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Li T, Zhang Y, Shao J, Hou R, Zhang Z, Ye C, Wang H, Zhu B, Zhang Y. Enhancement of non-covalent interaction between soy protein isolate and quercetin by sodium alginate. Food Chem 2024; 460:140422. [PMID: 39068794 DOI: 10.1016/j.foodchem.2024.140422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/16/2024] [Accepted: 07/09/2024] [Indexed: 07/30/2024]
Abstract
Effects of sodium alginate (SA) on the non-covalent interaction between soybean protein isolate (SPI) and quercetin (Que) were investigated by multispectral technology, molecular docking and dynamics simulation technology. Structural alterations of the binary complexes were observed after SA addition, characterized by a red shift of maximum fluorescence emission wavelength. The introduction of 0.1% (w/v) SA led to a reduction of 12.3% in the α-helix and β-sheet structures, accompanied by 12.6% increase in the β-turn and random coil conformations. The binding of SA to SPI provided electrostatic interactions and facilitated the subsequent binding of SPI to Que. Molecular docking confirmed that hydrophobic interactions and electrostatic interactions were also the main driving force. Molecular dynamics simulation emphasized that the ternary complexes with SA exhibited greater stability compared to the binary ones. The foaming and emulsifying properties of SPI-Que complexes were enhanced by 33.76% and 68.28%, respectively, due to the addition of SA.
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Affiliation(s)
- Taoran Li
- College of Public Health and Health Sciences, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yubo Zhang
- College of Public Health and Health Sciences, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Juanjuan Shao
- Department of Science and Technology, Hebei Agricultural University, Hebei 061100, China
| | - Ruiyang Hou
- College of Public Health and Health Sciences, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Zifan Zhang
- College of Public Health and Health Sciences, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Chengxiang Ye
- College of Public Health and Health Sciences, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Hongwu Wang
- College of Public Health and Health Sciences, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Beibei Zhu
- College of Chinese Medicine Pharmaceutical Engineering, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yating Zhang
- College of Public Health and Health Sciences, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
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Moussaoui M, Baassi M, Baammi S, Soufi H, Salah M, Daoud R, El Allali A, Belghiti ME, Belaaouad S. In silico design of novel CDK2 inhibitors through QSAR, ADMET, molecular docking and molecular dynamics simulation studies. J Biomol Struct Dyn 2023; 41:13646-13662. [PMID: 37203327 DOI: 10.1080/07391102.2023.2212304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 02/04/2023] [Indexed: 05/20/2023]
Abstract
The present study aims to investigate about the quantitative structure-activity relationship (QSAR) of a series of Thiazole derivatives reported as anticancer agents (hepatocellular carcinoma), using principally the electronic descriptors calculated by the DFT method and by applying the multiple linear regression method. The developed model showed good statistical parameters (R2 = 0.725, R2adj = 0.653, MSE = 0.060, R2test = 0.827, Q2cv = 0.536). The energy EHOMO orbital, electronic energy (TE), shape coefficient (I), number of rotatable bonds (NROT), and index of refraction (n) were revealed to be the main descriptors influencing the anti-cancer activity. Further, new Thiazole derivatives have been designed and their activities and pharmacokinetic properties have been predicted using the validated QSAR model. The designed molecules were then assessed to molecular docking (MD), and molecular dynamic (MDs) simulation accompanied by the calculation of the binding affinity using MMPBSA script according to 100 ns a simulation trajectory, to study both their affinity and their stability towards CDK2 as a target protein for the cancer disease treatment. This research concluded with the identification of four new CDK2 inhibitors which are A1, A3, A5, and A6 showing good pharmacokinetic properties. The MDs results revealed that the newly designed compound A5 remained stable in the active center of the discovered CDK2 protein, indicating its potential as a novel inhibitor for the treatment of hepatocellular carcinoma. The current findings may eventually contribute to the development of robust CDK2 inhibitors in the future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohamed Moussaoui
- Laboratory of Physical Chemistry of Materials, Faculty of Sciences Ben M'Sick, Hassan II University of Casablanca, Casablanca, Morocco
| | - Mouna Baassi
- Laboratory of Physical Chemistry of Materials, Faculty of Sciences Ben M'Sick, Hassan II University of Casablanca, Casablanca, Morocco
| | - Soukayna Baammi
- African Genome Centre (AGC), Mohammed VI Polytechnic University, Benguerir, Morocco
| | - Hatim Soufi
- Laboratory of Physical Chemistry of Materials, Faculty of Sciences Ben M'Sick, Hassan II University of Casablanca, Casablanca, Morocco
| | - Mohammed Salah
