86 results about "Rational design" patented technology

The invention belongs to the technical field of antibacterial peptide activity identification and evaluation, and relates to an antibacterial peptide activity and MIC value combined prediction framework based on cross-modal deep learning, and the framework uses a protein language model ESM2 to respectively carry out token-level semantic embedding coding on an antibacterial peptide sequence and a pathogen protein sequence; performing cross-modal feature extraction and fusion through a multi-branch structure comprising a Mama module, a multi-head self-attention mechanism and DASM 1D convolution; a multi-task decoding structure is adopted to realize antibacterial peptide activity classification and MIC value regression prediction at the same time; according to the method, functional characteristics in the sequence can be effectively mined, the accuracy and generalization ability of antibacterial peptide activity and MIC value prediction are remarkably improved, and a reliable calculation tool is provided for high-throughput screening and rational design of the antibacterial peptide.

The invention belongs to the field of medical technology analysis, and discloses an analysis method and system for revealing a hidden binding pocket of a drug target, and the method comprises the steps: firstly obtaining a representative conformation metastable state of a target protein through conventional molecular dynamics simulation and clustering analysis; secondly, constructing a Markov state model to analyze a dynamic transformation rule between conformations; carrying out enhanced sampling by adopting meta-dynamics, and deeply exploring a rare conformation space; and finally, constructing a free energy landscape to quantitatively evaluate the relative stability of the conformation, and identifying a hidden binding pocket in the stable rare conformation. According to the method, the limitation of a single calculation means is overcome, a full-chain calculation system of dynamic conformation analysis-hidden cavity feature mining-novel ligand rational design is constructed, and the formation mechanism and potential druggability of the hidden pocket can be comprehensively revealed from the two dimensions of dynamics and thermodynamics; and an efficient and accurate calculation framework is provided for research and development of innovative drugs targeting difficult drug targets.

The present application relates to the technical field of synthetic biology, and particularly relates to a fully synthetic yeast inducible promoter and a construction method thereof.The method splits the upstream activation region and the core promoter region of the promoter by modularizing the framework of the promoter, and uses rational design, computer model assistance and high-throughput library construction to screen the spacer sequence, explores the framework mode of the promoter with saccharomyces cerevisiae as the chassis microorganism, obtains the fully synthetic non-natural yeast inducible promoter sequence, and solves the problems of insufficient number of good characteristic promoters caused by high background leakage of the promoter, insufficient induction intensity and few types, or the problem of easy homologous recombination in the saccharomyces cerevisiae.

The invention discloses a method for constructing a two-dimensional layered material machine learning potential function, and belongs to the field of material science and computational simulation, and the method comprises the steps: S1, carrying out the modeling of a two-dimensional layered material through employing a first principle, completing the calculation of the first principle, and taking a result as a data source; s2, extracting structure and force information from the data source, and vectorizing the data to form a data set for training a neural network model; s3, training the processed data set based on a deep learning model DeepMD, and generating a potential function model of machine learning; s4, model detection: calculating an error between a model prediction value and a first principle calculation result; s5, carrying out molecular dynamics simulation; by reasonably designing the modeling process and optimizing the data processing and training steps, the generated potential function model is ensured to have high precision and high efficiency, and the method can be widely applied to the field of material science and molecular dynamics simulation.

The invention relates to the technical field of agricultural biology, in particular to a rational design method of a rice growth-promoting synthetic microbial community based on collaborative optimization of directed evolution and a metabolism model. The method comprises the following steps: continuously subculturing a multi-source soil microbial community to be stable, co-culturing the multi-source soil microbial community and rice seeds, and selecting an optimal community based on a growth phenotype; the method comprises the following steps: selecting an optimal community, applying a bottleneck to the optimal community, externally adding flora disturbance, constructing a filial generation community, repeating'screening-disturbance-subculture 'for five rounds to obtain a growth promoting function enhanced directed evolution synthesis microbial community, dividing the microbial community into a plurality of modules, and constructing a genome scale metabolism model to simulate the influence of interaction between different modules on rice growth. And combining the directed evolution synthesized microbial communities in pairs according to different proportions so as to obtain rational design synthesized microbial communities with better growth promoting effects. According to the method, the problem of model prediction deviation caused by lack of a host-microorganism interaction mechanism in an existing method is solved.

