> Genes & Molecular Sequences > Amino Acid Sequence > Catalytic Domain

Catalytic Domain

Q: What are the different types or variations of Catalytic Domains?

Catalytic Domains can have diverse structures and functions depending on the enzyme they are part of. Some common variations include serine proteases, cysteine proteases, metalloproteinases, and kinase domains. Each type of catalytic domain has unique active site characteristics and catalytic mechanisms that are important to understand for specific applications.

The Catalytic Domain is a discrete structural unit within an enzyme that is responsible for its catalytic activity.
This region of the protein typically contains the active site where the substrate binds and the chemical reaction occurs.
Identifying and understanding the catalytic domain is crucial for studying enzyme function, mechanism, and inhibition.
PubCompare.ai's AI-driven platform can help researchers efforlessly locate and compare catalytic domain protocols from literature, preprints, and patents to optimize their research proccess and make data-driven decisions.

Most cited protocols related to «Catalytic Domain»

Hydrogenase Catalytic Subunit Sequence Database

The database was constructed using the amino acid sequences of all curated non-redundant 3248 hydrogenase catalytic subunits represented in the NCBI RefSeq database in August 20142 (link) (Dataset S1). In order to test the classification tool, additional sequences from newly-sequenced archaeal and bacterial phyla were retrieved from the Joint Genome Institute’s Integrated Microbial Genomes database43 (link).

Søndergaard D., Pedersen C.N, & Greening C. (2016). HydDB: A web tool for hydrogenase classification and analysis. Scientific Reports, 6, 34212.

Publication 2016

Amino Acid Sequence Archaea Bacteria Catalytic Domain Genome Genome, Microbial Hydrogenase Joints

Structural Determination of HDAC Complexes

For the zCD1-TSA complex, the zCD2-TSA complex, and the zCD2-SAHA complex, X-ray diffraction data were recorded at the Stanford Synchrotron Radiation Lightsource (SSRL), beamline 14-1 (λ = 1.28184 Å). For the MBP-hCD2-TSA complex, unliganded zCD2, the H574A zCD2-substrate 8 complex, and the zCD2-Belinostat complex, X-ray diffraction data were recorded at the Advanced Photon Source (APS), beamline NE-CAT 24-ID-E (λ = 0.97918 Å). For all other structures, X-ray diffraction data were recorded at the Advanced Light Source (ALS), beamline 4.2.2 (λ = 1.00003 Å). Data reduction and integration for all datasets was achieved with HKL2000;⁵⁰ data collection and reduction statistics are recorded in Supplementary Tables 2–4. Although R_merge values were relatively high for some datasets, analysis of CC_1/2 values indicated that these datasets were of sufficient quality for satisfactory structure determination and refinement.
All structures were solved by molecular replacement using the program Phaser.^{51 (link)} For the structure of the zCD2–SAHA complex, a model of the HDAC4 catalytic domain in a closed-loop conformation (PDB entry 4CBT)^{52 (link)} was used as the search probe for rotation and translation function calculations. For all other zCD1 and zCD2 structures, the structure of the zCD2-SAHA complex less inhibitor and water molecules was used as a search probe. For the structure determination of the fusion protein MBP-hCD2–TSA complex, maltose binding protein (PDB entry 4EDQ) and the zCD2–TSA complex less ligands and solvent molecules were used as search probes. The graphics program Coot was used for model building^{53 (link)} and Phenix was used for crystallographic refinement.^{54 (link)} Refinement statistics for each final model are recorded in Supplementary Tables 2–4. The quality of each model was verified with PROCHECK⁵⁵ and MolProbity.^{56 (link)} Figures were prepared with Pymol and UCSF Chimera.^{57 (link)} The Ramachandran statistics for each model are as follows: zCD1-TSA complex: 90.3% allowed, 9.4% additionally allowed; zCD2-TSA complex: 91.6% allowed, 7.8% additionally allowed; MBP-hCD2-TSA complex: 88.5% allowed, 10.8% additionally allowed; unliganded zCD2: 91.1% allowed, 8.6% additionally allowed; H574A zCD2-substrate 8 complex: 92.2% allowed, 7.3% additionally allowed; Y785F zCD2-substrate 1 complex: 90.6% allowed, 8.7% additionally allowed; Y785F zCD2-substrate 1 complex: 90.6% allowed, 8.7% additionally allowed; zCD2-HC toxin complex: 90.6% allowed, 8.8% additionally allowed; zCD2-trifluoroketone inhibitor complex: 90.5% allowed, 9.0% additionally allowed; zCD2-acetate complex: 90.4% allowed, 9.1% additionally allowed; zCD2-SAHA complex: 91.4% allowed, 8.0% additionally allowed; zCD2-Belinostat complex: 91.1% allowed, 8.5% additionally allowed; zCD2-HPOB complex: 91.0% allowed, 8.7% additionally allowed; zCD2-Panobinostat complex: 89.9% allowed, 9.6% additionally allowed; zCD2-Oxamflatin complex: 89.3% allowed, 10.0% additionally allowed. No backbone torsion angles adopt disallowed conformations in any structure.