- Team of Chemoinformatics Research and Spectroscopy and Quantum Chemistry, Department of chemistry, Faculty of Science, University Chouaib Doukkali, El Jadida, Morocco
| | - Rachid Daoud
- African Genome Centre (AGC), Mohammed VI Polytechnic University, Benguerir, Morocco
| | - Achraf El Allali
- African Genome Centre (AGC), Mohammed VI Polytechnic University, Benguerir, Morocco
| | - M E Belghiti
- Laboratory of Physical Chemistry of Materials, Faculty of Sciences Ben M'Sick, Hassan II University of Casablanca, Casablanca, Morocco
- Laboratory of Nernest Technology, Sherbrook, Quebec, Canada
| | - Said Belaaouad
- Laboratory of Physical Chemistry of Materials, Faculty of Sciences Ben M'Sick, Hassan II University of Casablanca, Casablanca, Morocco
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Pinto ÉSM, Krause MJ, Dorn M, Feltes BC. The nucleotide excision repair proteins through the lens of molecular dynamics simulations. DNA Repair (Amst) 2023; 127:103510. [PMID: 37148846 DOI: 10.1016/j.dnarep.2023.103510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 04/07/2023] [Accepted: 04/23/2023] [Indexed: 05/08/2023]
Abstract
Mutations that affect the proteins responsible for the nucleotide excision repair (NER) pathway can lead to diseases such as xeroderma pigmentosum, trichothiodystrophy, Cockayne syndrome, and Cerebro-oculo-facio-skeletal syndrome. Hence, understanding their molecular behavior is needed to elucidate these diseases' phenotypes and how the NER pathway is organized and coordinated. Molecular dynamics techniques enable the study of different protein conformations, adaptable to any research question, shedding light on the dynamics of biomolecules. However, as important as they are, molecular dynamics studies focused on DNA repair pathways are still becoming more widespread. Currently, there are no review articles compiling the advancements made in molecular dynamics approaches applied to NER and discussing: (i) how this technique is currently employed in the field of DNA repair, focusing on NER proteins; (ii) which technical setups are being employed, their strengths and limitations; (iii) which insights or information are they providing to understand the NER pathway or NER-associated proteins; (iv) which open questions would be suited for this technique to answer; and (v) where can we go from here. These questions become even more crucial considering the numerous 3D structures published regarding the NER pathway's proteins in recent years. In this work, we tackle each one of these questions, revising and critically discussing the results published in the context of the NER pathway.
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Affiliation(s)
| | - Mathias J Krause
- Institute for Applied and Numerical Mathematics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Márcio Dorn
- Center for Biotechnology, Federal University of Rio Grande do Sul, RS, Brazil; Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil
| | - Bruno César Feltes
- Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
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Alakbaree M, Abdulsalam AH, Ahmed HH, Ali FH, Al-Hili A, Omar MSS, Alonazi M, Jamalis J, Latif NA, Hamza MA, Amran SI. A computational study of structural analysis of Class I human glucose-6-phosphate dehydrogenase (G6PD) variants: Elaborating the correlation to chronic non-spherocytic hemolytic anemia (CNSHA). Comput Biol Chem 2023; 104:107873. [PMID: 37141793 DOI: 10.1016/j.compbiolchem.2023.107873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/11/2023] [Accepted: 04/19/2023] [Indexed: 05/06/2023]
Abstract
Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common human enzyme defect that affects more than 500 million people worldwide. Individuals affected with G6PD deficiency may occasionally suffer mild-to-severe chronic hemolytic anemia. Chronic non-spherocytic hemolytic anemia (CNSHA) is a potential result of the Class I G6PD variants. This comparative computational study attempted to correct the defect in variants structure by docking the AG1 molecule to selected Class I G6PD variants [G6PDNashville (Arg393His), G6PDAlhambra (Val394Leu), and G6PDDurham (Lys238Arg)] at the dimer interface and structural NADP+ binding site. It was followed by an analysis of the enzyme conformations before and after binding to the AG1 molecule using the molecular dynamics simulation (MDS) approach, while the severity of CNSHA was determined via root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), hydrogen bonds, salt bridges, radius of gyration (Rg), solvent accessible surface area analysis (SASA), and principal component analysis (PCA). The results revealed that G6PDNashville (Arg393His) and G6PDDurham (Lys238Arg) had lost the direct contact with structural NADP+ and salt bridges at Glu419 - Arg427 and Glu206 - Lys407 were disrupted in all selected variants. Furthermore, the AG1 molecule re-stabilized the enzyme structure by restoring the missing interactions. Bioinformatics approaches were also used to conduct a detailed structural analysis of the G6PD enzyme at a molecular level to understand the implications of these variants toward enzyme function. Our findings suggest that despite the lack of treatment for G6PDD to date, AG1 remains a novel molecule that promotes activation in a variety of G6PD variants.
