Complex network analysis of thermostable mutants of Bacillus subtilis Lipase A

Exploring the molecular mechanism of cold-adaption of an alkaline protease mutant by molecular dynamics simulations and residue interaction network

Psychrophilic proteases have attracted enormous attention in past decades, due to their high catalytic activity at low temperatures in a wide range of industrial processes, especially in the detergent and leather industries. Among them, H5 is an alkaline protease mutant, which featuring psychrophilic-like behavior, but the reasons that H5 with higher activity at low temperatures are still poorly understood. Herein, the molecular dynamics (MD) simulations combined with residue interaction network (RIN) were utilized to investigate the mechanisms of the cold-adaption of mutant H5. The results demonstrated that two loops involved in the substrate binding G100-S104 and S125-S129 in H5 had higher mobility, and the distance enlargement between the two loops modulated the substrate's accessibility compared with wild type counterpart. Besides, H5 enhanced conformational flexibility by weakening salt bridges and increasing interaction with the solvent. In particular, the absence of Lys251-Asp197-Arg247 salt bridge network may contribute to the structural mobility. Based on the free energy landscape and molecular mechanics Poisson-Boltzmann surface area of the wild type and H5, it was elucidated that H5 possessed a large population of interconvertible conformations, resulting in the weaker substrate binding free energy. The calculated RIN topology parameters such as the average degree, average cluster coefficient, and average path length further verified that the mutant H5 attenuated residue-to-residue interactions. The investigation of the mechanisms by which how the residue mutation affects the stability and activity of enzymes provides a theoretical basis for the development of cold-adapted protease.

Probing structural basis for enhanced binding of SARS-CoV-2 P.1 variant spike protein with the human ACE2 receptor

The initial step of infection by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) involves the binding of receptor binding domain (RBD) of the spike protein to the angiotensin converting enzyme 2 (ACE2) receptor. Each successive wave of SARS‐CoV‐2 reports emergence of many new variants, which is associated with mutations in the RBD as well as other parts of the spike protein. These mutations are reported to have enhanced affinity towards the ACE2 receptor as well as are also crucial for the virus transmission. Many computational and experimental studies have demonstrated the effect of individual mutation on the RBD‐ACE2 binding. However, the cumulative effect of mutations on the RBD and away from the RBD was not investigated in detail. We report here a comparative analysis on the structural communication and dynamics of the RBD and truncated S1 domain of spike protein in complex with the ACE2 receptor from SARS‐CoV‐2 wild type and its P.1 variant. Our integrative network and dynamics approaches highlighted a subtle conformational changes in the RBD as well as truncated S1 domain of spike protein at the protein contact level, responsible for the increased affinity with the ACE2 receptor. Moreover, our study also identified the commonalities and differences in the dynamics of the interactions between spike protein of SARS‐CoV‐2 wild type and its P.1 variant with the ACE2 receptor. Further, our investigation yielded an understanding towards identification of the unique RBD residues crucial for the interaction with the ACE2 host receptor. Overall, the study provides an insight for designing better therapeutics against the circulating P.1 variants as well as other future variants.

Emerging landscape of molecular interaction networks: Opportunities, challenges and prospects

Network biology finds application in interpreting molecular interaction networks and providing insightful inferences using graph theoretical analysis of biological systems. The integration of computational bio-modelling approaches with different hybrid network-based techniques provides additional information about the behaviour of complex systems. With increasing advances in high-throughput technologies in biological research, attempts have been made to incorporate this information into network structures, which has led to a continuous update of network biology approaches over time. The newly minted centrality measures accommodate the details of omics data and regulatory network structure information. The unification of graph network properties with classical mathematical and computational modelling approaches and technologically advanced approaches like machine-learning- and artificial intelligence-based algorithms leverages the potential application of these techniques. These computational advances prove beneficial and serve various applications such as essential gene prediction, identification of drug–disease interaction and gene prioritization. Hence, in this review, we have provided a comprehensive overview of the emerging landscape of molecular interaction networks using graph theoretical approaches. With the aim to provide information on the wide range of applications of network biology approaches in understanding the interaction and regulation of genes, proteins, enzymes and metabolites at different molecular levels, we have reviewed the methods that utilize network topological properties, emerging hybrid network-based approaches and applications that integrate machine learning techniques to analyse molecular interaction networks. Further, we have discussed the applications of these approaches in biomedical research with a note on future prospects.