The invention discloses efficient synthesis of guanidinoacetic acid by a carbamyl phosphoric acid synthesis-enhanced multi-enzyme cascade system, and belongs to the field of biological catalysis engineering. The invention provides a dominant mutant E31K / G351N of L-arginine: glycine amidino transferase, the catalytic efficiency of guanidinoacetic acid is improved by 34.6% compared with that of wild type, an eight-enzyme synergistic arginine circulation system is subsequently constructed based on a mutant strain, 18.35 g / L GAA (56.75 mM) is realized by a 5L fermentation tank, the arginine conversion rate reaches 261.12%, and the yield of the glycine amidino transferase is greatly improved. The highest level of catalytic synthesis of guanidinoacetic acid by escherichia coli is publically reported at home and abroad at present. According to the research, an efficient technical route is provided for GAA industrial production, and a universal strategy framework is established for rational design of a multi-enzyme system and multi-gene co-expression optimization.

The invention discloses a high-efficiency PET hydrolase mutant and an application of the high-efficiency PET hydrolase mutant in PET plastic degradation. The PET hydrolase is characterized in that the PET hydrolase is a protein of the following (a) or (b): (a) a protein as shown in SEQ ID NO.1; and (b) a protein which is derived from (a) by substituting, deleting or adding one or more amino acids in the amino acid sequence in (a), has hydrolase activity and is derived from (a). The high-yield PET hydrolase ClbPETase (the expression quantity is 80 mg / L) is excavated from an environmental metagenome through an HMM method, and the high-yield PET hydrolase ClbPETase has great industrial application potential. A plurality of single-point mutants and a series of combined mutants are constructed through a rational design method assisted by machine learning, a mutant UltraPETase with the optimal catalytic performance is obtained through superposition of single-point mutation, complete depolymerization of PET powder can be achieved by reacting for 8 hours at the temperature of 65 DEG C or reacting for 6 hours at the temperature of 60 DEG C. And a novel efficient depolymerization enzyme resource is provided for biological enzyme depolymerization of polyester plastics.

This invention belongs to the field of enzyme engineering technology, specifically providing a nitrile hydratase mutant and its application. The nitrile hydratase mutant is derived from *Aurantimonas manganoxydans*. Am NHase)SI859A was modified using rational design methods based on its three-dimensional protein structure. The resulting nitrile hydratase mutant ultimately achieved an enzyme activity that was up to 6.74 times higher than that of the wild enzyme, and its stability did not decrease significantly within two hours under heating conditions at 50°C.

The invention discloses a construction method of a high-activity mutant of chondroitin 6-O sulfotransferase, and belongs to the field of biological enzyme engineering and synthetic biology. Interaction sites of MusC6 protein and a substrate PAPS are accurately analyzed through a computer-aided molecular docking technology, and key active sites are directionally modified by adopting a strategy of combining rational design and saturated mutation. Experimental results show that the catalytic performance of the obtained mutant S139T / S140L / Y364M / K412V is remarkably improved, and the enzyme activity of the mutant reaches 1182U / L and is improved by 4.4 times compared with the enzyme activity of a wild type 270U / L. According to the invention, the technical bottleneck of low catalytic efficiency of a wild type enzyme on a natural substrate is solved through a multi-site synergistic mutation strategy, and a biocatalyst with industrial application value is provided for efficiently synthesizing chondroitin sulfate C by a microbiological method.

The invention discloses a glycosyl transferase mutant with improved thermal stability and activity, and belongs to the technical field of biological catalytic synthesis. Through rational design, the 102nd site, the 110th site, the 208th site and the 251th site of glycosyl transferase are mutated to obtain a combined mutant UGT94E13M3 phase starting enzyme, the half-life period of the combined mutant UGT94E13M3 phase starting enzyme at the temperature of 45 DEG C is prolonged from 0.60 h to 8.88 h, the thermal stability is improved by 14.8 times, and the enzyme activity is improved by 1.08 times. According to the invention, the mutant and sucrose synthase are subjected to a coupling reaction, so that the Reb D conversion rate reaches 71.40%, and an efficient and green new way is provided for production of rebaudioside M8.

