+. Taken together, these data suggest a preliminary model in which YME1L modulates its affinity for the nucleotide to stabilize against degradation or instability inherent to such stress conditions.

Molecular dynamics simulation, free energy landscape and binding free energy computations in exploration the anti-invasive activity of amygdalin against metastasis

BACKGROUND AND OBJECTIVE

Historically, amygdalin has been used as alternative medicine or in vitro and in vivo studies, but no single study exists which discusses the structural mechanism of amygdalin at a molecular level. This paper inquiries into the inhibitory actions of amygdalin on the selected targets: AKT1, FAK, and ILK, which are regulators for various mediated signaling pathways, and are associated with cell adhesion, migration, and differentiation. In order to get details at the molecular level of amygdalin's inhibitory activities against chosen proteins, molecular modeling and simulation techniques including double docking, molecular dynamics simulation, free energy landscape analysis, and binding free energy calculation were exerted.

METHODS

To get molecular level details of amygdalin inhibitory effects against the relevant proteins; here the utilized tools are the following: the double docking, molecular dynamics simulation, free energy landscape analysis, g_mmpbsa, and interaction entropy were used to evaluate the inhibitory activity against targeted proteins.

RESULTS

The computational calculations revealed that amygdalin inhibits the selected targets via block the ATP-binding pocket of AKT1, FAK, and ILK by forming stable hydrogen bonds. Moreover, free energy landscape, FEL exposed that amygdalin stabilized the global conformations of both FAK and ILK proteins to the minimum global energy besides it reduced the essential dynamics of FAK and ILK proteins. MMPBSA computations provided further evidence for amygdalin's stability inside the ATP-binding pocket of AKT1, FAK, and ILK with a binding free energy of 45.067, -13.033, 13.109 kJ/mol, respectively. The binding free energies are lastly consistent with the hydrogen bonding and pairs within 0.35 nm results. The decomposition of binding energy shows the pivotal amino acid residues responsible for the stability of amygdalin's interactions inside the ATP-binding sites by forming hydrogen bonds.

CONCLUSIONS

Before this work, it was enigmatic to make predictions about how amygdalin inhibits metastasis of cancer. But the computational results contribute in several ways to our understanding of amygdalin activity and provide a basic insight into the activity of amygdalin as a multi-target drug in the metastasis and invasion of cancer.

Insights Into the Role of Exposed Surface Charged Residues in the Alkali-Tolerance of GH11 Xylanase

Thermostable and alkaline- or acid-stable xylanases are more advantageous in agricultural and industrial fields. In this study, a rational structure-based design was conducted based on a thermostable GH11 xylanase TlXynA from Thermomyces lanuginosus to improved pH-tolerance. Four mutant enzymes (P1, P2, P3, and P4) and five variants (N1, N2, N3, N4, and N5) were constructed by substituting surface charged residue combinations using site-directed mutagenesis. Compared to the native enzyme, two mutants P1 and P2 showed higher acid tolerance, especially at pH 3.0, presented 50 and 40% of their maximum activity, respectively. In addition, four mutants N1, N2, N3 and N4 had higher tolerance than the native enzyme to alkaline environments (pH 7.0-9.0). At pH 9.0, the residual activities of N1, N2, N3, and N4 were 86, 78, 77, and 66%, respectively. In summary, an improved pH-tolerance design principle is being reported.

Integrated Computational Approaches and Tools forAllosteric Drug Discovery

Understanding molecular mechanisms underlying the complexity of allosteric regulationin proteins has attracted considerable attention in drug discovery due to the benefits and versatilityof allosteric modulators in providing desirable selectivity against protein targets while minimizingtoxicity and other side effects. The proliferation of novel computational approaches for predictingligand-protein interactions and binding using dynamic and network-centric perspectives has ledto new insights into allosteric mechanisms and facilitated computer-based discovery of allostericdrugs. Although no absolute method of experimental and in silico allosteric drug/site discoveryexists, current methods are still being improved. As such, the critical analysis and integration ofestablished approaches into robust, reproducible, and customizable computational pipelines withexperimental feedback could make allosteric drug discovery more efficient and reliable. In this article,we review computational approaches for allosteric drug discovery and discuss how these tools can beutilized to develop consensus workflows for in silico identification of allosteric sites and modulatorswith some applications to pathogen resistance and precision medicine. The emerging realization thatallosteric modulators can exploit distinct regulatory mechanisms and can provide access to targetedmodulation of protein activities could open opportunities for probing biological processes and insilico design of drug combinations with improved therapeutic indices and a broad range of activities.