Comparative protein structure network analysis on 3CLpro from SARS-CoV-1 and SARS-CoV-2

The main protease M^pro, 3CL^pro is an important target from coronaviruses. In spite of having 96% sequence identity among M^pros from SARS‐CoV‐1 and SARS‐CoV‐2; the inhibitors used to block the activity of SARS‐CoV‐1 M^pro so far, were found to have differential inhibitory effect on M^pro of SARS‐CoV‐2. The possible reason could be due to the difference of few amino acids among the peptidases. Since, overall 3‐D crystallographic structure of M^pro from SARS‐CoV‐1 and SARS‐CoV‐2 is quite similar and mapping a subtle structural variation is seemingly impossible. Hence, we have attempted to study a structural comparison of SARS‐CoV‐1 and SARS‐CoV‐2 M^pro in apo and inhibitor bound states using protein structure network (PSN) based approach at contacts level. The comparative PSNs analysis of apo M^pros from SARS‐CoV‐1 and SARS‐CoV‐2 uncovers small but significant local changes occurring near the active site region and distributed throughout the structure. Additionally, we have shown how inhibitor binding perturbs the PSG and the communication pathways in M^pros. Moreover, we have also investigated the network connectivity on the quaternary structure of M^pro and identified critical residue pairs for complex formation using three centrality measurement parameters along with the modularity analysis. Taken together, these results on the comparative PSN provide an insight into conformational changes that may be used as an additional guidance towards specific drug development.

Facile One-Pot Immobilization of a Novel Thermostable Carboxylesterase from Geobacillus uzenensis for Continuous Pesticide Degradation in a Packed-Bed Column Reactor

The novel carboxylesterase gene (est741) was cloned from Geobacillus uzenensis. The optimal pH and temperature of Est741 were 8.0 and 50 °C. Through site-directed mutation, the optimum temperature of the mutant M160K(EstM160K) was increased from 50 to 60 °C, and showed enhanced T1/2 of 2.5 h at 70 °C in comparison to the wild type (1.3 h). EstM160K was successfully expressed Pichia pastoris and EstM160K fermentation broth was directly immobilized on epoxy-functionalized supports via a one-pot strategy to obtain the immobilized enzyme lx-EstM160K. Additionally, lx-EstM160K showed enhanced T1/2 of 36.8 h at 70 °C in comparison to free enzyme. lx-EstM160K could degrade various pyrethroid pesticides. After 40 min reaction with 50 U of the lx-EstM160K, the malathion removal was 95.8% with a malathion concentration of 20 mg/L. When 2.5 g lx-EstM160K was added to the 10 mL column reactor with the concentration of bifenthrin was 500 mg/L and the transfer rate of the pump was 0.7 mL/min, the degradation rate of lx-EstM160K to bifenthrin was 90.4%. lx-EstM160K exhibited high operational stability and maintained 72% initial activity after ten batches of continuous reaction for bifenthrin pesticide biodegradation.

Small Conformational Changes Underlie Evolution of Resistance to NNRTI in HIV Reverse Transcriptase

Despite achieving considerable success in reducing the number of fatalities due to acquired immunodeficiency syndrome, emergence of resistance against the reverse transcriptase (RT) inhibitor drugs remains one of the biggest challenges of the human immunodeficiency virus antiretroviral therapy (ART). Non-nucleoside reverse transcriptase inhibitors (NNRTIs) form a large class of drugs and a crucial component of ART. In NNRTIs, even a single resistance mutation is known to make the drugs completely ineffective. Additionally, several inhibitor-bound RTs with single resistance mutations do not exhibit any significant variations in their three-dimensional structures compared with the inhibitor-bound RT but completely nullify their inhibitory functions. This makes understanding the structural mechanism of these resistance mutations crucial for drug development. Here, we study several single resistance mutations in the allosteric inhibitor (nevirapine)-bound RT to analyze the mechanism of small structural changes leading to these large functional effects. In this study, we have shown that in absence of significant conformational variations in the inhibitor-bound wild-type RT and RT with single resistance mutations, the protein contact network analysis of their static structures, along with molecular dynamics simulations, can be a useful approach to understand the functional effect of small local conformational variations. The simple network analysis exposes the localized contact changes that lead to global rearrangement in the communication pattern within RT. Furthermore, these conformational changes have implications on the overall dynamics of RT. Using various measures, we show that a single resistance mutation can change the network structure and dynamics of RT to behave more like unbound RT, even in the presence of the inhibitor. This combined coarse-grained contact network and molecular dynamics approach promises to be a useful tool to analyze structure-function studies of proteins that show large functional changes with negligible variations in their overall conformation.

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.