The invention relates to the technical field of enzyme engineering, and particularly discloses a phytase mutant and application thereof. The mutant T273K with improved heat resistance is obtained through rational design and site-directed mutagenesis screening on the basis of aspergillus tubingensis phytase. The thermal stability and catalytic ability of the mutant are obviously improved compared with those before mutation; after heat preservation is carried out for 90 min at the temperature of 60 DEG C, the relative enzyme activity is 69.4%, and compared with WT, the relative enzyme activity is improved by 20.4%; the specific activity is improved by about 77.78% compared with that of WT, and the catalytic efficiency kcat / Km is improved by 50.56% compared with that of WT; and the enzyme activity retention rate reaches 33.8% under the condition of 10% salinity. The phytase mutant T273K has the comprehensive characteristics of salt resistance, heat resistance and the like, the phytase mutant T273K can better exert the phytic acid enzymolysis effect in the food processing process, turbidity generated by phytic acid in liquid food such as soy sauce, vinegar, cooking wine and the like can be remarkably reduced, so that the product quality is improved, and the phytase mutant T273K has a wide application prospect.

The application belongs to the field of biological enzyme engineering, and provides a rational design method for enzyme modification based on deep learning, which comprises the following steps: constructing a protein crystal structure data set; adding an atomic microenvironment centered on an amino acid residue based on the protein crystal structure data set, and reconstructing the protein crystal structure data set; predicting the amino acid residue of the reconstructed protein crystal structure data set by using a pre-trained amino acid residue prediction model according to the reconstructed protein crystal structure data set; and determining potential sites for enzyme function optimization according to the difference between the predicted amino acid residue probability and the actual amino acid probability of the natural enzyme. The application takes the protein crystal structure data as a basic data set, fully utilizes the physicochemical properties of the protein, and rationally designs and modifies the enzyme based on artificial intelligence, thereby avoiding the inconvenience caused by manual screening.

The invention discloses a method for enhancing the thermal stability of a mycotoxin degrading enzyme based on structural activity protection. The invention belongs to the technical field of biology, and relates to a mycotoxin degrading enzyme mutant, which is prepared by mutating wild mycotoxin degrading enzyme with an amino acid sequence of SEQ ID No: 1: mutating N at the 6th site of SEQ ID No: 1 into Y, and mutating N at the 6th site of SEQ ID No: 1 into Y at the 6th site of SEQ ID No: 1; and / or mutating the 15th site of SEQ ID No: 1 from W to I; and / or mutating the 92nd site of SEQ ID No: 1 from A to G; and / or the 114 site of SEQ ID No: 1 is mutated from D to L. Through a rational design strategy combining structure prediction and active site protection, damage to a catalytic core is effectively avoided, the mutation success rate and the experiment efficiency are greatly improved, dual guarantee of enzyme activity and temperature resistance is considered, and the method is more systematic and reliable compared with a conventional method.

The invention belongs to the technical field of molecular biology, and particularly discloses a theophylline aptamer and a virtual screening method and application thereof. The theophylline aptamer is selected from one or more of MUT9, MUT16, MUT67, MUT78 or MUT89. The invention further discloses a preparation method of the theophylline aptamer. The invention discloses a theophylline aptamer as well as a virtual screening method and application thereof, the theophylline aptamer is high in affinity and specificity, the virtual screening method remarkably improves the accuracy and efficiency of virtual screening, the theophylline aptamer can be quickly obtained at low cost, and a powerful calculation tool is provided for rational design and application of the aptamer.

The invention belongs to the field of biotechnology and biomass conversion, and particularly relates to a lignin peroxidase mutant based on semi-rational design, a preparation method of an enzyme preparation and application of the lignin peroxidase mutant and the enzyme preparation in straw degradation. According to the method, a three-dimensional model constructed by wild type lignin peroxidase is evaluated, a potential mutation hot spot is screened out in combination with a molecular docking technology, and then the high-activity lignin peroxidase mutant is successfully obtained through alanine scanning, saturated mutation and combined mutation three rounds. After an enzyme activity improvement mechanism is simulated and analyzed through molecular dynamics, an optimized high-activity mutant is optimized according to codon preference of pichia pastoris and then integrated into an expression vector pPIC9K of the pichia pastoris, so that secretory expression of the mutant is realized; the composite material shows significantly improved catalytic efficiency in straw degradation. While the outstanding degradation effect is achieved, the method also has important significance for promoting the green and efficient development of the feed industry.

