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Xu D, Shao Q, Zhou C, Mahmood A, Zhang J. In Silico Analysis of nsSNPs of Human KRAS Gene and Protein Modeling Using Bioinformatic Tools. ACS OMEGA 2023; 8:13362-13370. [PMID: 37065036 PMCID: PMC10099408 DOI: 10.1021/acsomega.3c00804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 03/23/2023] [Indexed: 06/19/2023]
Abstract
The KRAS gene belongs to the RAS family and codes for 188 amino acid residues of KRAS protein, with a molecular mass of 21.6 kD. Non-synonymous single-nucleotide polymorphisms (nsSNPs) have been identified within the coding region in which some are associated with different diseases. However, structural changes are not well defined yet. In this study, we first categorized SNPs in the KRAS coding area and then used computational methods to determine their impact on the protein structure and stability. In addition, the three-dimensional model of KRAS was taken from the Protein Data Bank for structural modeling. Furthermore, genomic data were extracted from a variety of sources, including the 1000 Genome Project, dbSNPs, and ENSEMBLE, and assessed through in silico methods. Based on various tools used in this study, 10 out of 48 missense SNPs with rsIDs were found deleterious. The substitution of alanine for proline at position 146 pushed several residues toward the center of the protein. Arginine instead of leucine has a minor effect on protein structure and stability. In addition, the substitution of proline for leucine at the 34th position disrupted the structure and led to a bigger size than the wild-type protein, hence interrupting the protein interaction. Using the well-intended computational approach and applying several bioinformatic tools, we characterized and identified most damaging nsSNPs and further explored the structural dynamics and stability of KRAS protein.
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Affiliation(s)
- Duoduo Xu
- Oncology
Department, Wenzhou Hospital of Traditional
Chinese Medicine Affiliated to Zhejiang Chinese Medicine University, Wenzhou 325000, China
| | - Qiqi Shao
- Department
of Nursing, Central Health Center of Zeya
Town, Ouhai District, Wenzhou 325000, China
| | - Chen Zhou
- Ultrasonography
Department, Wenzhou Hospital of Traditional
Chinese Medicine Affiliated to Zhejiang Chinese Medicine University, Wenzhou 325099, China
| | - Arif Mahmood
- Center
for Medical Genetics and Hunan Key Laboratory of Medical Genetics,
School of Life Sciences, Central South University, Changsha 410078, Hunan, China
| | - Jizhou Zhang
- Oncology
Department, Wenzhou Hospital of Traditional
Chinese Medicine Affiliated to Zhejiang Chinese Medicine University, Wenzhou 325000, China
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Moreno-Del Álamo M, Tabone M, Muñoz-Martínez J, Valverde JR, Alonso JC. Toxin ζ Reduces the ATP and Modulates the Uridine Diphosphate-N-acetylglucosamine Pool. Toxins (Basel) 2019; 11:E29. [PMID: 30634431 PMCID: PMC6356619 DOI: 10.3390/toxins11010029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 12/21/2018] [Accepted: 01/04/2019] [Indexed: 11/20/2022] Open
Abstract
Toxin ζ expression triggers a reversible state of dormancy, diminishes the pool of purine nucleotides, promotes (p)ppGpp synthesis, phosphorylates a fraction of the peptidoglycan precursor uridine diphosphate-N-acetylglucosamine (UNAG), leading to unreactive UNAG-P, induces persistence in a reduced subpopulation, and sensitizes cells to different antibiotics. Here, we combined computational analyses with biochemical experiments to examine the mechanism of toxin ζ action. Free ζ toxin showed low affinity for UNAG. Toxin ζ bound to UNAG hydrolyzed ATP·Mg2+, with the accumulation of ADP, Pi, and produced low levels of phosphorylated UNAG (UNAG-P). Toxin ζ, which has a large ATP binding pocket, may temporally favor ATP binding in a position that is distant from UNAG, hindering UNAG phosphorylation upon ATP hydrolysis. The residues D67, E116, R158 and R171, involved in the interaction with metal, ATP, and UNAG, were essential for the toxic and ATPase activities of toxin ζ; whereas the E100 and T128 residues were partially dispensable. The results indicate that ζ bound to UNAG reduces the ATP concentration, which indirectly induces a reversible dormant state, and modulates the pool of UNAG.
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Affiliation(s)
- María Moreno-Del Álamo
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str., 28049 Madrid, Spain.
| | - Mariangela Tabone
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str., 28049 Madrid, Spain.
| | - Juan Muñoz-Martínez
- Scientific Computing Service, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str., 28049 Madrid, Spain.
| | - José R Valverde
- Scientific Computing Service, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str., 28049 Madrid, Spain.
| | - Juan C Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str., 28049 Madrid, Spain.