Hai Y, & Christianson D.W. (2016). Histone deacetylase 6 structure and molecular basis of catalysis and inhibition. Nature chemical biology, 12(9), 741-747.

Publication 2016

Acetate belinostat Catalytic Domain Chimera Crystallography HC toxin Ligands Light Maltose-Binding Proteins oxamflatin Panobinostat Proteins Radiation Solvents Vertebral Column Vorinostat X-Ray Diffraction

Structural and Functional Analysis of Human Pol η

The full-length human Pol η gene codon-optimized for E. coli expression was synthesized by GenScript. The catalytic core (aa 1–432, hPol η) was cloned into modified pET28a45 (link), expressed in E. coli and purified by Ni²⁺-affinity, MonoS and Superdex75 chromatography. The His-tag was removed by PreScission protease. Mutagenesis was performed using QuikChange (Stratagene). Non-hydrolyzable dNMPNPPs were purchased from Jena Bioscience, and phosphoramidites of CPD from Glen Research. CPD oligos were synthesized and purified by TriLink Biotechnogies. Ternary complexes were prepared by mixing WT or C406M mutant hPol η and annealed DNA at a 1:1.05 molar ratio and addition of 5 mM Mg²⁺ and 1 mM non-hydrolyzable deoxynucleotides (dNMPNPP). The final protein concentration was 6–7 mg/ml. Crystals were grown in 0.1 M MES (pH 6.0), 19–21% (w/v) PEG 2K-MME and 5 mM MgCl₂ after several rounds of microseeding. Diffraction data were collected at sectors 22 and 23 of the APS. Phases were determined by molecular replacement46 (link) and multi-wavelength anomalous dispersion using selenomethionine-labeled hPol η47 (link). Structures were refined using CNS48 and interspersed with manual model building using COOT49 . All residues are in the most favorable (97%) and allowed (2.3%) regions of Ramachandran plot except for two that are well defined by electron densities. For functional assays, the C-terminal truncated human Pol η (1–511aa), which has the same TLS activity as the full-length hPol η43 (link), was subcloned into pET21a and readily expressed in E. coli. Q38A and R61A mutations were made using Mutant-K (TaKaRa BIO Inc). Steady-state kinetic assays and primer extension reactions were carried out as described43 (link).

Biertümpfel C., Zhao Y., Kondo Y., Ramón-Maiques S., Gregory M., Lee J.Y., Masutani C., Lehmann A.R., Hanaoka F, & Yang W. (2010). Structure and Mechanism of Human DNA Polymerase η. Nature, 465(7301), 1044-1048.

Publication 2010

2',5'-oligoadenylate Biological Assay Catalytic Domain Cell Motility Assays Chromatography Codon Electrons Escherichia coli Homo sapiens Magnesium Chloride Molar Mono-S Mutagenesis Mutation Oligonucleotide Primers Peptide Hydrolases phosphoramidite Proteins Selenomethionine

CRISPR Construction and Cloning

The constitutive Cas9 expression construct was derived by subcloning the 5’ 3×FLAG tagged human-codon optimized Cas9 cDNA from Streptococcus pyogenes (addgene: # 49535) into the MSCV-PGK-Puro vector (Clontech: # 634401). The U6-sgRNA-EFS-GFP and the U6-sgRNA-EFS-mCherry vectors were derived from the lentiCRISPR plasmid (addgene: # 49535) by removing the hCas9 cDNA and replacing the Puro cassette with GFP or mCherry. The wild-type RPA3 was PCR cloned directly from human cDNA into the MSCV-IRES-GFP (MigR1) vector. All cloning procedures were performed using the In-Fusion cloning system (Clontech: #638909). sgRNAs were cloned by annealing two DNA oligos and ligating into a BsmB1-digested U6-sgRNA-EFS-GFP/mCherry vectors, as described^{26 (link)}. To improve U6 promoter efficiency, we added an extra 5’ G nucleotide to all of the sgRNAs that did not start with a 5’ G.
All sgRNAs in this study were designed using http://crispr.mit.edu/^{25 (link)}. The majority of sgRNAs used in this study had a quality score above 70 to minimize off-target effects. In Figure 1, sgRNAs were designed targeting 5’ constitutive coding exons of each target gene. For the chromatin regulatory domain-focused CRISPR screen, sgRNAs were designed to target the catalytic domain or bromodomain of each protein based on the NCBI database annotation.
All sgRNA sequences used in this study are provided in a Supplementary Table 1.