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Affiliation(s)
- Maysaa Alakbaree
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.
| | | | - Haron H Ahmed
- Ibn Sina University for Medical and Pharmaceutical Sciences, Faculty of Medicine, Baghdad, Iraq
| | - Farah Hasan Ali
- Department of Radiology and Ultrasound, Al-Farahidi University, Collage of Medical Technology, Baghdad, Iraq
| | - Ahmed Al-Hili
- Department of Anesthesia, Al-Farahidi University, Collage of Medical Technology, Baghdad, Iraq
| | | | - Mona Alonazi
- Department of Biochemistry, Science College, King Saud University, Riyadh, Saudi Arabia
| | - Joazaizulfazli Jamalis
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Nurriza Ab Latif
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Muaawia Ahmed Hamza
- Faculty of Medicine, King Fahad Medical City, Research Center, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Syazwani Itri Amran
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
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Sur VP, Simonik O, Novotna M, Mazumdar A, Liska F, Vimberg V, Komrskova K. Dynamic study of small toxic hydrophobic proteins PepA1 and PepG1 of Staphylococcus aureus. Int J Biol Macromol 2022; 219:1360-1371. [PMID: 35932805 DOI: 10.1016/j.ijbiomac.2022.07.192] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/22/2022] [Accepted: 07/23/2022] [Indexed: 11/16/2022]
Abstract
Toxin-antitoxin (TA) systems are small genetic elements which encode toxin proteins that interfere with vital cellular functions. PepA1 and PepG1 toxin proteins, known also as SprA1 and SprG1, are type I TA. In Staphylococcus aureus (S. aureus), their expression without the antitoxin counterparts (SprA1AS and SprF1), is lethal to the pathogen. Molecular Dynamics (MD) simulation was performed for PepA1 and PepG1 to understand their dynamic state, conformational changes, and their toxicity. The protein structures were constructed and used for MD simulation and the conformational changes, stability, flexibility, fluctuations, hydrophobicity, and role of their dynamic state on function prediction were studied extensively by GROMACS MD simulation analysis tools. In silico study indicated that the PepA1 and PepG1 proteins change their structural conformation from an open to closed state where PepA1 conformational changes were faster (10 ns) than PepG1 (20 ns) while PepG1 exerted more stability and flexibility than PepA1. According to SASA values, PepG1 is more hydrophobic than the PepA1 and forms fewer hydrogen bonds than PepA1. The in vivo study with PepA1 and PepG1 proteins provided evidence that both the conformation changes between the open and closed states and the amino acid sequence are crucial for peptide toxicity.
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Affiliation(s)
- Vishma Pratap Sur
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, Prumyslova 595, 25250 Vestec, Czech Republic
| | - Ondrej Simonik
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, Prumyslova 595, 25250 Vestec, Czech Republic
| | - Michaela Novotna
- Laboratory for Biology of Secondary Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Aninda Mazumdar
- Laboratory for Biology of Secondary Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Frantisek Liska
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague, Albertov 4, 128 00 Prague, Czech Republic
| | - Vladimir Vimberg
- Laboratory for Biology of Secondary Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Katerina Komrskova
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, Prumyslova 595, 25250 Vestec, Czech Republic; Department of Zoology, Faculty of Science, Charles University, Vinicna 7, 128 44 Prague, Czech Republic.