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Gurung AB, Bhattacharjee A. Impact of a non-synonymous Q281R polymorphism on structure of human Lipoprotein-Associated Phospholipase A 2 (Lp-PLA 2 ). J Cell Biochem 2018; 119:7009-7021. [PMID: 29737567 DOI: 10.1002/jcb.26909] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 03/28/2018] [Indexed: 01/27/2023]
Abstract
Non-synonymous single nucleotide polymorphisms (nsSNPs) are genetic variations at single base resulting in an amino acid change which have been associated with various complex human diseases. The human Lipoprotein-associated phospholipase A2 (Lp-PLA2 ) gene harbours a rare Q281R polymorphism which was previously reported to cause loss of enzymatic function. Lp-PLA2 is an important enzyme which catalyzes the hydrolysis of polar phospholipids releasing pro-atherogenic and pro-inflammatory mediators involved in the pathogenesis of atherosclerosis. Our current study is aimed at elucidating the structural and functional consequences of Q281R polymorphism on Lp-PLA2 . The Q281R mutation is classified as deleterious and causes protein instability as deduced from evolutionary, folding free energy changes and Support vector machine (SVM)-based methods. A Q281R mutant structure was deciphered using homology modelling approach and was validated using phi and psi dihedral angles distribution, ERRAT, Verify_3D scores, Protein Structure Analysis (ProSA) energ,y and Z-score. A decreased hydrophobic interactions and weaker substrate binding affinity was observed in the mutant compared to the wild- type (WT) using molecular docking. Further, the mutant displayed enhanced structural flexibility particularly in the low density lipoprotein (LDL) binding domain, decreased solvent accessibility of catalytic residues-Phe274 and Ser273 and increased Cɑ distance between Phe274 and Leu153 and large conformational entropy change as inferred from all-atom molecular dynamics (MD) simulation and essential dynamics (ED) studies. Our results corroborate well with previous experimental studies and thus these aberrations in the Q281R mutant structure may help explain the molecular basis of loss of enzyme activity.
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Affiliation(s)
- Arun B Gurung
- Computational Biology Laboratory, Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya, India
| | - Atanu Bhattacharjee
- Computational Biology Laboratory, Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya, India.,Bioinformatics Centre, North-Eastern Hill University, Shillong, Meghalaya, India
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4
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Affimer proteins inhibit immune complex binding to FcγRIIIa with high specificity through competitive and allosteric modes of action. Proc Natl Acad Sci U S A 2017; 115:E72-E81. [PMID: 29247053 DOI: 10.1073/pnas.1707856115] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Protein-protein interactions are essential for the control of cellular functions and are critical for regulation of the immune system. One example is the binding of Fc regions of IgG to the Fc gamma receptors (FcγRs). High sequence identity (98%) between the genes encoding FcγRIIIa (expressed on macrophages and natural killer cells) and FcγRIIIb (expressed on neutrophils) has prevented the development of monospecific agents against these therapeutic targets. We now report the identification of FcγRIIIa-specific artificial binding proteins called "Affimer" that block IgG binding and abrogate FcγRIIIa-mediated downstream effector functions in macrophages, namely TNF release and phagocytosis. Cocrystal structures and molecular dynamics simulations have revealed the structural basis of this specificity for two Affimer proteins: One binds directly to the Fc binding site, whereas the other acts allosterically.
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Hollman AL, Tchounwou PB, Huang HC. The Association between Gene-Environment Interactions and Diseases Involving the Human GST Superfamily with SNP Variants. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2016; 13:379. [PMID: 27043589 PMCID: PMC4847041 DOI: 10.3390/ijerph13040379] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 03/11/2016] [Accepted: 03/14/2016] [Indexed: 12/25/2022]
Abstract
Exposure to environmental hazards has been associated with diseases in humans. The identification of single nucleotide polymorphisms (SNPs) in human populations exposed to different environmental hazards, is vital for detecting the genetic risks of some important human diseases. Several studies in this field have been conducted on glutathione S-transferases (GSTs), a phase II detoxification superfamily, to investigate its role in the occurrence of diseases. Human GSTs consist of cytosolic and microsomal superfamilies that are further divided into subfamilies. Based on scientific search engines and a review of the literature, we have found a large amount of published articles on human GST super- and subfamilies that have greatly assisted in our efforts to examine their role in health and disease. Because of its polymorphic variations in relation to environmental hazards such as air pollutants, cigarette smoke, pesticides, heavy metals, carcinogens, pharmaceutical drugs, and xenobiotics, GST is considered as a significant biomarker. This review examines the studies on gene-environment interactions related to various diseases with respect to single nucleotide polymorphisms (SNPs) found in the GST superfamily. Overall, it can be concluded that interactions between GST genes and environmental factors play an important role in human diseases.
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Affiliation(s)
- Antoinesha L Hollman
- NIH/NIMHD RCMI Center for Environmental Heath, College of Science, Engineering, and Technology (CSET), Jackson State University, Jackson, MS 39217, USA.
| | - Paul B Tchounwou
- NIH/NIMHD RCMI Center for Environmental Heath, College of Science, Engineering, and Technology (CSET), Jackson State University, Jackson, MS 39217, USA.