Shi J., Wang E., Milazzo J.P., Wang Z., Kinney J.B, & Vakoc C.R. (2015). Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains. Nature biotechnology, 33(6), 661-667.

Publication 2015

2',5'-oligoadenylate Amber Stop Codon Catalytic Domain Chromatin Cloning Vectors Clustered Regularly Interspaced Short Palindromic Repeats DNA, Complementary Exons Homo sapiens Internal Ribosome Entry Sites Nucleotides Plasmids Proteins RPA3 protein, human Streptococcus pyogenes

Genetic Analysis of DNA Methylation Mutants

Plants were grown under continuous light conditions. The drm1–1, drm2–1, cmt3–7, rdr2–1, drd1–6, rdr6–1, sgs3/sde2–1, sde3–1, dcl2–1, rdr1–1, nrpd2a-1, and nrpd2b-1 mutants have been previously described [18 (link),20 (link),23 ,27 (link),31 (link)]. drm1–1 and drm2–1 are T-DNA alleles isolated in the Wassilewskija (WS) ecotype—both T-DNAs are predicted to disrupt essential catalytic domains. These mutations were backcrossed five times into Ler prior to this analysis. cmt3–7 is a point mutation isolated in the Ler ecotype that creates a stop codon, truncating the CMT3 protein after 27 amino acids. drm1–2, drm2–2, and cmt3–11 are T-DNA insertions in the predicted methyltransferase domains of DRM1, DRM2, and CMT3 that would be expected to create null mutations (T-DNAs SALK_031705, SALK_150863, and SALK_148381 respectively). kyp-6 is T-DNA SALK_041474. The phenotypes of drm1 drm2 cmt3 in the Ler ecotype were scored at two main stages. Twisted rosette leaf shape was scored at approximately 2 wk, prior to bolting. Short stature was scored at approximate 5–6 wk, once the plants had made the majority of their siliques.

Chan S.W., Henderson I.R., Zhang X., Shah G., Chien J.S, & Jacobsen S.E. (2006). RNAi, DRD1, and Histone Methylation Actively Target Developmentally Important Non-CG DNA Methylation in Arabidopsis. PLoS Genetics, 2(6), e83.

Publication 2006

Alleles Amino Acids Catalytic Domain Codon, Terminator Disease, Dejerine-Sottas DNA Modification Methylases DRD1 protein, human Dwarfism Ecotype Insertion Mutation Light Mutation Null Mutation Phenotype Plant Leaves Plants Point Mutation Proteins T-DNA

Most recents protocols related to «Catalytic Domain»

Enzyme Kinetic Analysis with Substrate Inhibition

All graphs were drawn using Prism GraphPad. Michaelis−Menten kinetics data was also calculated using Prism. Substrate inhibition curves were plotted using Prism or the Dynafit software and the equations in Scheme 1 [53 (link)], where Ks and Kss are dissociation constants and kcat is the turnover of the enzyme in min⁻¹. The K_m and V_max were determined using Prism, using points below the substrate inhibition concentrations.

Scheme 1. Mechanism for substrate inhibition. This mechanism assumes that enzyme I has two substrate (S) binding sites: a catalytic site for normal catalysis and a second non-catalytic or allosteric binding site. When substrate is bound at both sites (SES), the product (P) is produced at a reduced rate.

Batt S.M., Toth S., Rodriguez B., Abrahams K.A., Veerapen N., Chiodarelli G., Cox L.R., Moynihan P.J., Lelievre J., Fütterer K, & Besra G.S. (2023). Assay development and inhibition of the Mt-DprE2 essential reductase from Mycobacterium tuberculosis. Microbiology, 169(1), 001288.