The invention relates to a thermal-stable KGF-2 derivative for increasing molecular internal interaction based on artificial intelligence, and a generation method, device and application of the thermal-stable KGF-2 derivative. The thermal stability type KGF-2 derivative is obtained by mutating a lysine residue at the 103th site of wild type KGF-2 into an aspartic acid residue, mutating a cysteine residue at the 106th site of the wild type KGF-2 into an aspartic acid residue and removing amino acid residues at the 2nd to 68th sites; the amino acid sequence of the heat-stable KGF-2 derivative is as shown in SEQ ID NO: 4. According to the scheme provided by the invention, the molecular structure of the KGF-2 protein can be improved by utilizing artificial intelligence rational design, a hydrogen bond network in the KGF-2 protein molecule is increased, and interaction among atom nodes is enhanced, so that the stability and druggability of the KGF-2 protein are effectively improved.

The invention discloses an LwaCas13a nuclease mutant and an application of the LwaCas13a nuclease mutant. According to the invention, the modification direction of enzyme is determined based on a rational design strategy, an amino acid saturation mutation method is adopted, serine at the 996th site of wild type LwaCas13a nuclease is respectively replaced by arginine or lysine (S996R, S996K), serine at the 778th site is replaced by asparagine, and meanwhile, serine at the 996th site is replaced by arginine (S778N / S996R). Experimental results show that the obtained LwaCas13a mutant shows trans-cleavage activity obviously higher than that of a wild type, and is more suitable for high-sensitivity molecular detection application.

The invention discloses a mutant containing flavin monooxygenase and application of the mutant. According to the invention, semi-rational design and screening are carried out on the flavin-containing monooxygenase to obtain the flavin-containing monooxygenase mutant, and the amino acid sequence of the flavin-containing monooxygenase mutant is shown as SEQ ID NO.4. The mutant provided by the invention can obviously improve the activity of the flavin-containing monooxygenase and is used for improving the yield of the teer violet. By using the engineering bacteria expressing the flavin-containing monooxygenase mutant, the activity of the flavin-containing monooxygenase can be remarkably improved, the engineering bacteria are used for producing the tylosin-containing monooxygenase mutant to improve the yield, the yield of the tylosin-containing monooxygenase mutant is improved to 74.6%, and the titer of the tylosin-containing monooxygenase mutant can reach 853.7 mg L <-1 >.

The invention discloses a glycosyl transferase mutant and application thereof in preparation of salidroside, and belongs to the technical field of bioengineering. The mutant is obtained by mutating UDP (User Datagram Protocol) glycosyl transferase AtUGT85A1 from arabidopsis thaliana, and the mutant comprises at least one mutation of C128G, F204A and F217V. The invention also discloses a gene for coding the mutant, a recombinant expression vector containing the gene and a genetically engineered bacterium. According to the present invention, the glycosyl transferase mutant with significantly improved catalytic activity is obtained through the structure-oriented rational design, the glycosyl transferase mutant is integrated into the de novo synthesis path of Escherichia coli, and after the constructed gene engineering bacterium is fermented for 72 h, the salidroside titer can achieve 9.1 g / L, and is improved by 200% compared with the wild type; the method provided by the invention gets rid of dependence on exogenous addition of expensive glycosyl donors, has the advantages of simple process, low cost, environmental friendliness and the like, and provides a new strategy for green industrial production of salidroside.

The invention belongs to the technical field of gene engineering, and relates to an optimized recombinase recognition site and application thereof, in particular to a method for improving the recombination activity of a large serine recombinase Bxb1 attB recognition site obtained through rational design and saturated mutation. The novel attB designed by the invention can be widely applied to gene therapy, synthetic biology and crop genetic improvement, and the editing efficiency and accuracy of a large serine recombinase system are improved.