- Department of Biology, CSET, Jackson State University, Jackson, MS 39217, USA.
| | - Hung-Chung Huang
- NIH/NIMHD RCMI Center for Environmental Heath, College of Science, Engineering, and Technology (CSET), Jackson State University, Jackson, MS 39217, USA.
- Department of Biology, CSET, Jackson State University, Jackson, MS 39217, USA.
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Frömmel J, Šebela M, Demo G, Lenobel R, Pospíšil T, Soural M, Kopečný D. N-acyl-ω-aminoaldehydes are efficient substrates of plant aminoaldehyde dehydrogenases. Amino Acids 2015; 47:175-87. [PMID: 25344796 DOI: 10.1007/s00726-014-1853-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 10/07/2014] [Indexed: 11/29/2022]
Abstract
Plant aminoaldehyde dehydrogenases (AMADHs, EC 1.2.1.19) belong to the family 10 of aldehyde dehydrogenases and participate in the metabolism of compounds related to amino acids such as polyamines or osmoprotectants. Their broad specificity covers ω-aminoaldehydes, aliphatic and aromatic aldehydes as well as nitrogen-containing heterocyclic aldehydes. The substrate preference of plant AMADHs is determined by the presence of aspartic acid and aromatic residues in the substrate channel. In this work, 15 new N-acyl derivates of 3-aminopropanal (APAL) and 4-aminobutanal (ABAL) were synthesized and confirmed as substrates of two pea AMADH isoenzymes (PsAMADH 1 and 2). The compounds were designed considering the previously demonstrated conversion of N-acetyl derivatives as well as substrate channel dimensions (5-8 Å × 14 Å). The acyl chain length and its branching were found less significant for substrate properties than the length of the initial natural substrate. In general, APAL derivatives were found more efficient than the corresponding ABAL derivatives because of the prevailing higher conversion rates and lower K m values. Differences in enzymatic performance between the two isoenzymes corresponded in part to their preferences to APAL to ABAL. The higher PsAMADH2 affinity to substrates correlated with more frequent occurrence of an excess substrate inhibition. Molecular docking indicated the possible auxiliary role of Tyr163, Ser295 and Gln451 in binding of the new substrates. The only derivative carrying a free carboxyl group (N-adipoyl APAL) was surprisingly better substrate than ABAL in PsAMADH2 reaction indicating that also negatively charged aldehydes might be good substrates for ALDH10 family.
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Affiliation(s)
- Jan Frömmel
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 11, 783 71, Olomouc, Czech Republic
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Demo G, Horská V, Fliedrová B, Stěpán J, Koča J, Weignerová L, Křen V, Wimmerová M. Protein engineering study of β-mannosidase to set up a potential chemically efficient biocatalyst. Glycobiology 2014; 24:1301-11. [PMID: 25049237 DOI: 10.1093/glycob/cwu074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
This study is focused on the analysis and mutagenesis of β-mannosidase from Bacteroides thetaiotaomicron with the aim of broadening its substrate specificity to 2-acetamido-2-deoxy-β-d-mannopyranosyl (β-ManNAc) derivatives. Various conformations ((4)C1, (4)H5 and (1)S5) of native and modified ligands were docked to the binding site of the protein to determine the most suitable conformation of sugars for further hydrolysis. Key amino acid residues were mutated in silico focusing on stabilizing the acetamido group of β-ManNAc as well as forming the oxazoline intermediate needed for hydrolysis. The results of large set of 5 ns molecular dynamic simulations showed that the majority of the active site residues are involved in substrate interaction and do not exhibit a higher flexibility except for Asn178. Mutations of Asn178 to alanine and Asp199 to serine could lead to a stabilization of the acetamido group in the binding site. So far, in vitro mutagenesis and the screen of a large variety of biological sources were unable to extend β-mannosidase's activity to include β-ManNAc derivatives.