Publication 2023

Binding Sites Catalysis Catalytic Domain Enzymes Kinetics prisma Psychological Inhibition

Molecular Docking of Anti-SARS-CoV-2 Drug Candidates

The molecular docking simulation was used to determine the binding energy of six antiretrovirals to the RdRp, ExoN-NSP10 and 3CLpro proteins of SARS-CoV-2. These proteins are necessary for viral RNA replication and polyprotein processing [12] (link). The crystal structures of RdRp (Identification code, ID: 6M71) [8] (link), ExoN-NSP10 (ID:7MC6) [37] (link) and 3CLpro (ID: 6M2N) [38] (link) were obtained from the Protein Data Bank (PDB) [39] (link). The resolution structures selected were lower than 3 Å [40] (link). The proteins were subjected to preparation by using Discovery Studio [41] and AutoDockTools (ADT). The active forms of the antiretrovirals [42] (link) were drawn and optimized by using Avogadro software [43] (link) and ADT. Remdesivir [44] (link),[45] (link), pibrentasvir [46] (link) and CQ [47] (link),[48] (link) were used as positive controls of the interaction with RdRp, ExoN-NSP10 and 3CLpro, respectively.
PrankWeb [49] (link) was used to determine the number of pockets and the amino acid residues that comprise them. This program also described the size (volume), depth, surface area or general hydrophobicity of each pocket (Table 1). In addition, Protein plus [50] (link) was implemented to verify the number of pockets obtained by PrankWeb [49] (link), and to describe their characteristics (size, shapes, amino acids composition and descriptor functional groups). The pockets were selected according to the active site or catalytic domain for each protein, as based on previous reports [16] (link),[51] (link),[52] (link).
Couplings were carried out using AutoDock Vina version 4.2.6 [53] (link), with an exhaustiveness value of 20 and a grid box of 24 Å × 24 Å × 24 Å, centered at (116.7829 Å, 109.9570 Å, 123.9430 Å) (XYZ coordinates) for RdRp (PDB ID: 6M71), (28.6904 Å, −1.9647 Å, 13.6836 Å) for ExoN-NSP10 (PDB: 7MC6) and (−47.585 Å, 1.135 Å, −5.600 Å) for 3CLpro (PDB ID:6M2N) (Table 1). The best docking conformation of protein-ligand interactions was predicted based on the binding energy value (kcal/mol). The docked structures were analyzed and visualized by using BIOVIA Discovery Studio Visualizer 16.1.

Zapata-Cardona M.I., Florez-Alvarez L., Guerra-Sandoval A.L., Chvatal-Medina M., Guerra-Almonacid C.M., Hincapie-Garcia J., Hernandez J.C., Rugeles M.T, & Zapata-Builes W. (2023). In vitro and in silico evaluation of antiretrovirals against SARS-CoV-2: A drug repurposing approach. AIMS Microbiology, 9(1), 20-40.

Publication 2023

Amino Acids Catalysis Catalytic Domain DNA Replication Exons Ligands Molecular Docking Simulation pibrentasvir Polyproteins Protein Domain Proteins remdesivir RNA, Viral RNA Replication SARS-CoV-2 Virus Replication

Structural Modeling and Validation of Catalytic Site

Three-dimensional structure of wild and mutant models of catalytic site domain was constructed using MODELLER v9.24 [33 (link)]. Thereafter, all models were refined using galaxy refine server and validated from Ramachandran plot using PROCHECK. Furthermore, energy minimization of both wild and mutant structures was executed using Chimera 1.1.5 software [34 (link)]. PyMOL software was used for calculating RMSD of mutant models w.r.t wild model.

Kaushal N, & Baranwal M. (2023). Mutational analysis of catalytic site domain of CCHFV L RNA segment. Journal of Molecular Modeling, 29(4), 88.

Publication 2023

Catalytic Domain Chimera

Auxin-Induced Degron Depletion of RNase H2

Strains carrying the auxin-inducible degron (AID*) for RNase H2 (catalytic subunit Rnh201) were created as described before^{27 (link)}. Plasmids and oligonucleotides are listed in Supplementary Data 3.

Schindler N., Tonn M., Kellner V., Fung J.J., Lockhart A., Vydzhak O., Juretschke T., Möckel S., Beli P., Khmelinskii A, & Luke B. (2023). Genetic requirements for repair of lesions caused by single genomic ribonucleotides in S phase. Nature Communications, 14, 1227.

