We leveraged a variety of sources of internal and external validation data to calibrate filters and evaluate the quality of filtered variants (Supplementary Information Table 7 ). We adjusted the standard GATK variant site filtering37 (link) to increase the number of singleton variants that pass this filter, while maintaining a singleton transmission rate of 50.1%, very near the expected 50%, within sequenced trios. We then used the remaining passing variants to assess depth and genotype quality filters compared to >10,000 samples that had been directly genotyped using SNP arrays (Illumina HumanExome) and achieved 97–99% heterozygous concordance, consistent with known error rates for rare variants in chip-based genotyping38 (link). Relative to a “platinum standard” genome sequenced using five different technologies39 (link), we achieved sensitivity of 99.8% and false discovery rates (FDR) of 0.056% for single nucleotide variants (SNVs), and corresponding rates of 95.1% and 2.17% for insertions and deletions (indels). Lastly, we compared 13 representative Non-Finnish European exomes included in the call set with their corresponding 30x PCR-Free genome. The overall SNV and indel FDR was 0.14% and 4.71%, while for SNV singletons was 0.389%. The overall FDR by annotation classes missense, synonymous and protein truncating variants (including indels) were 0.076%, 0.055% and 0.471% respectively (Supplementary Information Table 5 and 6 ). Full details of quality assessments are described in the Supplementary Information Section 1.6 .
>
Chemicals & Drugs
>
Amino Acid
>
Mutant Proteins
Mutant Proteins
Mutant Proteins are altered or modified versions of naturally occuring proteins.
These variants can arise from genetic mutations, post-translational modifications, or other processes that change the structure and/or function of the original protein.
Studying Mutant Proteins is crucial for understanding disease mechanisms, drug targeting, and protein engineering.
PubCompare.ai's AI-driven tools can help researchers optimize protocols and uncover insights by locating the best published protocols, pre-prints, and patents related to Mutant Proteins research.
Streamline your work and discover the optimal approach using PubCompare.ai's intellegent comparison features.
These variants can arise from genetic mutations, post-translational modifications, or other processes that change the structure and/or function of the original protein.
Studying Mutant Proteins is crucial for understanding disease mechanisms, drug targeting, and protein engineering.
PubCompare.ai's AI-driven tools can help researchers optimize protocols and uncover insights by locating the best published protocols, pre-prints, and patents related to Mutant Proteins research.
Streamline your work and discover the optimal approach using PubCompare.ai's intellegent comparison features.
Most cited protocols related to «Mutant Proteins»
DNA Chips
Europeans
Exome
Gene Deletion
Genome
Heterozygote
Hypersensitivity
INDEL Mutation
Insertion Mutation
Mutant Proteins
Nucleotides
Platinum
Transmission, Communicable Disease
TRIO protein, human
To assess the applicability of mCSM signatures in predicting the impact of mutations in protein stability, several data sets derived from the ProTherm (Kumar et al., 2006 (link)) database were considered. ProTherm is a collection of experimental thermodynamic parameters for wild-type and mutant proteins, including the change in Gibbs free energy ( ). Only single-point mutations were considered. The data sets were used in comparative experiments with other methods, in regression and classification tasks, which consist of predicting the numerical value and the direction of change in , respectively.
S2648 : The first data set, S2648, was used in comparative regression tasks where the aim is to predict the change in Gibbs free energy ( ) between wild-type and mutant protein. The data set comprises 2648 single-point mutations in 131 different globular proteins. For experiments with these data, we used 5-fold cross-validation, the same validation procedure use by the authors of the PoPMuSiC (Dehouck et al., 2009 (link)) algorithm.
S350 : The second data set, S350, comprised 350 mutations in 67 different proteins. It is a randomly selected subset of the S2648 data set, also used in comparative regression experiments. In this case, the remaining 2298 mutations from the S2648 data set were used to train the predictive model, whereas the S350 data set was used as a test set. This data set is widely used in the literature to compare the performance of different methods.
S1925 : The data set S1925 was used in both regression and classification experiments. It comprises 1925 mutations in 55 proteins, which are uniformly distributed across the four major SCOP classes (Murzin et al., 1995 (link)). Twenty-fold cross-validation protocol was used, the same protocol used in by the AUTOMUTE method Masso and Vaisman, 2008 (link)).
p53 : Finally, as a study case, we assembled a data set of 42 mutations within the DNA binding domain of the tumour suppressor protein p53, whose thermodynamic effects have previously been experimentally characterized (Ang et al., 2006 (link); Bullock et al. 2000 (link); Joerger et al., 2006 (link); Nikolova et al. 1998 (link), 2000 (link)). The full data set description is available as Supplementary Material .