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Affiliation(s)
- Gabriel Demo
- National Centre for Biomolecular Research, Faculty of Science Central European Institute of Technology, Masaryk University, Kamenice 5/A4, Brno 62500, Czech Republic
| | - Veronika Horská
- National Centre for Biomolecular Research, Faculty of Science
| | - Barbora Fliedrová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 142 20, Czech Republic
| | - Jakub Stěpán
- National Centre for Biomolecular Research, Faculty of Science Central European Institute of Technology, Masaryk University, Kamenice 5/A4, Brno 62500, Czech Republic
| | - Jaroslav Koča
- National Centre for Biomolecular Research, Faculty of Science Central European Institute of Technology, Masaryk University, Kamenice 5/A4, Brno 62500, Czech Republic
| | - Lenka Weignerová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 142 20, Czech Republic
| | - Vladimír Křen
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 142 20, Czech Republic
| | - Michaela Wimmerová
- National Centre for Biomolecular Research, Faculty of Science Central European Institute of Technology, Masaryk University, Kamenice 5/A4, Brno 62500, Czech Republic Department of Biochemistry, Faculty of Science, Masaryk University, Kamenice 5/A5, Brno 62500, Czech Republic
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8
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Tabassum A, Rajeshwari T, Soni N, Raju DSB, Yadav M, Nayarisseri A, Jahan P. Structural characterization and mutational assessment of podocin - a novel drug target to nephrotic syndrome - an in silico approach. Interdiscip Sci 2014; 6:32-9. [PMID: 24464702 DOI: 10.1007/s12539-014-0190-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 07/13/2013] [Accepted: 07/29/2013] [Indexed: 12/01/2022]
Abstract
Non-synonymous single nucleotide changes (nSNC) are coding variants that introduce amino acid changes in their corresponding proteins. They can affect protein function; they are believed to have the largest impact on human health compared with SNCs in other regions of the genome. Such a sequence alteration directly affects their structural stability through conformational changes. Presence of these conformational changes near catalytic site or active site may alter protein function and as a consequence receptor-ligand complex interactions. The present investigation includes assessment of human podocin mutations (G92C, P118L, R138Q, and D160G) on its structure. Podocin is an important glomerular integral membrane protein thought to play a key role in steroid resistant nephrotic syndrome. Podocin has a hairpin like structure with 383 amino acids, it is an integral protein homologous to stomatin, and acts as a molecular link in a stretch-sensitive system. We modeled 3D structure of podocin by means of Modeller and validated via PROCHECK to get a Ramachandran plot (88.5% in most favored region), main chain, side chain, bad contacts, gauche and pooled standard deviation. Further, a protein engineering tool Triton was used to induce mutagenesis corresponding to four variants G92C, P118L, R138Q and D160G in the wild type. Perusal of energies of wild and mutated type of podocin structures confirmed that mutated structures were thermodynamically more stable than wild type and therefore biological events favored synthesis of mutated forms of podocin than wild type. As a conclusive part, two mutations G92C (-8179.272 kJ/mol) and P118L (-8136.685 kJ/mol) are more stable and probable to take place in podocin structure over wild podocin structure (-8105.622 kJ/mol). Though there is lesser difference in mutated and wild type (approximately, 74 and 35 kJ/mol), it may play a crucial role in deciding why mutations are favored and occur at the genetic level.
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Affiliation(s)
- Asra Tabassum
- Department of Genetics, Osmania University, Hyderabad, 500007, India
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Ionescu CM, Geidl S, Svobodová Vařeková R, Koča J. Rapid Calculation of Accurate Atomic Charges for Proteins via the Electronegativity Equalization Method. J Chem Inf Model 2013; 53:2548-58. [DOI: 10.1021/ci400448n] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Crina-Maria Ionescu
- CEITEC—Central European
Institute of Technology, and National Centre for Biomolecular Research,
Faculty of Science, Masaryk University Brno, Kamenice 5, 625 00, Brno-Bohunice, Czech Republic
| | - Stanislav Geidl
- CEITEC—Central European
Institute of Technology, and National Centre for Biomolecular Research,
Faculty of Science, Masaryk University Brno, Kamenice 5, 625 00, Brno-Bohunice, Czech Republic
| | - Radka Svobodová Vařeková
- CEITEC—Central European
Institute of Technology, and National Centre for Biomolecular Research,
Faculty of Science, Masaryk University Brno, Kamenice 5, 625 00, Brno-Bohunice, Czech Republic
| | - Jaroslav Koča
- CEITEC—Central European
Institute of Technology, and National Centre for Biomolecular Research,
Faculty of Science, Masaryk University Brno, Kamenice 5, 625 00, Brno-Bohunice, Czech Republic
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Vuree S, Dunna NR, Khan IA, Alharbi KK, Vishnupriya S, Soni D, Shah P, Chandok H, Yadav M, Nayarisseri A. Pharmacogenomics of drug resistance in Breast Cancer Resistance Protein (BCRP) and its mutated variants. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.jopr.2013.06.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Predictions of Enzymatic Parameters: A Mini-Review with Focus on Enzymes for Biofuel. Appl Biochem Biotechnol 2013; 171:590-615. [DOI: 10.1007/s12010-013-0328-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 06/11/2013] [Indexed: 12/25/2022]
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Kříž Z, Klusák J, Krištofíková Z, Koča J. How ionic strength affects the conformational behavior of human and rat beta amyloids--a computational study. PLoS One 2013; 8:e62914. [PMID: 23717395 PMCID: PMC3662769 DOI: 10.1371/journal.pone.0062914] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 03/26/2013] [Indexed: 11/21/2022] Open
Abstract
Progressive cerebral deposition of amyloid beta occurs in Alzheimeŕs disease and during the aging of certain mammals (human, monkey, dog, bear, cow, cat) but not others (rat, mouse). It is possibly due to different amino acid sequences at positions 5, 10 and 13. To address this issue, we performed series of 100 ns long trajectories (each trajectory was run twice with different initial velocity distribution) on amyloid beta (1–42) with the human and rat amino acid sequence in three different environments: water with only counter ions, water with NaCl at a concentration of 0.15 M as a model of intracellular Na+ concentration at steady state, and water with NaCl at a concentration of 0.30 M as a model of intracellular Na+ concentration under stimulated conditions. We analyzed secondary structure stability, internal hydrogen bonds, and residual fluctuation. It was observed that the change in ionic strength affects the stability of internal hydrogen bonds. Increasing the ionic strength increases atomic fluctuation in the hydrophobic core of the human amyloid, and decreases the atomic fluctuation in the case of rat amyloid. The secondary structure analyses show a stable α-helix part between residues 10 and 20. However, C-terminus of investigated amyloids is much more flexible showing no stable secondary structure elements. Increasing ionic strength of the solvent leads to decreasing stability of the secondary structural elements. The difference in conformational behavior of the three amino acids at position 5, 10 and 13 for human and rat amyloids significantly changes the conformational behavior of the whole peptide.