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Attri P, Kurita H, Koga K, Shiratani M. Impact of Reactive Oxygen and Nitrogen Species Produced by Plasma on Mdm2-p53 Complex. Int J Mol Sci 2021; 22:ijms22179585. [PMID: 34502494 PMCID: PMC8431430 DOI: 10.3390/ijms22179585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 08/27/2021] [Accepted: 08/31/2021] [Indexed: 12/11/2022] Open
Abstract
The study of protein–protein interactions is of great interest. Several early studies focused on the murine double minute 2 (Mdm2)–tumor suppressor protein p53 interactions. However, the effect of plasma treatment on Mdm2 and p53 is still absent from the literature. This study investigated the structural changes in Mdm2, p53, and the Mdm2–p53 complex before and after possible plasma oxidation through molecular dynamic (MD) simulations. MD calculation revealed that the oxidized Mdm2 bounded or unbounded showed high flexibility that might increase the availability of tumor suppressor protein p53 in plasma-treated cells. This study provides insight into Mdm2 and p53 for a better understanding of plasma oncology.
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Affiliation(s)
- Pankaj Attri
- Center of Plasma Nano-Interface Engineering, Kyushu University, Fukuoka 819-0395, Japan;
- Graduate School of Information Science and Electrical Engineering, Kyushu University, Fukuoka 819-0395, Japan
- Correspondence:
| | - Hirofumi Kurita
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi 441-8580, Aichi, Japan;
| | - Kazunori Koga
- Faculty of Information Science and Electrical Engineering, Kyushu University, Fukuoka 819-0395, Japan;
- Center for Novel Science Initiatives, National Institute of Natural Science, Tokyo 105-0001, Japan
| | - Masaharu Shiratani
- Center of Plasma Nano-Interface Engineering, Kyushu University, Fukuoka 819-0395, Japan;
- Faculty of Information Science and Electrical Engineering, Kyushu University, Fukuoka 819-0395, Japan;
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XPF -673C>T variation is associated with the susceptibility to breast cancer. Cancer Epidemiol 2021; 74:102007. [PMID: 34416547 DOI: 10.1016/j.canep.2021.102007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 08/02/2021] [Accepted: 08/08/2021] [Indexed: 11/22/2022]
Abstract
PURPOSE XPF variations might decrease the DNA repair capacity and further contribute to cancer development. This study aimed to investigate the association of XPF polymorphisms with risk of developing breast cancer. METHODS TCGA, the Human Protein Atlas and Kaplan-Meier plotter were used to analyze the expression of XPF in breast cancer tissues and its effect on the survival of breast cancer patients. The expression of XPF in breast cancer tissues was detected by qRT-PCR. This case-control study included 467 breast cancer patients and 467 healthy controls. The genotype of genetic variation was detected by polymerase chain reaction restriction fragment length polymorphism. Odds ratios and 95 % confidence intervals were calculated. Correlations between XPF variation and clinicopathological parameters were assessed through Kendall's Tau-b test. The relationship between XPF gene function variation and XPF gene expression was analyzed by GTEx. RESULTS The expression of XPF in breast cancer tissues is higher than that in normal tissues. Breast cancer patients with high XPF expression have a higher relapse free survival rate (HR = 0.88, 95 % CI = 0.80-0.97), but have no effect on the overall survival rate (logrank P = 0.28). XPF -673C > T variant can reduce the risk of breast cancer patients (OR = 0.35, 95 %CI = 0.20-0.63 for codominant mode; OR = 0.66, 95 %CI = 0.51-0.85 for dominant model; OR = 0.40, 95 %CI = 0.23-0.70 for recessive model). The XPF 11985 GG genotype reduced the risk of early breast cancer (OR = 0.49, 95 %CI = 0.24-0.97), but not the risk of advanced breast cancer (OR = 1.20, 95 % CI = 0.58-2.48). XPF 11985A > G variant can also reduce the risk of ERBB2 expression in patients (OR = 0.50, 95 %CI = 0.27-0.94). There is no correlation between XPF -673C > T/XPF11985A > G variants and ER and PR. XPF -673C > T variant can reduce XPF expression (P < 0.05). CONCLUSIONS Genetic variations of XPF gene may affect its expression and the risk of breast cancer in the Chinese population.