Full text: Click here
Eye
Mutant Proteins
Mutation
Oncoprotein p53
Point Mutation
Proteins
The APPRIS annotation pipeline deploys a range of computational methods to provide value to the annotations of the human genome. The server flags variants that code for proteins with altered structure, function or localization, and exons that are evolving in a non-neutral fashion. APPRIS also selects one of the CDS for each gene as the principal functional isoform. The pipeline is made up of separate modules that combine protein structure and function information and evolutionary evidence. Each module has been implemented as a separate web service.
firestar (Lopez et al. 2007 (link), 2011 (link)) is a method that predicts functionally important residues in protein sequences.
Matador3D is locally installed and checks for structural homologs for each transcript in the PDB (Berman et al. 2000 (link)).
SPADE uses a locally installed version of the program Pfamscan (Finn et al. 2010 (link)) to identify the conservation of protein functional domains.
INERTIA detects exons with non-neutral evolutionary rates. Transcripts are aligned against related species using three different alignment methods, Kalign (Lassmann and Sonnhammer 2005 (link)), multiz (Blanchette et al. 2004 (link)), and PRANK (Loytynoja and Goldman 2005 (link)), and evolutionary rates of exons for each of the three alignments are contrasted using SLR (Massingham and Goldman 2005 (link)).
CRASH makes conservative predictions of signal peptides and mitochondrial signal sequences by using locally installed versions of the SignalP and TargetP programs (Emanuelsson et al. 2007 (link)) .
THUMP makes conservative predictions of trans-membrane helices by analyzing the output of three locally installed trans-membrane prediction methods, MemSat (Jones 2007 (link)), PRODIV (Viklund and Elofsson 2004 (link)), and PHOBIUS (Kall et al. 2004 (link)).
CExonic is a locally developed method that uses exonerate (Slater and Birney 2005 (link)) to align mouse and human transcripts and then looks for patterns of conservation in exonic structure.
CORSAIR is a locally installed method that checks for orthologs for each variant in a locally installed vertebrate protein sequence database.
Amino Acid Sequence
Biological Evolution
Evolution, Neutral
Exons
Genes
Genome, Human
Helix (Snails)
Homo sapiens
Mitochondria
Mus
Mutant Proteins
Protein Domain
Protein Isoforms
Proteins
Signal Peptides
Tissue, Membrane
Vertebrates
In this work, we used the previously established S2648 dataset (15–18 (link)), derived from the ProTherm database (19 (link)). This dataset is comprised of 2648 different point-mutations across 131 globular proteins with experimentally determined structures whose impact on protein stability has been experimentally measured (602 stabilizing and 2046 destabilizing). The DynaMut training set comprises 2297 mutations randomly selected from the original dataset. A blind test set composed of 351 non-redundant mutations derived from the S2648 set was also compiled. This blind test set has been widely used in the literature (15–18 (link)), enabling direct comparative performance of methods that quantify the impact of mutations on the folding free energy.
Previous studies have reported performance comparisons of difference methods on predicting changes in folding free energy (ΔΔG) using these datasets (20–22 (link)). Given the unbalanced nature of the original dataset, here we have considered the hypothetical reverse mutations (22 (link)) in order to build a more robust, balanced and self-consistent predictive method. The change in folding free energy is a thermodynamic state function, and it has been proposed that the change in folding free energy of a mutation from a wild-type protein to its mutant (ΔΔGWT→MT) should be equivalent to the negative change in folding free energy of the hypothetical reverse mutation—from the mutant to the wild-type protein (–ΔΔGMT→WT) (16 (link),22–24 (link)). Including the hypothetical reverse mutations, our predictive model was trained using 4594 mutations and our blind test was comprised of 702 single-point mutations.
Previous studies have reported performance comparisons of difference methods on predicting changes in folding free energy (ΔΔG) using these datasets (20–22 (link)). Given the unbalanced nature of the original dataset, here we have considered the hypothetical reverse mutations (22 (link)) in order to build a more robust, balanced and self-consistent predictive method. The change in folding free energy is a thermodynamic state function, and it has been proposed that the change in folding free energy of a mutation from a wild-type protein to its mutant (ΔΔGWT→MT) should be equivalent to the negative change in folding free energy of the hypothetical reverse mutation—from the mutant to the wild-type protein (–ΔΔGMT→WT) (16 (link),22–24 (link)). Including the hypothetical reverse mutations, our predictive model was trained using 4594 mutations and our blind test was comprised of 702 single-point mutations.