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Affiliation(s)
- Zdeněk Kříž
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jiří Klusák
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Zdena Krištofíková
- Alzheimer Disease Centre, Prague Psychiatric Centre, Prague, Czech Republic
| | - Jaroslav Koča
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
- * E-mail:
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Velliquette RW, Hue-Roye K, Lomas-Francis C, Gillen B, Schierts J, Gentzkow K, Peyrard T, von Zabern I, Flegel WA, Rodberg K, Debnath AK, Lee S, Reid ME. Molecular basis of two novel and related high-prevalence antigens in the Kell blood group system, KUCI and KANT, and their serologic and spatial association with K11 and KETI. Transfusion 2013; 53:2872-81. [PMID: 23560718 DOI: 10.1111/trf.12200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 02/17/2013] [Accepted: 03/03/2013] [Indexed: 11/27/2022]
Abstract
BACKGROUND The numerous antigens in the Kell blood group system result from missense nucleotide changes in KEL. Antibodies to antigens in this system can be clinically important. We describe six probands whose plasma contained antibodies to high-prevalence Kell antigens and discuss their relationship. STUDY DESIGN AND METHODS Polymerase chain reaction amplification, direct sequencing, restriction fragment length polymorphism assays, hemagglutination, flow cytometry, and protein modeling were performed by standard methods. RESULTS Proband 1 (KUCI) and her serologically compatible sister were heterozygous for a nucleotide change in Exon 11 (KEL*1271C/T; Ala424Val). Proband 2 (KANT) was heterozygous for KEL*1283G/T (Arg428Leu) and KEL*1216C/T (Arg406Stop) in Exon 11. Red blood cells (RBCs) from Proband 1 and her sister were not agglutinated by plasma from Proband 2; however, RBCs from Proband 2 were agglutinated by plasma from Proband 1. Probands 3, 4, 5, and 6 had the KEL*1391C>T change associated with the previously reported KETI- phenotype. Proband 5 was also homozygous for KEL*905T>C encoding the K11-K17+ phenotype. Hemagglutination studies revealed an association between KUCI, KANT, KETI, and K11. Protein modeling indicated that whereas Ala424 and Arg428 are clustered, Val302 and Thr464 are not. CONCLUSION Ala424 in the Kell glycoprotein is associated with the high-prevalence Kell antigen, KUCI (ISBT 006032), which is detected by the antibody of Proband 1. Arg428 is associated with the high-prevalence Kell antigen, KANT (ISBT 006033). The association between KUCI, KANT, KETI, and K11 and the results of protein modeling are discussed.