The invention discloses a protein degradation targeting chimera for an EGFR-VHL system. The protein degradation targeting chimera comprises an EGFR binding molecule and a VHL binding molecule, the EGFR binding molecule is any one of proteins as shown in SEQ ID NO.1 to SEQ ID NO.3; the VHL binding molecule is any one of proteins as shown in SEQ ID NO. 4 to 37. The invention also discloses application of the protein degradation targeting chimera in preparation of drugs targeting EGFR and VHL. The invention provides a set of complete calculation design framework, a diversified candidate binding protein library is generated, and finally three high-quality EGFR binding proteins and 34 high-quality VHL binding proteins are obtained and show excellent prediction evaluation indexes. The invention establishes a general framework which is preliminarily verified and is suitable for the rational design of the next generation of protein PROTAC, and lays a foundation for a targeted protein degradation treatment strategy of tumors and other diseases.

The invention discloses a (-)-alpha-bisabolol synthase mutant and application thereof, and belongs to the technical field of enzyme engineering and microbial engineering. According to the invention, (-)-alpha-bisabolol synthase BOS from cynara scolymus is taken as an object, based on sequence conservative analysis and semi-rational design, a series of BOS mutants obtained by the invention are obviously improved in the aspect of FPP substrate conversion efficiency, and the optimal (-)-alpha-bisabolol synthase BOSG119W-H151Y-F282Y-H302Q has the advantages that the conversion efficiency of the FPP substrate is obviously improved, and the optimal (-)-alpha-bisabolol synthase BOSG119W-H151Y-F282Y-H302Q is obviously improved; the yield of the generated (-)-alpha-bisabolol is 16.7 times that of a wild type, and the yield exceeds 2g / L. The (-)-alpha-bisabolol synthase mutant enhances the performance of microbial synthesis of (-)-alpha-bisabolol, and provides an effective technical route for green production of industrial high-purity (-)-alpha-bisabolol.

The invention discloses photoresponsive protein hydrogel with wide-area mechanical regulation characteristics. The photoresponsive protein hydrogel is formed by polymerizing a specific mutant of photoactivated xanthoprotein (PYP) and a multi-arm polyethylene glycol derivative with the tail end modified with a maleimide group. Through rational design of molecular dynamics and material mechanics, cysteine mutation is carried out on the 48th site and the 85th site of a wild type PYP sequence, and the PYP (48 / 85) double mutant with an anisotropic unfolding energy scene is constructed. According to the mutant, exposed sulfydryl and a multi-arm polyethylene glycol derivative are subjected to Michael addition reaction to form a cross-linked network. Compared with the prior art (such as PYP 36 / 128 hydrogel), the method has the advantages that higher mechanical sensitivity and unfolding probability of PYP 48 / 85 under network tension are utilized, the limitation that traditional design only depends on chain length change is overcome, and remarkably larger macroscopic rigidity adjusting amplitude (the mechanical switch ratio can reach 70% or above) is achieved. The material has the characteristics of good biocompatibility, high response speed (millisecond level), complete reversibility and wide rigidity dynamic range, and can meet the biological application requirements of stem cell differentiation, tissue fibrosis model construction and the like with high requirements on a mechanical signal threshold.

The invention discloses a high-fidelity Cas9 homolog based on structure orientation and a screening method and application thereof, and belongs to the technical field of gene editing. According to the method, cross-database searching is carried out, a sequence comparison tool is used for finding a homologous sequence, duplicate removal is carried out, three candidate enzymes are effectively recognized from 24 and 544 Cas9 homologues by combining the sequence and three-dimensional structure evaluation, engineering variants with improved editing efficiency are obtained through PAM recognition area replacement and rational design, and the eSeqCas9 editing efficiency reaches 82.9%. The high-fidelity Cas9 homologue and the engineered variant thereof have good performance in a base editing system, the editing efficiency of A-to-G and C-to-T is considerable, and whole genome off-target detection shows that the Cas9 homologue and the engineered variant thereof have higher specificity. A new thought is provided for discovering the high-fidelity Cas9 homologue, and when the Cas9 homologue is applied to a gene editing tool, accuracy and safety can be improved, off-target can be reduced, and development of the fields of gene therapy, biological breeding and the like can be promoted.