Publication 2023

Auxins Catalytic Domain Endoribonucleases Oligonucleotides Plasmids Strains

CRISPR Activation and Methylation Plasmid Construction

Plasmid MLM3636, expressing single-guide RNAs in mammalian cells, was a kind gift from Keith Joung (Addgene plasmid # 43860). Plasmid pMLM2.0 was constructed from MLM3636 by replacing the sgRNA expression cassette with the sgRNA2.0 expression cassette of the lentiviral plasmid sgRNA (MS2)_zeo backbone (Addgene plasmid # 61427) [26 (link)]. Stretches of 20 bp sgRNA to target UCHL1 were designed using the online tool (http://crispr.mit.edu/). Double-stranded oligonucleotides containing these targeting sites (listed in Supplemental Table 2) were cloned into BsmBI-digested pMLM2.0.
The plasmid containing the gene of the mammalian codon-optimized dCas9-VP64 activator (a tetramer of the viral VP16 transcriptional activator) was a kind gift from Keith Joung (Addgene; pMLM3705, #47754). An additional multiple-cloning site was inserted by replacing the VP64 coding sequence in dCas9-VP64 with a sequence containing a PacI restriction site, the new plasmid was referred to as No Effector Domain, pdCas9-NED (Addgene #109358) [53 (link)].
Plasmids expressing C-terminally mCherry-tagged dCas9-MSssI (Q147L/E186A) in mammalian cells were constructed as follows [54 (link)]: to create in-frame fusion between dCas9-MSssI and the P2A-mCherry-tag, the double-stranded oligonucleotide AK473-AK474 (5’-CGCGCCCAT ATGTTAATTAACAATTAA/5’-CCGGTTAATTGTTAATTAACATATGGG) was inserted between the SgsI (AscI) and BshTI (AgeI) restriction sites of pSYC-187 (Addgene#74,794). Insertion of AK473-AK474 preserved the flanking restriction sites, introduced a unique PacI site (underlined) and an in-frame stop codon. To abolish the stop codon, a short oligo-duplex (AK481-AK482, 5’-TAAGGTACCGA/5’-CCGGTCGGTACCTTAAT) was cloned between the PacI and the BshTI (AgeI) sites to obtain the plasmid pMCS-P2A-mCherry. (MCS stands for a sequence containing several restriction sites.) The SgsI (AscI) and Eco105I (SnaBI) fragment encoding the ‘MCS-P2A-mChery’ fragment was excised from pMCS-P2A-mCherry and cloned between the SgsI (AscI) and MssI (PmeI) sites of pdCas9-NED. The resulting plasmid pM-dCas9-(NED)-P2A_mCherry encodes a dCas9-P2A-mCherry fusion. The coding sequences of the MSssI (Q147L) and MSssI (E186A) variants were inserted, on SgsI-PacI fragments, between the SgsI and PacI sites of pdCas9-(NED)-P2A_mCherry. The new plasmids named pM-dCas9-MsssI (Q147L)-P2A-mCherry and pM-dCas9-MsssI (E186A)-P2A-mCherry express the respective dCas9-MSssI variant carrying the self-cleavable mCherry-tag. The catalytic domain of H3K27 histone methyltransferase enhancer of zeste homolog 2 (EZH2) was amplified with overhangs containing AscI and PacI restriction sites by PCR from pdCas9-EZH2. The EZH2 catalytic domain was subcloned into the pM-dCas9-NED-P2A-mCherry plasmid to yield pM-dCas9-EZH2-P2A-mCherry. The P2A-mCherry coding sequence was from the plasmid pSYC-187 [55 (link)], which was a kind gift from Seok-Yong Choi (Addgene plasmid # 74794). The catalytic domain of PRDM9 and DOT1L from dCas9-PRDM9 and dCas9-DOT1L, constructed as previously described [47 (link)], were subcloned into the pM-dCas9-NED-P2A-mCherry plasmid.
UCHL1 full-length cDNA (669 bp) was amplified from BEAS-2B cells and inserted into pcDNA4/HisMaxA between the BamHI and XbaI sites to generate the pcDNA4-UCHL1. Structure of the recombinant plasmids was confirmed by sequencing.

Wu D.D., Lau A.T., Xu Y.M., Reinders-Luinge M., Koncz M., Kiss A., Timens W., Rots M.G, & Hylkema M.N. (2023). Targeted epigenetic silencing of UCHL1 expression suppresses collagen-1 production in human lung epithelial cells. Epigenetics, 18(1), 2175522.