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Identification and structural characterization of deleterious non-synonymous single nucleotide polymorphisms in the human SKP2 gene. Comput Biol Chem 2019; 79:127-136. [PMID: 30802828 DOI: 10.1016/j.compbiolchem.2019.02.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 01/27/2019] [Accepted: 02/13/2019] [Indexed: 12/17/2022]
Abstract
In SCF (Skp, Cullin, F-box) ubiquitin-protein ligase complexes, S-phase kinase 2 (SKP2) is one of the major players of F-box family, that is responsible for the degradation of several important cell regulators and tumor suppressor proteins. Despite of having significant evidence for the role of SKP2 on tumorgenesis, there is a lack of available data regarding the effect of non-synonymous polymorphisms. In this communication, the structural and functional consequences of non-synonymous single nucleotide polymorphisms (nsSNPs) of SKP2 have been reported by employing various computational approaches and molecular dynamics simulation. Initially, several computational tools like SIFT, PolyPhen-2, PredictSNP, I-Mutant 2.0 and ConSurf have been implicated in this study to explore the damaging SNPs. In total of 172 nsSNPs, 5 nsSNPs were identified as deleterious and 3 of them were predicted to be decreased the stability of protein. Guided from ConSurf analysis, P101L (rs761253702) and Y346C (rs755010517) were categorized as the highly conserved and functional disrupting mutations. Therefore, these mutations were subjected to three dimensional model building and molecular dynamics simulation study for the detailed structural consequences upon the mutations. The study revealed that P101L and Y346C mutations increased the flexibility and changed the structural dynamics. As both these mutations are located in the most functional regions of SKP2 protein, these computational insights might be helpful to consider these nsSNPs for wet-lab confirmatory analysis as well as in rationalizing future population based studies and structure based drug design against SKP2.
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Ghosh M, Sodhi SS, Sharma N, Mongre RK, Kim N, Singh AK, Lee SJ, Kim DC, Kim SW, Lee HK, Song KD, Jeong DK. An integrated in silico approach for functional and structural impact of non- synonymous SNPs in the MYH1 gene in Jeju Native Pigs. BMC Genet 2016; 17:35. [PMID: 26847462 PMCID: PMC4741023 DOI: 10.1186/s12863-016-0341-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 01/25/2016] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND This study was performed to identify the non- synonymous polymorphisms in the myosin heavy chain 1 gene (MYH1) association with skeletal muscle development in economically important Jeju Native Pig (JNP) and Berkshire breeds. Herein, we present an in silico analysis, with a focus on (a) in silico approaches to predict the functional effect of non-synonymous SNP (nsSNP) in MYH1 on growth, and (b) molecular docking and dynamic simulation of MYH1 to predict the effects of those nsSNP on protein-protein association. RESULTS The NextGENe (V 2.3.4.) tool was used to identify the variants in MYH1 from JNP and Berkshire using RNA seq. Gene ontology analysis of MYH1 revealed significant association with muscle contraction and muscle organ development. The 95 % confidence intervals clearly indicate that the mRNA expression of MYH1 is significantly higher in the Berkshire longissimus dorsi muscle samples than JNP breed. Concordant in silico analysis of MYH1, the open-source software tools identified 4 potential nsSNP (L884T, K972C, N981G, and Q1285C) in JNP and 1 nsSNP (H973G) in Berkshire pigs. Moreover, protein-protein interactions were studied to investigate the effect of MYH1 mutations on association with hub proteins, and MYH1 was found to be closely associated with the protein myosin light chain, phosphorylatable, fast skeletal muscle MYLPF. The results of molecular docking studies on MYH1 (native and 4 mutants) and MYLFP demonstrated that the native complex showed higher electrostatic energy (-466.5 Kcal mol(-1)), van der Walls energy (-87.3 Kcal mol(-1)), and interaction energy (-835.7 Kcal mol(-1)) than the mutant complexes. Furthermore, the molecular dynamic simulation revealed that the native complex yielded a higher root-mean-square deviation (0.2-0.55 nm) and lower root-mean-square fluctuation (approximately 0.08-0.3 nm) as compared to the mutant complexes. CONCLUSIONS The results suggest that the variants at L884T, K972C, N981G, and Q1285C in MYH1 in JNP might represent a cause for the poor growth performance for this breed. This study is a pioneering in-depth in silico analysis of polymorphic MYH1 and will serve as a valuable resource for further targeted molecular diagnosis and population-based studies conducted for improving the growth performance of JNP.