Molecular investigation against the resistant mechanism of PncA mutated pyrazinamide resistance and insight into the role of pH environment for pyrazinamide activation

Pyrazinamide (PZA), a crucial component of anti-TB therapy, is a prodrug. PZA interacts with PncA protein to be converted into its functional form i.e. pyrazinoic acid (POA). It has unique feature to kill dormant tubercle bacilli of acidic environment. Although significance of pH environment in PZA activation has been investigated in several of previous studies, insight into the significant atomistic variations in the interaction pattern of PZA with PncA, at different pH environments, are still required to be explored. On the other hand, continuously emerging PncA mutants, associated with PZA resistance, have also become a serious threat for global TB control program. Therefore, the current study was designed to understand the role of pH environment in the PZA activation and to explore the PZA resistance mechanism in various PncA mutants. The study included various in silico experiments like molecular docking, MD simulation, binding free energy estimation, PCA and FEL. In our study, we have found pH-3 and pH-5 environment as a highly significant environment for PZA activation. It was found that protonation or deprotonation of PZA activation site (PAS) residues, majorly K48, D56, K96 and E107, resulted in rearrangement of the PAS according to the pH conditions. It has also been observed that positioning of PZA binding near to Fe²⁺ and residues of catalytic triad (i.e. D8, K96 and C138) also play a very crucial role in the activation of PZA. The overall insight from the current study may help to develop new therapeutics against PncA mutated PZA resistance.Communicated by Ramaswamy H. Sarma.

Thermostability of Lipase A and Dynamic Communication Based on Residue Interaction Network

OBJECTIVE

Dynamic communication caused by mutation affects protein stability. The main objective of this study is to explore how mutations affect communication and to provide further insight into the relationship between heat resistance and signal propagation of Bacillus subtilis lipase (Lip A).

METHODS

The relationship between dynamic communication and Lip A thermostability is studied by long-time MD simulation and residue interaction network. The Dijkstra algorithm is used to get the shortest path of each residue pair. Subsequently, time-series frequent paths and spatio-temporal frequent paths are mined through an Apriori-like algorithm.

RESULTS

Time-series frequent paths show that the communication between residue pairs, both in wild-type lipase (WTL) and mutant 6B, becomes chaotic with an increase in temperature; however, more residues in 6B can maintain stable communication at high temperature, which may be associated with the structural rigidity. Furthermore, spatio-temporal frequent paths reflect the interactions among secondary structures. For WTL at 300K, β7, αC, αB, the longest loop, αA and αF contact frequently. The 310-helix between β3 and αA is penetrated by spatio-temporal frequent paths. At 400K, only αC can be frequently transmitted. For 6B, when at 300K, αA and αF are in more tight contact by spatio-temporal frequent paths though I157M and N166Y. Moreover, the rigidity of the active site His156 and the C-terminal of Lip A are increased, as reflected by the spatio-temporal frequent paths. At 400K, αA and αF, 310-helix between β3 and αA, the longest loop, and the loop where the active site Asp133 is located can still maintain stable communication.

CONCLUSION

From the perspective of residue dynamic communication, it is obviously found that mutations cause changes in interactions between secondary structures and enhance the rigidity of the structure, contributing to the thermal stability and functional activity of 6B.

Changes of Thermostability, Organic Solvent, and pH Stability in Geobacillus zalihae HT1 and Its Mutant by Calcium Ion