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Affiliation(s)
- Randall W Velliquette
- Laboratory of Immunohematology and Genomics, New York Blood Center, Long Island City, New York; Laboratory of Immunochemistry, New York Blood Center, New York, New York; Laboratory of Molecular Modeling and Drug Design, New York Blood Center, New York, New York; Laboratory of Membrane Biochemistry, New York Blood Center, New York, New York; Memorial Blood Centers, St Paul, Minnesota; Medcenter One, Bismarck, North Dakota; National Reference Center for Blood Groups, National Institute of Blood Transfusion, Paris, France; Department of Transfusion Medicine, University Hospital Ulm, Institute of Clinical Transfusion Medicine and Immunogenetics, Ulm and German Red Cross Blood Donor Service, Baden-Württemberg-Hessen, Institute Ulm, Ulm, Germany; Laboratory Services Section, Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland; American Red Cross, Southern California Region, Pomona, California
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Hasan K, Gora A, Brezovsky J, Chaloupkova R, Moskalikova H, Fortova A, Nagata Y, Damborsky J, Prokop Z. The effect of a unique halide-stabilizing residue on the catalytic properties of haloalkane dehalogenase DatA from Agrobacterium tumefaciens C58. FEBS J 2013; 280:3149-59. [PMID: 23490078 DOI: 10.1111/febs.12238] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 03/05/2013] [Accepted: 03/06/2013] [Indexed: 11/28/2022]
Abstract
Haloalkane dehalogenases catalyze the hydrolysis of carbon-halogen bonds in various chlorinated, brominated and iodinated compounds. These enzymes have a conserved pair of halide-stabilizing residues that are important in substrate binding and stabilization of the transition state and the halide ion product via hydrogen bonding. In all previously known haloalkane dehalogenases, these residues are either a pair of tryptophans or a tryptophan-asparagine pair. The newly-isolated haloalkane dehalogenase DatA from Agrobacterium tumefaciens C58 (EC 3.8.1.5) possesses a unique halide-stabilizing tyrosine residue, Y109, in place of the conventional tryptophan. A variant of DatA with the Y109W mutation was created and the effects of this mutation on the structure and catalytic properties of the enzyme were studied using spectroscopy and pre-steady-state kinetic experiments. Quantum mechanical and molecular dynamics calculations were used to obtain a detailed analysis of the hydrogen-bonding patterns within the active sites of the wild-type and the mutant, as well as of the stabilization of the ligands as the reaction proceeds. Fluorescence quenching experiments suggested that replacing the tyrosine with tryptophan improves halide binding by 3.7-fold, presumably as a result of the introduction of an additional hydrogen bond. Kinetic analysis revealed that the mutation affected the substrate specificity of the enzyme and reduced its K(0.5) for selected halogenated substrates by a factor of 2-4, without impacting the rate-determining hydrolytic step. We conclude that DatA is the first natural haloalkane dehalogenase that stabilizes its substrate in the active site using only a single hydrogen bond, which is a new paradigm in catalysis by this enzyme family.
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Affiliation(s)
- Khomaini Hasan
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Brno, Czech Republic
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15
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Sonawane P, Patel K, Vishwakarma RK, Singh S, Khan BM. in Silico mutagenesis and docking studies of active site residues suggest altered substrate specificity and possible physiological role of Cinnamoyl CoA Reductase 1 (Ll-CCRH1). Bioinformation 2013; 9:224-32. [PMID: 23515358 PMCID: PMC3602876 DOI: 10.6026/97320630009224] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 02/11/2013] [Indexed: 11/23/2022] Open
Abstract
Cinnamoyl CoA reductase (CCR) carries out the first committed step in monolignol biosynthesis and acts as a first regulatory point
in lignin formation. CCR shows multiple substrate specificity towards various cinnamoyl CoA esters. Here, in Silico mutagenesis
studies of active site residues of Ll-CCRH1 were carried out. Homology modeling based modeled 3D structure of Ll-CCRH1 was
used as template for in Silico mutant preparations. Docking simulations of Ll-CCRH1 mutants with CoA esters by AutoDock Vina
tools showed altered substrate specificity as compared to wild type. The study evidences that conformational changes, and change
in geometry or architecture of active site pocket occurred following mutations. The altered substrate specificity for active site
mutants suggests the possible physiological role of CCR either in lignin formation or in defense system in plants.
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Affiliation(s)
- Prashant Sonawane
- Plant Tissue Culture and Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India
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16
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Verma R, Schwaneberg U, Roccatano D. Computer-Aided Protein Directed Evolution: a Review of Web Servers, Databases and other Computational Tools for Protein Engineering. Comput Struct Biotechnol J 2012; 2:e201209008. [PMID: 24688649 PMCID: PMC3962222 DOI: 10.5936/csbj.201209008] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 10/07/2012] [Accepted: 10/12/2012] [Indexed: 12/01/2022] Open
Abstract
The combination of computational and directed evolution methods has proven a winning strategy for protein engineering. We refer to this approach as computer-aided protein directed evolution (CAPDE) and the review summarizes the recent developments in this rapidly growing field. We will restrict ourselves to overview the availability, usability and limitations of web servers, databases and other computational tools proposed in the last five years. The goal of this review is to provide concise information about currently available computational resources to assist the design of directed evolution based protein engineering experiment.