Publication 2023

Catalytic Domain Cells Clustered Regularly Interspaced Short Palindromic Repeats Codon Codon, Terminator DNA, Complementary DOT1L protein, human Exons EZH2 protein, human Genes Mammals Methyltransferase, Histone Oligonucleotides Open Reading Frames Paramyotonia Congenita Plasmids Reading Frames RNA, Single Guide Tetrameres UCHL1 protein, human Vertebral Column Viral Transcription VP-16

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What is the Catalytic Domain and why is it important?

The Catalytic Domain is a discrete structural unit within an enzyme that is responsible for its catalytic activity. This region of the protein typically contains the active site where the substrate binds and the chemical reaction occurs. Identifying and understanding the catalytic domain is crucial for studying enzyme function, mechanism, and inhibition. Knowing the structure and properties of the catalytic domain is essential for developing effective enzyme-targeted drugs and optimizing enzymatic processes.

What are the different types or variations of Catalytic Domains?

How can the Catalytic Domain be used in practical applications?

The Catalytic Domain has many practical applications, such as: 1. Drug discovery: Identifying and targeting the catalytic domain of enzymes involved in disease pathways is a key strategy for developing enzyme inhibitors as therapeutic drugs. 2. Enzyme engineering: Modifying the catalytic domain can alter an enzyme's activity, specificity, and efficiency for industrial, agricultural, or medical uses. 3. Diagnostic assays: Detecting and quantifying the activity of certain catalytic domains can serve as biomarkers for disease diagnosis and monitoring.

What challenges are commonly faced when working with Catalytic Domains?

Some common challenges when working with Catalytic Domains include: 1. Identifying the precise boundaries and location of the catalytic domain within a larger enzyme structure. 2. Ensuring the catalytic domain retains its activity and native conformation when expressed or purified in isolation. 3. Accurately measuring catalytic activity and kinetics, especially for complex multi-subunit enzymes. 4. Selectivily targeting the catalytic domain without affecting other functional domains of the enzyme.

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PubCompare.ai's AI-driven platfrom can be extremely helpful for Catalytic Domain research in several ways: 1. Screen protocol literature more efficiently: The platform can rapidly identify and curate relevant publications, preprints, and patents containing Catalytic Domain protocols and methods. 2. Leverage AI to pinpoint Critical Insights: PubCompare.ai's AI analysis can highlight key differences in protocol effectiveness, enzyme characteristics, and catalytic domain performance to help you choose the best approach. 3. Identify the most effective Catalytic Domain protocols: The platform enables researchers to effortlessly compare multiple protocols side-by-side and select the most reproducible and accurate methods for their specific needs.

More about "Catalytic Domain"

Catalytic Domain: The Heart of Enzyme Function Enzymes are the workhorses of biological processes, catalyzing a wide range of chemical reactions essential for life.
At the core of an enzyme's function is its catalytic domain - a discrete structural unit responsible for its catalytic activity.
This region of the protein typically contains the active site where the substrate binds and the chemical transformation occurs.
Understanding the catalytic domain is crucial for studying enzyme mechanism, function, and inhibition.
Researchers utilize various techniques to identify and characterize this crucial domain, including the use of tools like Lipofectamine 2000 for transfection, TRIzol reagent for RNA extraction, Ni-NTA agarose for protein purification, and AutoDock Tools for molecular docking simulations.
The catalytic domain often contains key amino acid residues that participate in catalysis, such as those involved in substrate binding, proton transfer, or stabilizing reaction intermediates.
By studying the structure and dynamics of the catalytic domain, scientists can gain valuable insights into the enzyme's mechanism of action and potential target sites for inhibition, as demonstrated by the use of molecules like ATP and the PyMOL Molecular Graphics System.
Moreover, techniques like site-directed mutagenesis, using tools like the Q5 Site-Directed Mutagenesis Kit, allow researchers to systematically investigate the role of specific amino acids within the catalytic domain, revealing their contributions to enzyme function and potential for therapeutic targeting.
Computational approaches, such as those employing the Maestro software and Superdex 200 column for protein purification, also play a crucial role in understanding catalytic domains.
These methods can help predict and analyze the structure, dynamics, and interactions of the catalytic domain, ultimately leading to the development of more effective enzyme-targeted therapies.
By harnessing the power of PubCompare.ai's AI-driven platform, researchers can effortlessly locate and compare catalytic domain protocols from literature, preprints, and patents, optimizing their research process and making data-driven decisions to advance our understanding of this critical enzyme component.