Full text: Click here
Eye
Mutant Proteins
Mutation
Point Mutation
Proteins
Staphylococcal Protein A
Visually Impaired Persons
Antibodies
Baculoviridae
Cell Lines
Clip
Digestion
Electrophoretic Mobility Shift Assay
FMR1 protein, human
Mus
Mutant Proteins
Pharmaceutical Preparations
Plasmids
Ribonuclease T1
Western Blot
Most recents protocols related to «Mutant Proteins»
Example 2
This study demonstrates the efficacy of one embodiment of the Porcine Circovirus Type 2 ORF2b Vaccine against a PCV2a and/or PCV2b challenge. Cesarean-derived colostrum-deprived (CDCD) piglets are used in this study and separated into 2 groups; 1) pigs vaccinated with an experimental Porcine Circovirus Vaccine including the PCV2b ORF2 R63T variant of Example 1 (Killed Baculovirus Vector) that are challenged with virulent PCV2b and, 2) non-vaccinated challenged control pigs that are challenged with virulent PCV2b. On Day 0, Group 1 is administered 1 mL of vaccine intramuscularly (IM) whereas Group 2, non-vaccinated challenge control pigs do not receive any treatment. On Day 28, all pigs in groups 1 and 2 are challenged with virulent PCV2b 1 mL intranasally (IN) and 1 mL IM with an approximate dosage of 3.0 Log10 TCID5/mL of live virus. All pigs receive 2.0 mL Keyhole Limpet Hemocyanin emulsified in Incomplete Freunds Adjuvant (KLH/ICFA) IM on Days 25 and 31. Pigs are monitored daily for clinical signs, and blood is drawn for serologic testing periodically. On Day 56 all pigs are necropsied and select tissues are collected and gross pathology observations are made.
As a whole, vaccinated animals exhibit reduction when compared to their respective challenge control group in all parameters tested.
Full text: Click here
Animals
Baculoviridae
BLOOD
Cloning Vectors
Colostrum
incomplete Freund's adjuvant
keyhole-limpet hemocyanin
MLL protein, human
Mutant Proteins
Porcine Circovirus
Sus scrofa
Tissues
Vaccines
Virion
Virus
Example 3
Several other substitutions at amino acid site 63 were produced to compare to the PCV2b ORF BDH native strain. The results from the evaluation of the PCV2b ORF2 BDH mutant constructs are shown in
Full text: Click here
Amino Acids
Amino Acid Substitution
Arginine
Aspartate
Cells
Figs
Glutamine
Glycine
Mutant Proteins
Mutation
Strains
Threonine
Virion
Three-dimensional structural models of wild-type and mutant SMARCE1 were predicted based on the whole sequence using AlphaFold2 v2.0.0 in casp14 mode [81 (link)]. Pairwise TM-scores of the predicted tertiary structures were calculated with TM-align [82 (link), 83 (link)], with the mutant protein of SMARCE1 compared against that of the wild-type using Student’s t test to determine whether variation in conformation existed between the models. Structures with a TM-score > 0.5 assume generally the same fold.
Full text: Click here
Base Sequence
Mutant Proteins
SMARCE1 protein, human
Student
Cultures were grown following the same protocol described by Mehlhoff et al. (2020) (link). Briefly, we tracked the optical density of monocultures over six hours of induced growth with a dilution after three hours. We calculated the fitness using Equation 4 from the dilution factor (d) and the starting and final OD's (Oo, Of) of the mutant and wild-type cultures under the assumption that the correlation between OD and cell density was the same for cells whether they were expressing wild-type or any mutant TEM-1 allele. Thus, fitness represents the mean growth rate of the cells expressing the mutant protein relative to the growth rate of cells expressing the wildtype protein.