Thermostable T1 lipase from Geobacillus zalihae has been crystallized using counter-diffusion method under space and Earth conditions. The comparison of the three-dimensional structures from both crystallized proteins show differences in the formation of hydrogen bond and ion interactions. Hydrogen bond and ion interaction are important in the stabilization of protein structure towards extreme temperature and organic solvents. In this study, the differences of hydrogen bond interactions at position Asp43, Thr118, Glu250, and Asn304 and ion interaction at position Glu226 was chosen to imitate space-grown crystal structure, and the impact of these combined interactions in T1 lipase-mutated structure was studied. Using space-grown T1 lipase structure as a reference, subsequent simultaneous mutation D43E, T118N, E226D, E250L, and N304E was performed on recombinant wild-type T1 lipase (wt-HT1) to generate a quintuple mutant term as 5M mutant lipase. This mutant lipase shared similar characteristics to its wild-type in terms of optimal pH and temperature. The stability of mutant 5M lipase improved significantly in acidic and alkaline pH as compared to wt-HT1. 5M lipase was highly stable in organic solvents such as dimethyl sulfoxide (DMSO), methanol, and n-hexane compared to wt-HT1. Both wild-type and mutant lipases were found highly activated in calcium as compared to other metal ions due to the presence of calcium-binding site for thermostability. The presence of calcium prolonged the half-life of mutant 5M and wt-HT1, and at the same time increased their melting temperature (T_m). The melting temperature of 5M and wt-HT1 lipases increased at 8.4 and 12.1 °C, respectively, in the presence of calcium as compared to those without. Calcium enhanced the stability of mutant 5M in 25% (v/v) DMSO, n-hexane, and n-heptane. The lipase activity of wt-HT1 also increased in 25% (v/v) ethanol, methanol, acetonitrile, n-hexane, and n-heptane in the presence of calcium. The current study showed that the accumulation of amino acid substitutions D43E, T118N, E226D, E250L, and N304E produced highly stable T1 mutant when hydrolyzing oil in selected organic solvents such as DMSO, n-hexane, and n-heptane. It is also believed that calcium ion plays important role in regulating lipase thermostability.

Improvements of thermophilic enzymes: From genetic modifications to applications

Thermozymes (from thermophiles or hyperthermophiles) offer obvious advantages due to their excellent thermostability, broad pH adaptation, and hydrolysis ability, resulting in diverse industrial applications including food, paper, and textile processing, biofuel production. However, natural thermozymes with low yield and poor adaptability severely hinder their large-scale applications. Extensive studies demonstrated that using genetic modifications such as directed evolution, semi-rational design, and rational design, expression regulations and chemical modifications effectively improved enzyme's yield, thermostability and catalytic efficiency. However, mechanism-based techniques for thermozymes improvements and applications need more attention. In this review, stabilizing mechanisms of thermozymes are summarized for thermozymes improvements, and these improved thermozymes eventually have large-scale industrial applications.

Influence of Calcium Ions on the Thermal Characteristics of α-amylase from Thermophilic Anoxybacillus sp. GXS-BL

BACKGROUND

α-Amylases are starch-degrading enzymes and used widely, the study on thermostability of α-amylase is a central requirement for its application in life science and biotechnology.

OBJECTIVE

In this article, our motivation is to study how the effect of Ca2+ ions on the structure and thermal characterization of α-amylase (AGXA) from thermophilic Anoxybacillus sp.GXS-BL.

METHODS

α-Amylase activity was assayed with soluble starch as the substrate, and the amount of sugar released was determined by DNS method. For AGXA with calcium ions and without calcium ions, optimum temperature (Topt), half-inactivation temperature (T50) and thermal inactivation (halflife, t1/2) was evaluated. The thermal denaturation of the enzymes was determined by DSC and CD methods. 3D structure of AGXA was homology modeled with α-amylase (5A2A) as the template.

RESULTS

With calcium ions, the values of Topt, T50, t1/2, Tm and ΔH in AGXA were significantly higher than those of AGXA without calcium ions, showing calcium ions had stabilizing effects on α-amylase structure with the increased temperature. Based on DSC measurements AGXA underwent thermal denaturation by adopting two-state irreversible unfolding processes. Based on the CD spectra, AGXA without calcium ions exhibited two transition states upon unfolding, including α- helical contents increasing, and the transition from α-helices to β-sheet structures, which was obviously different in AGXA with Ca2+ ions, and up to 4 Ca2+ ions were located on the inter-domain or intra-domain regions according to the modeling structure.

CONCLUSION

These results reveal that Ca2+ ions have pronounced influences on the thermostability of AGXA structure.

Role of simple descriptors and applicability domain in predicting change in protein thermostability

The melting temperature (Tm) of a protein is the temperature at which half of the protein population is in a folded state. Therefore, Tm is a measure of the thermostability of a protein. Increasing the Tm of a protein is a critical goal in biotechnology and biomedicine. However, predicting the change in melting temperature (dTm) due to mutations at a single residue is difficult because it depends on an intricate balance of forces. Existing methods for predicting dTm have had similar levels of success using generally complex models. We find that training a machine learning model with a simple set of easy to calculate physicochemical descriptors describing the local environment of the mutation performed as well as more complicated machine learning models and is 2-6 orders of magnitude faster. Importantly, unlike in most previous publications, we perform a blind prospective test on our simple model by designing 96 variants of a protein not in the training set. Results from retrospective and prospective predictions reveal the limited applicability domain of each model. This study highlights the current deficiencies in the available dTm dataset and is a call to the community to systematically design a larger and more diverse experimental dataset of mutants to prospectively predict dTm with greater certainty.

