Investigation of Single and Multiple Mutations Prediction Using Binary Classification Approach

The mutation is a critical element in determining the proteins’stability,becoming a core element in portraying the effects of a drug in the pharmaceutical industry.Doing wet laboratory tests to provide a better perspective on protein mutations is expensive and time-intensive since there are so many potential muta-tions,computational approaches that can reliably anticipate the consequences of amino acid mutations are critical.This work presents a robust methodology to analyze and identify the effects of mutation on a single protein structure.Initially,the context in a collection of words is determined using a knowledge graph for feature selection purposes.The proposed prediction is based on an easier and sim-pler logistic regression inferred binary classification technique.This approach can able to obtain a classification accuracy(AUC)Area Under the Curve of 87%when randomly validated against experimental energy changes.Moreover,for each cross-fold validation,the precision,recall,and F-Score are presented.These results support the validity of our strategy since it performs the vast majority of prior studies in this domain.

DNA duplex membrane effect for the electrochemical detection of single-base DNA mutations

Here we report a new method to detect DNA point mutations.The method is based on the formation and deformation of double-stranded DNA(dsDNA)membranes on a gold surface.It can encage reporter molecules between the gold surface and the double-stranded DNA or keep them away from the gold surface.In these systems,Fe(CN)63−was used as the reporter.As the temperature increases,a sharp electrochemical signal change in the melting curve of wild-type dsDNA appears.At a special temperature,the method gives 100:1 selectivity for the perfect complement and single base mutation target.Thus,the system provides a simple and sensitive method to detect DNA point mutations without labeling targets.

An automated fluorescent single strand conformation polymorphism technique for high throughput mutation screening

Objective To develop a high throughput mutational detection method by mutiple fluorescence-labeled polymerase chain reaction(PCR)products.Methods A total of 27 known mutations including 22 substitutions,3 insertions(1,2 and 7 bp)and 2 deletions(1 and 2 bp)in the hepatocyte nuclear factor(HNF)-4α,glucokinase and HNF-1α genes were tested.During nested PCR,amplified fragments were labeled with three fluorescent dyes.PCR products were visualized with an ABI-377 fluorescence sequencer using 5% glycerol or 10% sucrose in nondenaturing gel conditions.Results Twenty-five of 27 variants(93%)could be detected by combining 5% glycerol and 10% sucrosegel matrix conditions.Twenty-two of 27(82%)and 18 of 27(67%)variants were identified using 5%glycerol and 10% sucrose conditions,respectively.Conclusion This fluorescence-based PCR single strand conformation polymorphism technique represents a simple,non-hazardous,time-saving and sensitive method for high throughput mutation detection.

Eyes of diff ering colors in Alvinocaris longirostris from deep-sea chemosynthetic ecosystems: genetic and molecular evidence of its formation mechanism

Coloration is an important phenotypic trait for multiple adaptive functions.It is interesting to fi nd white-eye(AW)and orange-eye(AO)phenotypes in the shrimp Alvinocaris longirostris inhabiting the deep-sea cold seep and hydrothermal vent areas of the northwestern Pacifi c.By comparative transcriptome analyses,1491 diff erentially expressed genes(DEGs)were identified between AW and AO.Among them,many DEGs were associated with immunity,antioxidation,and detoxifi cation.Two signifi cant enzyme encoding genes,xanthine dehydrogenase,and tryptophan oxidase involved in pigment biosynthesis pathways were up-regulated in AW and AO,respectively,which might be related to the diff erences of white and orange eye phenotypes.Moreover,single nucleotide polymorphism(SNP)calling detected that genotypes of 28 SNP distributing in 14 unigenes were completely diff erent between AW and AO.Particularly,there were three and two non-synonymous mutations in immune genes crustin Pm5 and antimicrobial peptide,respectively.Results indicate that the diff erence in eye color is probably resulted from immune response to variable micro-environmental stressors encountered in the dispersal process of the shrimps,such as symbiotic microbes,pathogens,and toxic substances,and might be genetically fi xed at last.The suggested pathway preliminarily explained the formation mechanism of diff erent eye phenotypes in Alvinocaridid shrimps,providing a basis for further study on adaptive evolution of eyes in deep-sea chemosynthetic faunas.

Naturally occurring spike mutations influence the infectivity and immunogenicity of SARS-CoV-2

Mutations in SARS-CoV-2 variants of concern(VOCs)have enhanced transmissibility and immune evasion with respect to current vaccines and neutralizing antibodies(NAbs).How naturally occurring spike mutations affect the infectivity and antigenicity of VOCs remains to be investigated.The entry efficiency of individual spike mutations was determined in vitro using pseudotyped viruses.BALB/c mice were immunized with 2-dose DNA vaccines encoding B.1.1.7,B.1.351,B.1.1.529 and their single mutations.Cellular and humoral immune responses were then compared to determine the impact of individual mutations on immunogenicity.In the B.1.1.7 lineage,Del69–70 and Del 144 in NTD,A570D and P681H in SD1 and S982A and D1118H in S2 significantly increased viral entry,whereas T716I resulted in a decrease.In the B.1.351 lineage,L18F and Del 242–244 in the NTD,K417N in the RBD and A701V in S2 also increased viral entry.S982A weakened the generation of binding antibodies.All sera showed reduced cross-neutralization activity against B.1.351,B.1.617.2(Delta)and B.1.1.529(Omicron BA.1).S982A,L18F,and Del 242–244 hindered the induction of cross-NAbs,whereas Del 69–70,Del144,R246I,and K417N showed the opposite effects.B.1.351 elicited adequate broad cross-NAbs against both B.1.351 and B.1.617.2.All immunogens tested,however,showed low neutralization against circulating B.1.1.529.In addition,T-cell responses were unlikely affected by mutations tested in the spike.We conclude that individual spike mutations influence viral infectivity and vaccine immunogenicity.Designing VOC-targeted vaccines is likely necessary to overcome immune evasion from current vaccines and neutralizing antibodies.

Using DelPhi Capabilities to Mimic Protein’s Conformational Reorganization with Amino Acid Specific Dielectric Constants

Many molecular events are associated with small or large conformational changes occurring in the corresponding proteins.Modeling such changes is a challenge and requires significant amount of computing time.From point of view of electrostatics,these changes can be viewed as a reorganization of local charges and dipoles in response to the changes of the electrostatic field,if the cause is insertion or deletion of a charged amino acid.Here we report a large scale investigation of modeling the changes of the folding energy due to single mutations involving charged group.This allows the changes of the folding energy to be considered mostly electrostatics in origin and to be calculated with DelPhi assigning residue-specific value of the internal dielectric constant of protein.The predicted energy changes are benchmarked against experimentally measured changes of the folding energy on a set of 257 single mutations.The best fit between experimental values and predicted changes is used to find out the effective value of the internal dielectric constant for each type of amino acid.The predicted folding free energy changes with the optimal,amino acid specific,dielectric constants are within RMSD=0.86 kcal/mol from experimentally measured changes.