Alleles
Cells
Factor D, Complement
Mutant Proteins
Proteins
Technique, Dilution
Vision
For AP-MS experiments, Caco-2 cells were seeded 24 h before transfection in 10-cm dishes in normal growth medium and grown to 70–80% of confluency. Cells were transfected with 15 μg of pMDS-TetOn3G-kozak-FLAG-GOI plasmids (containing FLAG-KRASWT or FLAG-KRASG12D or FLAG-KRASG12V or FLAG-KRASG12C as GOI) using Lipofectamine 2000 (11668-019; Invitrogen) according to the manufacturer’s instructions in Opti-MEM reduced serum medium (31985-062; Gibco, Thermo Fisher Scientific) for 4 h. Then, the medium was changed and supplemented with culture medium containing the various growth conditions. To note, cells transfected with the KRASWT plasmids were always supplemented with 15 ng/ml of doxycycline (Sigma-Aldrich). Cells were incubated for 24 h at 37°C and harvested. FLAG-KRAS mutant plasmid transfections were not supplemented with doxycycline as the promoter is leaky and KRAS mutant proteins were already expressed at WT levels without adding doxycycline.
Full text: Click here
Caco-2 Cells
Cells
Culture Media
Doxycycline
Growth Disorders
Hyperostosis, Diffuse Idiopathic Skeletal
K-ras Genes
lipofectamine 2000
Mutant Proteins
Persistent Mullerian duct syndrome
Plasmids
Serum
Transfection
Top products related to «Mutant Proteins»
Sourced in United States, China, Germany, United Kingdom, Canada, Japan, France, Italy, Switzerland, Australia, Spain, Belgium, Denmark, Singapore, India, Netherlands, Sweden, New Zealand, Portugal, Poland, Israel, Lithuania, Hong Kong, Argentina, Ireland, Austria, Czechia, Cameroon, Taiwan, Province of China, Morocco
Lipofectamine 2000 is a cationic lipid-based transfection reagent designed for efficient and reliable delivery of nucleic acids, such as plasmid DNA and small interfering RNA (siRNA), into a wide range of eukaryotic cell types. It facilitates the formation of complexes between the nucleic acid and the lipid components, which can then be introduced into cells to enable gene expression or gene silencing studies.
Sourced in United States, Germany, United Kingdom, Canada, Japan, Belgium, France, China
The QuikChange site-directed mutagenesis kit is a tool used in molecular biology for introducing specific mutations into double-stranded plasmid or linear DNA templates. The kit provides a fast and efficient method for generating site-specific mutations, insertions, or deletions without the need for subcloning, library construction, or other specialized techniques.
Sourced in United States, China, Germany, Japan, United Kingdom, France, Canada, Italy, Australia, Switzerland, Denmark, Spain, Singapore, Belgium, Lithuania, Israel, Sweden, Austria, Moldova, Republic of, Greece, Azerbaijan, Finland
Lipofectamine 3000 is a transfection reagent used for the efficient delivery of nucleic acids, such as plasmid DNA, siRNA, and mRNA, into a variety of mammalian cell types. It facilitates the entry of these molecules into the cells, enabling their expression or silencing.
Sourced in United States, Japan, United Kingdom, Austria, Canada, Germany, Poland, Belgium, Lao People's Democratic Republic, China, Switzerland, Sweden, Finland, Spain, France
GraphPad Prism 7 is a data analysis and graphing software. It provides tools for data organization, curve fitting, statistical analysis, and visualization. Prism 7 supports a variety of data types and file formats, enabling users to create high-quality scientific graphs and publications.
Sourced in United States, China, United Kingdom, Germany, Australia, Japan, Canada, Italy, France, Switzerland, New Zealand, Brazil, Belgium, India, Spain, Israel, Austria, Poland, Ireland, Sweden, Macao, Netherlands, Denmark, Cameroon, Singapore, Portugal, Argentina, Holy See (Vatican City State), Morocco, Uruguay, Mexico, Thailand, Sao Tome and Principe, Hungary, Panama, Hong Kong, Norway, United Arab Emirates, Czechia, Russian Federation, Chile, Moldova, Republic of, Gabon, Palestine, State of, Saudi Arabia, Senegal
Fetal Bovine Serum (FBS) is a cell culture supplement derived from the blood of bovine fetuses. FBS provides a source of proteins, growth factors, and other components that support the growth and maintenance of various cell types in in vitro cell culture applications.
Sourced in United States, Germany, United Kingdom, Spain, Canada, Italy, Sweden, Austria
SYPRO Orange is a fluorescent dye used in protein analysis. It binds to proteins and emits a fluorescent signal that can be detected and quantified. The dye is commonly used in techniques such as thermal shift assays and protein folding studies to monitor protein stability and unfolding.