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Affiliation(s)
- Rajni Verma
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany ; Department of Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074 Aachen, Germany
| | - Ulrich Schwaneberg
- Department of Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074 Aachen, Germany
| | - Danilo Roccatano
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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17
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Frömmel J, Soural M, Tylichová M, Kopečný D, Demo G, Wimmerová M, Sebela M. Plant aminoaldehyde dehydrogenases oxidize a wide range of nitrogenous heterocyclic aldehydes. Amino Acids 2012; 43:1189-202. [PMID: 22160258 DOI: 10.1007/s00726-011-1174-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Accepted: 11/21/2011] [Indexed: 11/29/2022]
Abstract
The metabolic degradation of aldehydes is catalyzed by oxidoreductases from which aldehyde dehydrogenases (EC 1.2.1) comprise nonspecific or substrate-specific enzymes. The latter subset is represented, e.g., by NAD(+)-dependent aminoaldehyde dehydrogenases (AMADHs; EC 1.2.1.19) oxidizing a group of naturally occurring ω-aminoaldehydes including polyamine oxidation products. Recombinant isoenzymes from pea (PsAMADH1 and 2) and tomato (LeAMADH1 and 2) were subjected to kinetic measurements with synthetic aldehydes containing a nitrogenous heterocycle such as pyridinecarbaldehydes and their halogenated derivatives, (pyridinylmethylamino)-aldehydes, pyridinyl propanals and aldehydes derived from purine, 7-deazapurine and pyrimidine to characterize their substrate specificity and significance of the resulting data for in vivo reactions. The enzymatic production of the corresponding carboxylic acids was analyzed by liquid chromatography coupled to electrospray ionization mass spectrometry. Although the studied AMADHs are largely homologous and supposed to have a very similar active site architecture, significant differences were observed. LeAMADH1 displayed the broadest specificity oxidizing almost all compounds followed by PsAMADH2 and 1. In contrast, LeAMADH2 accepted only a few compounds as substrates. Pyridinyl propanals were converted by all isoenzymes, usually better than pyridinecarbaldehydes and aldehydes with fused rings. The K (m) values for the best substrates were in the range of 10(-5)-10(-4) M. Nevertheless, the catalytic efficiency values (V (max)/K (m)) reached only a very small fraction of that with 3-aminopropanal (except for LeAMADH1 activity with two pyridine-derived compounds). Docking experiments using the crystal structure of PsAMADH2 were involved to discuss differences in results with position isomers or alkyl chain homologs.
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Affiliation(s)
- Jan Frömmel
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 11, Olomouc, Czech Republic
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Charge profile analysis reveals that activation of pro-apoptotic regulators Bax and Bak relies on charge transfer mediated allosteric regulation. PLoS Comput Biol 2012; 8:e1002565. [PMID: 22719244 PMCID: PMC3375244 DOI: 10.1371/journal.pcbi.1002565] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Accepted: 05/04/2012] [Indexed: 11/22/2022] Open
Abstract
The pro-apoptotic proteins Bax and Bak are essential for executing programmed cell death (apoptosis), yet the mechanism of their activation is not properly understood at the structural level. For the first time in cell death research, we calculated intra-protein charge transfer in order to study the structural alterations and their functional consequences during Bax activation. Using an electronegativity equalization model, we investigated the changes in the Bax charge profile upon activation by a functional peptide of its natural activator protein, Bim. We found that charge reorganizations upon activator binding mediate the exposure of the functional sites of Bax, rendering Bax active. The affinity of the Bax C-domain for its binding groove is decreased due to the Arg94-mediated abrogation of the Ser184-Asp98 interaction. We further identified a network of charge reorganizations that confirms previous speculations of allosteric sensing, whereby the activation information is conveyed from the activation site, through the hydrophobic core of Bax, to the well-distanced functional sites of Bax. The network was mediated by a hub of three residues on helix 5 of the hydrophobic core of Bax. Sequence and structural alignment revealed that this hub was conserved in the Bak amino acid sequence, and in the 3D structure of folded Bak. Our results suggest that allostery mediated by charge transfer is responsible for the activation of both Bax and Bak, and that this might be a prototypical mechanism for a fast activation of proteins during signal transduction. Our method can be applied to any protein or protein complex in order to map the progress of allosteric changes through the proteins' structure. Apoptosis is a physiological form of cell death that is fundamental for development, growth and homeostasis in multi-cellular organisms. Deviations in the apoptosis machinery are known to be involved in cancer, neurodegenerative disorders, and autoimmune diseases. The proteins Bax and Bak are essential for executing apoptosis, yet the mechanism of their activation is not properly understood at the structural level. To understand this mechanism, we investigated how the electronic density is reorganized (i.e., how charge is transferred) inside the Bax molecule when Bax binds a functional peptide of its natural activator protein. We identified the specific interactions responsible for the exposure of the functional sites of Bax, rendering Bax active. Furthermore, we found a network of charge transfer that conveys activation information from the Bax activation site, through the hydrophobic core of Bax, to the well-distanced functional sites of Bax. This network consists of three residues inside the hydrophobic core of Bax, which are present also in the hydrophobic core of Bak, suggesting that these residues are functionally important and thus potential drug targets. We provide a straightforward and accessible methodology to identify the key residues involved in the fast activation of proteins during signal transduction.