Insight into the inhibitor discrimination by FLT3 F691L

Fms-like tyrosine kinase 3 (FLT3) belongs to the receptor tyrosine kinase family and expressed in hematopoietic progenitor cells. FLT3 gene mutations are reported in ~30% of acute myeloid leukemia cases. FLT3 kinase domain mutation F691L is one of the common causes of acquired resistance to the FLT3 inhibitors including quizartinib. MZH29 and crenolanib were previously reported to inhibit FLT3 F691L. However, crenolanib was reported for the moderate inhibition. We found that Glu661and Asp829 were the most significant residues to target the FLT3 F691L which contribute most significantly to the binding energy with MZH29 and crenolanib. These interactions were found absent with quizartinib. Further free energy landscape analysis revealed that FLT3 F691L bound to MZH29 and crenolanib was more stable as compared to quizartinib.

Structural investigations on mechanism of lapatinib resistance caused by HER-2 mutants

HER-2 belongs to the human epidermal growth factor receptor (HER) family. Via different signal transduction pathways, HER-2 regulates normal cell proliferation, survival, and differentiation. Recently, it was reported that MCF10A, BT474, and MDA-MB-231 cells bearing the HER2 K753E mutation were resistant to lapatinib. Present study revealed that HER-2 mutant K753E showed some contrasting behaviour as compared to wild, L768S and V773L HER-2 in complex with lapatinib while similar to previously known lapatinib resistant L755S HER-2 mutant. Lapatinib showed stable but reverse orientation in binding site of K753E and the highest binding energy among studied HER2-lapatinib complexes but slightly lesser than L755S mutant. Results indicate that K753E has similar profile as L755S mutant for lapatinib. The interacting residues were also found different from other three studied forms as revealed by free energy decomposition and ligplot analysis.

Histidine substitution in the most flexible fragments of firefly luciferase modifies its thermal stability

Molecular dynamics (MD) at two temperatures of 300 and 340 K identified two histidine residues, His461 and His489, in the most flexible regions of firefly luciferase, a light emitting enzyme. We therefore designed four protein mutants H461D, H489K, H489D and H489M to investigate their enzyme kinetic and thermodynamic stability changes. Substitution of His461 by aspartate (H461D) decreased ATP binding affinity, reduced the melting temperature of protein by around 25 °C and shifted its optimum temperature of activity to 10 °C. In line with the common feature of psychrophilic enzymes, the MD data showed that the overall flexibility of H461D was relatively high at low temperature, probably due to a decrease in the number of salt bridges around the mutation site. On the other hand, substitution of His489 by aspartate (H489D) introduced a new salt bridge between the C-terminal and N-terminal domains and increased protein rigidity but only slightly improved its thermal stability. Similar changes were observed for H489K and, to a lesser degree, H489M mutations. Based on our results we conclude that the MD simulation-based rational substitution of histidines by salt-bridge forming residues can modulate conformational dynamics in luciferase and shift its optimal temperature activity.

Two strategies to engineer flexible loops for improved enzyme thermostability

Flexible sites are potential targets for engineering the stability of enzymes. Nevertheless, the success rate of the rigidifying flexible sites (RFS) strategy is still low due to a limited understanding of how to determine the best mutation candidates. In this study, two parallel strategies were applied to identify mutation candidates within the flexible loops of Escherichia coli transketolase (TK). The first was a “back to consensus mutations” approach, and the second was computational design based on ΔΔG calculations in Rosetta. Forty-nine single variants were generated and characterised experimentally. From these, three single-variants I189H, A282P, D143K were found to be more thermostable than wild-type TK. The combination of A282P with H192P, a variant constructed previously, resulted in the best all-round variant with a 3-fold improved half-life at 60 °C, 5-fold increased specific activity at 65 °C, 1.3-fold improved k_cat and a T_m increased by 5 °C above that of wild type. Based on a statistical analysis of the stability changes for all variants, the qualitative prediction accuracy of the Rosetta program reached 65.3%. Both of the two strategies investigated were useful in guiding mutation candidates to flexible loops, and had the potential to be used for other enzymes.