Sourced in United States, China, United Kingdom, Germany, Japan, Canada, France, Sweden, Netherlands, Italy, Portugal, Spain, Australia, Denmark
The PcDNA3.1 is a plasmid vector used for the expression of recombinant proteins in mammalian cells. It contains a powerful human cytomegalovirus (CMV) promoter, which drives high-level expression of the inserted gene. The vector also includes a neomycin resistance gene for selection of stable transfectants.
Sourced in United States, Germany, China, United Kingdom, Japan, Sao Tome and Principe, Belgium, Canada, Sweden
The Anti-FLAG antibody is a laboratory reagent used to detect and purify proteins that have been engineered to contain a specific amino acid sequence known as the FLAG tag. The antibody binds specifically to this tag, allowing for the identification and isolation of the tagged protein from complex mixtures. The Anti-FLAG antibody is a valuable tool for researchers studying protein expression, localization, and interactions.
Sourced in United States, Germany, Canada, United Kingdom, France
The QuikChange II XL Site-Directed Mutagenesis Kit is a lab equipment product designed for introducing site-specific mutations in double-stranded plasmid DNA. It utilizes a proprietary DNA polymerase enzyme and specialized reaction components to efficiently generate desired mutations.
Sourced in United States, Germany, Canada, United Kingdom, France, China
The QuikChange Lightning Site-Directed Mutagenesis Kit is a laboratory tool used to perform rapid and efficient site-specific mutations in double-stranded plasmid DNA. The kit provides a reliable and straightforward method for introducing desired sequence changes without the need for subcloning.
More about "Mutant Proteins"
Mutant proteins, also known as variant proteins or modified proteins, are altered or modified versions of naturally occurring proteins.
These protein variants can arise from genetic mutations, post-translational modifications, or other processes that change the structure and/or function of the original protein.
Studying mutant proteins is crucial for understanding disease mechanisms, drug targeting, and protein engineering.
Researchers can leverage powerful tools like PubCompare.ai to optimize their protocols and uncover valuable insights for mutant proteins research.
PubCompare.ai's AI-driven features can help locate the best published protocols, pre-prints, and patents related to mutant proteins, allowing researchers to streamline their work and discover the optimal approach.
Techniques such as Lipofectamine 2000, QuikChange site-directed mutagenesis kit, Lipofectamine 3000, and QuikChange II XL Site-Directed Mutagenesis Kit are commonly used in mutant proteins research.
These tools can be used to introduce specific mutations or modifications into proteins, enabling researchers to study the effects of these changes.
Data analysis tools like GraphPad Prism 7 can be employed to analyze the results of mutant proteins experiments, while reagents like FBS and SYPRO Orange can be used to support the research process.
Expression vectors like pcDNA3.1 and antibodies like Anti-FLAG antibody can also be valuable for studying mutant proteins.
By harnessing the power of PubCompare.ai's intelligent comparison features, researchers can streamline their mutant proteins research, uncover new insights, and discover the optimal protocols and approaches to drive their work forward.
These protein variants can arise from genetic mutations, post-translational modifications, or other processes that change the structure and/or function of the original protein.
Studying mutant proteins is crucial for understanding disease mechanisms, drug targeting, and protein engineering.
Researchers can leverage powerful tools like PubCompare.ai to optimize their protocols and uncover valuable insights for mutant proteins research.
PubCompare.ai's AI-driven features can help locate the best published protocols, pre-prints, and patents related to mutant proteins, allowing researchers to streamline their work and discover the optimal approach.
Techniques such as Lipofectamine 2000, QuikChange site-directed mutagenesis kit, Lipofectamine 3000, and QuikChange II XL Site-Directed Mutagenesis Kit are commonly used in mutant proteins research.
These tools can be used to introduce specific mutations or modifications into proteins, enabling researchers to study the effects of these changes.
Data analysis tools like GraphPad Prism 7 can be employed to analyze the results of mutant proteins experiments, while reagents like FBS and SYPRO Orange can be used to support the research process.
Expression vectors like pcDNA3.1 and antibodies like Anti-FLAG antibody can also be valuable for studying mutant proteins.
By harnessing the power of PubCompare.ai's intelligent comparison features, researchers can streamline their mutant proteins research, uncover new insights, and discover the optimal protocols and approaches to drive their work forward.