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Affiliation(s)
- Mrinmoy Ghosh
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju-Do, 690-756, Republic of Korea.
| | - Simrinder Singh Sodhi
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju-Do, 690-756, Republic of Korea.
| | - Neelesh Sharma
- Sher-e-Kashmir University of Agricultural Sciences and Technology, R.S. Pura, Jammu, India.
| | - Raj Kumar Mongre
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju-Do, 690-756, Republic of Korea.
| | - Nameun Kim
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju-Do, 690-756, Republic of Korea.
| | - Amit Kumar Singh
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju-Do, 690-756, Republic of Korea.
| | - Sung Jin Lee
- Department of Animal Biotechnology, College of Animal Bioscience and Technology, Kangwon National University, Chuncheon, 200-701, Republic of Korea.
| | - Dae Cheol Kim
- Livestock Promotion Institute, Jeju Special Self-governing Province, Jeju-Do, 690-756, Republic of Korea.
| | - Sung Woo Kim
- Animal Genetic Resources Station, National Institute of Animal Science, Rural Administration, Namwon, Republic of Korea.
| | - Hak Kyo Lee
- Department of Animal Biotechnology, Chonbuk National University, Jeonju, 561-756, Republic of Korea.
| | - Ki-Duk Song
- Department of Animal Biotechnology, Chonbuk National University, Jeonju, 561-756, Republic of Korea.
| | - Dong Kee Jeong
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju-Do, 690-756, Republic of Korea.
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Ramesh M, Vepuri SB, Oosthuizen F, Soliman ME. Adenosine Monophosphate-Activated Protein Kinase (AMPK) as a Diverse Therapeutic Target: A Computational Perspective. Appl Biochem Biotechnol 2015; 178:810-30. [DOI: 10.1007/s12010-015-1911-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 10/26/2015] [Indexed: 12/12/2022]
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11
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An Integrated In Silico Approach for the Structural and Functional Exploration of Lipocalin 2 and its Functional Insights with Metalloproteinase 9 and Lipoprotein Receptor-Related Protein 2. Appl Biochem Biotechnol 2015; 176:712-29. [DOI: 10.1007/s12010-015-1606-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 04/06/2015] [Indexed: 12/17/2022]
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Liu Y, Cao L, Chang J, Lin J, He B, Rao J, Zhang Z, Zhang X. XPF-673C>T polymorphism effect on the susceptibility to esophageal cancer in Chinese population. PLoS One 2014; 9:e94136. [PMID: 24709955 PMCID: PMC3978021 DOI: 10.1371/journal.pone.0094136] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 03/12/2014] [Indexed: 12/12/2022] Open
Abstract
Purpose Xeroderma pigmentsum group F (XPF) plays a pivotal role in DNA nucleotide excision repair and has been linked to the development of various cancers. This study aims to assess the association of XPF genetic variants with the susceptibility to esophageal squamous cell carcinoma (ESCC) in Chinese population. Methods This two-stage case-control study was conducted in a total of 1524 patients with ESCC and 1524 controls. Genotype of XPF -673C>T and 11985A>G variants were determined by polymerase chain reaction-based restriction fragment length polymorphism (PCR-RFLP). Logistic regression analysis was performed to estimate odd ratios (ORs) and 95% confidence intervals (95% CI). Results Our case-control study showed that XPF -673TT genotype was associated with a decreased risk of ESCC compared with CC genotype in both case-control sets (Tangshan set: OR = 0.58; 95%CI = 0.34–0.99, P = 0.040; Beijing set: OR = 0.66; 95%CI = 0.46–0.95, P = 0.027). Stratified analyses revealed that a multiplicative interaction between -673C>T variant and age, sex or smoking status was evident (Gene-age: Pinteraction = 0.002; Gene-sex: Pinteraction = 0.002; Gene-smoking: Pinteraction = 0.002). For XPF 11985A>G polymorphism, there was no significant difference of genotype distribution between ESCC cases and controls. Conclusion These findings indicated that genetic variants in XPF might contribute to the susceptibility to ESCC.
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Affiliation(s)
- Yingwen Liu
- Department of Molecular Genetics, College of Life Science, Hebei United University, Tangshan, China
- Department of Epidemiology, College of Public Health, Hebei United University, Tangshan, China
| | - Lei Cao
- Department of Molecular Genetics, College of Life Science, Hebei United University, Tangshan, China
| | - Jiang Chang
- Department of Etiology and Carcinogenesis, Cancer Institute and Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Jia Lin
- Department of Molecular Genetics, College of Life Science, Hebei United University, Tangshan, China
| | - Bing He
- Department of Molecular Genetics, College of Life Science, Hebei United University, Tangshan, China
| | - Juan Rao
- Department of Molecular Genetics, College of Life Science, Hebei United University, Tangshan, China
| | - Zhi Zhang
- Hebei United University Affiliated Tangshan Gongren Hospital, Tangshan, China
| | - Xuemei Zhang
- Department of Molecular Genetics, College of Life Science, Hebei United University, Tangshan, China
- * E-mail:
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