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19
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Mishra SK, Adam J, Wimmerová M, Koča J. In silico mutagenesis and docking study of Ralstonia solanacearum RSL lectin: performance of docking software to predict saccharide binding. J Chem Inf Model 2012; 52:1250-61. [PMID: 22506916 DOI: 10.1021/ci200529n] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, in silico mutagenesis and docking in Ralstonia solanacearum lectin (RSL) were carried out, and the ability of several docking software programs to calculate binding affinity was evaluated. In silico mutation of six amino acid residues (Agr17, Glu28, Gly39, Ala40, Trp76, and Trp81) was done, and a total of 114 in silico mutants of RSL were docked with Me-α-L-fucoside. Our results show that polar residues Arg17 and Glu28, as well as nonpolar amino acids Trp76 and Trp81, are crucial for binding. Gly39 may also influence ligand binding because any mutations at this position lead to a change in the binding pocket shape. The Ala40 residue was found to be the most interesting residue for mutagenesis and can affect the selectivity and/or affinity. In general, the docking software used performs better for high affinity binders and fails to place the binding affinities in the correct order.
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Affiliation(s)
- Sushil Kumar Mishra
- Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
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20
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Méndez-Lucio O, Romo-Mancillas A, Medina-Franco JL, Castillo R. Computational study on the inhibition mechanism of cruzain by nitrile-containing molecules. J Mol Graph Model 2012; 35:28-35. [DOI: 10.1016/j.jmgm.2012.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 01/06/2012] [Accepted: 01/10/2012] [Indexed: 10/14/2022]
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21
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Méndez-Lucio O, Pérez-Villanueva J, Romo-Mancillas A, Castillo R. 3D-QSAR studies on purine-carbonitriles as cruzain inhibitors: comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). MEDCHEMCOMM 2011. [DOI: 10.1039/c1md00163a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Recognition of selected monosaccharides by Pseudomonas aeruginosa Lectin II analyzed by molecular dynamics and free energy calculations. Carbohydr Res 2010; 345:1432-41. [PMID: 20546713 DOI: 10.1016/j.carres.2010.04.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Revised: 04/19/2010] [Accepted: 04/23/2010] [Indexed: 12/24/2022]
Abstract
In this study, interactions of selected monosaccharides with the Pseudomonas aeruginosa Lectin II (PA-IIL) are analyzed in detail. An interesting feature of the PA-IIL binding is that the monosaccharide is interacting via two calcium ions and the binding is unusually strong for protein-saccharide interaction. We have used Molecular Mechanics Poisson-Boltzmann Surface Area (MM/PBSA) and normal mode analysis to calculate the free energy of binding. The impact of intramolecular hydrogen bond network for the lectin/monosaccharide interaction is also analyzed.
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Wimmerová M, Mishra NK, Pokorná M, Koca J. Importance of oligomerisation on Pseudomonas aeruginosaLectin-II binding affinity. In silico and in vitro mutagenesis. J Mol Model 2009; 15:673-9. [PMID: 19277730 DOI: 10.1007/s00894-009-0464-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2008] [Accepted: 01/13/2009] [Indexed: 01/07/2023]
Abstract
The effect of terminal GLY114* deletion on the binding affinity of the PA-IIL lectin toward L: -fucose was investigated. Both experimental (isothermal titration calorimetry) and computational (molecular dynamics simulations) methods have shown that the deletion mutation decreases the L-fucose affinity. It implies that the PA-IIL saccharide binding affinity is influenced by the dimerization of the lectin. A detailed analysis of computational data confirms the key role of electrostatic interactions in the PA-IIL/saccharide binding.
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Affiliation(s)
- Michaela Wimmerová
- National Centre for Biomolecular Research, Masaryk University, Faculty Science, Kotlárská 2, 611 37 Brno, Czech Republic.
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24
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Adam J, Kříž Z, Prokop M, Wimmerová M, Koča J. In Silico Mutagenesis and Docking Studies of Pseudomonas aeruginosa PA-IIL Lectin — Predicting Binding Modes and Energies. J Chem Inf Model 2008; 48:2234-42. [DOI: 10.1021/ci8002107] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jan Adam
- National Centre for Biomolecular Research, Department of Biochemistry, and Department of Chemistry, Faculty of Science, Kotlářská 2, Masaryk University, 611 37 Brno, Czech Republic
| | - Zdeněk Kříž
- National Centre for Biomolecular Research, Department of Biochemistry, and Department of Chemistry, Faculty of Science, Kotlářská 2, Masaryk University, 611 37 Brno, Czech Republic
| | - Martin Prokop
- National Centre for Biomolecular Research, Department of Biochemistry, and Department of Chemistry, Faculty of Science, Kotlářská 2, Masaryk University, 611 37 Brno, Czech Republic
| | - Michaela Wimmerová
- National Centre for Biomolecular Research, Department of Biochemistry, and Department of Chemistry, Faculty of Science, Kotlářská 2, Masaryk University, 611 37 Brno, Czech Republic
| | - Jaroslav Koča
- National Centre for Biomolecular Research, Department of Biochemistry, and Department of Chemistry, Faculty of Science, Kotlářská 2, Masaryk University, 611 37 Brno, Czech Republic
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