The application discloses a dye-decolorizing peroxidase mutant and application thereof, and a novel dye-decolorizing peroxidase GA1DyPB screened from Rhodococcus globerulus GA1 is used as a starting enzyme, computer-aided semi-rational design enzyme engineering is used for site-directed modification and saturation mutation modification, and comparative analysis is conducted on the enzymatic properties of the mutant and the original enzyme, so as to provide a theoretical basis and technical support for subsequent directional mutation and catalytic performance improvement of the dye-decolorizing peroxidase. Finally, lignin is used as a substrate to conduct long-time lignin enzymatic depolymerization reaction for 48 hours, and the ability of the mutant in the lignin depolymerization is verified.

The invention belongs to the technical field of gene engineering, and relates to a gRNA library of a targeted SARS-CoV-2 virus subgenome. The library is obtained through multi-step rational design screening, is composed of 65 gRNAs, can specifically recognize and target positive chain and negative chain subgenome RNAs of viruses ORF3a, E, M, ORF6, ORF7a, ORF7b, ORF8, N and ORF10, and has a sequence as shown in SEQ ID NO: 1 to 65. The gRNA can form a CRISPR-Cas13b (clustered regularly interspaced short palindromic repeats-associated protein 13b) system with a Cas13b protein, and is used for non-therapeutically inhibiting the replication of the SARS-CoV-2 virus.

The application provides a rational design method for improving thermal stability of lipase, and belongs to the field of enzyme engineering. A flexible region of the lipase to be reformed is determined through molecular dynamics simulation, a reforming region is determined through structure analysis, a reforming site is determined through comprehensive measurement of multiple calculation tools, a mutant library is established through site-directed saturation mutation using NNK degenerate codon, and an excellent mutant with improved thermal stability is screened through a microplate screening method based on spectrophotometry. The half-life of the Candida antarctica lipase B mutant of the application at 50 DEG C is 9 times that of the wild type, and the specific activity is also 6.32% higher than that of the wild type. The application breaks the trade-off between stability and activity, and realizes the improvement of the thermal stability of the lipase, which is conducive to the important role of the lipase mutant in the industrial application in the fields of food, medicine or biodiesel.

The invention discloses a phosphorylcholine cytidyltransferase mining method based on a deep learning model. According to the method, the limitation of traditional homologous comparison is broken through, and the CCT candidate enzyme which is high in catalytic activity, excellent in solubility and suitable for engineering application can be recognized in hundreds of millions of protein sequence spaces with higher screening efficiency and prediction precision. On the basis, a rational design and a zero sample mutation prediction strategy are combined to further obtain a CCT mutant with remarkably improved performance, so that a core catalytic element is provided for efficient biosynthesis of citicoline.

The invention discloses an endoglucanase mutant as well as a coding gene and application thereof. A mutant gene is obtained by carrying out semi-rational design on a wild endoglucanase A4 gene by adopting alanine scanning mutagenesis and saturation mutagenesis, and a recombinant expression vector is constructed. After the engineering bacterium escherichia coli Rosetta (DE3) is subjected to fermentation culture, mutant protein can be efficiently expressed. A high-efficiency expression system is established through genetic engineering, a new technology is provided for cellulose degradation and biomass resource utilization, and the method has application value in the field of biological energy sources. The results provide theoretical insights for enzyme activity and stability enhancement driven by mutation, and guide future enzyme engineering work.

This application relates to the technical fields of synthetic biology and enzyme engineering, and in particular to a computational-experimental closed-loop rational design method for polyketide synthases. The method includes: constructing a full-length FCHS model using AlphaFold3; identifying binding hotspots and verifying dynamic stability through molecular docking and kinetic simulations; and constructing a low-redundancy mutant library containing A, L, and F substitutions. This application solves the problems of difficult protein structure analysis and limited experimental throughput through a closed-loop process of computational pre-screening, dynamic verification, and evolutionary filtering, providing an efficient paradigm for the improvement of complex multifunctional enzymes.