Electrostatics-mediated α-chymotrypsin inhibition by functionalized single-walled carbon nanotubes

Electrostatics-mediated α-chymotrypsin inhibition by functionalized single-walled carbon nanotubes.

In Silico Designing of an Industrially Sustainable Carbonic Anhydrase Using Molecular Dynamics Simulation

Carbonic anhydrase (CA) is a family of metalloenzymes that has the potential to sequestrate carbon dioxide (CO₂) from the environment and reduce pollution. The goal of this study is to apply protein engineering to develop a modified CA enzyme that has both higher stability and activity and hence could be used for industrial purposes. In the current study, we have developed an in silico method to understand the molecular basis behind the stability of CA. We have performed comparative molecular dynamics simulation of two homologous α-CA, one of thermophilic origin (Sulfurihydrogenibium sp.) and its mesophilic counterpart (Neisseria gonorrhoeae), for 100 ns each at 300, 350, 400, and 500 K. Comparing the trajectories of two proteins using different stability-determining factors, we have designed a highly thermostable version of mesophilic α-CA by introducing three mutations (S44R, S139E, and K168R). The designed mutant α-CA maintains conformational stability at high temperatures. This study shows the potential to develop industrially stable variants of enzymes while maintaining high activity.

Structural insights into conformational stability of both wild-type and mutant EZH2 receptor

Polycomb group (PcG) proteins have been observed to maintain the pattern of histone by methylation of the histone tail responsible for the gene expression in various cellular processes, of which enhancer of zeste homolog 2 (EZH2) acts as tumor suppressor. Overexpression of EZH2 results in hyper activation found in a variety of cancer. Point mutation on two important residues were induced and the results were compared between the wild type and mutant EZH2. The mutation of Y641 and A677 present in the active region of the protein alters the interaction of the top ranked compound with the newly modeled binding groove of the SET domain, giving a GLIDE score of -12.26 kcal/mol, better than that of the wild type at -11.664 kcal/mol. In depth analysis were carried out for understanding the underlying molecular mechanism using techniques viz. molecular dynamics, principal component analysis, residue interaction network and free energy landscape analysis, which showed that the mutated residues changed the overall conformation of the system along with the residue-residue interaction network. The insight from this study could be of great relevance while designing new compounds for EZH2 enzyme inhibition and the effect of mutation on the overall binding mechanism of the system.

Molecular dynamics simulation and free energy landscape methods in probing L215H, L217R and L225M βI-tubulin mutations causing paclitaxel resistance in cancer cells

Drug resistance poses a threatening challenge for mankind, as the development of resistance to already well-established drugs causes serious therapeutic problems. Resistance to paclitaxel (Ptxl), a complex diterpenoid working as microtubule stabilizer, is one such issue in cancer treatment. Microtubule stabilizer drugs, stabilises microtubules upon binding to β-tubulin subunit of tubulin heterodimer thus causing mitotic arrest leading to death of cancer cell. Leucine point mutations viz. L215H, L217R, and L225M were reported for Ptxl resistance in various cancers. In the current study, molecular mechanism of these resistance causing mutations was explored using molecular docking, molecular dynamics (MD) simulation, binding energy estimation (MMPBSA), free energy decomposition, principle component analysis (PCA) and free energy landscape (FEL) methods. A total of five systems including unbound βI-tubulin (Apo), docked wild+Ptxl, L215H+Ptxl, L217R+Ptxl and L225M+Ptxl were prepared, and 50 ns MD simulation was performed for each system. Binding energy estimation indicated that leucine mutation reduces the binding affinity of Ptxl in mutant types (MTs) as compared to wild type (WT). Further, in contrast to WT Ptxl interactions with the M-loop (PHE270-VAL286), S6-S7 loop and H9-H10 were significantly altered in MTs. Results showed that in MTs, Ptxl had weak interaction with M-loop residues, while having strong affinity with S6-S7 loop and H6-H7 loop. Moreover, PCA and FEL analysis revealed that M-loop flexible region (THR274-LEU284) was strongly bound with Ptxl in WT preventing its flexible movement and the causing factor for microtubule stabilization. In MTs due to poor interaction with Ptxl, M-loop flexible region retains its flexibility, therefore unable to stabilize microtubule. This study will give an insight into the importance of M-loop flexible region interaction with Ptxl for microtubule stabilization. In addition, it clearly provides the molecular basis of Ptxl resistance mechanism in leucine MTs. This work will help in developing novel microtubule stabilizers molecules active against MTs.