1
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Cheng GP, Wang YF, Li YY, Guo SM, Li HG, Ji DM, Yi NH, Zhou LQ. Deficiency of nucleosome-destabilizing factor GLYR1 dampens spermatogenesis in mice. Mol Cell Endocrinol 2024; 586:112194. [PMID: 38395189 DOI: 10.1016/j.mce.2024.112194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 02/25/2024]
Abstract
Aberrant sperm morphology hinders sperm motility and causes male subfertility. Spermatogenesis, a complex process in male germ cell development, necessitates precise regulation of numerous developmental genes. However, the regulatory pathways involved in this process remain partially understood. We have observed the widespread expression of Glyr1, the gene encoding a nucleosome-destabilizing factor, in mouse testicular cells. Our study demonstrates that mice experiencing Glyr1 depletion in spermatogenic cells exhibit subfertility characterized by a diminished count and motility of spermatozoa. Furthermore, the rate of sperm malformation significantly increases in the absence of Glyr1, with a predominant occurrence of head and neck malformation in spermatozoa within the cauda epididymis. Additionally, a reduction in spermatocyte numbers across different meiotic stages is observed, accompanied by diminished histone acetylation in spermatogenic cells upon Glyr1 depletion. Our findings underscore the crucial roles of Glyr1 in mouse spermiogenesis and unveil novel insights into the etiology of male reproductive diseases.
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Affiliation(s)
- Gui-Ping Cheng
- Department of Women Health Care, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu-Fan Wang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuan-Yuan Li
- Department of Gynecology and Obstetrics, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shi-Meng Guo
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hong-Gang Li
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dong-Mei Ji
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Anhui, China.
| | - Nian-Hua Yi
- Department of Women Health Care, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Li-Quan Zhou
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Anhui, China.
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2
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Caroli J, Mattevi A. The NPAC-LSD2 complex in nucleosome demethylation. Enzymes 2023; 53:97-111. [PMID: 37748839 DOI: 10.1016/bs.enz.2023.03.003] [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] [Indexed: 09/27/2023]
Abstract
NPAC is a transcriptional co-activator widely associated with the H3K36me3 epigenetic marks present in the gene bodies. NPAC plays a fundamental role in RNA polymerase progression, and its depletion downregulates gene transcription. In this chapter, we review the current knowledge on the functional and structural features of this multi-domain protein. NPAC (also named GLYR1 or NP60) contains a PWWP motif, a chromatin binder and epigenetic reader that is proposed to weaken the DNA-histone contacts facilitating polymerase passage through the nucleosomes. The C-terminus of NPAC is a catalytically inactive dehydrogenase domain that forms a stable and rigid tetramer acting as an oligomerization module for the formation of co-transcriptional multimeric complexes. The PWWP and dehydrogenase domains are connected by a long, mostly disordered, linker that comprises putative sites for protein and DNA interactions. A short dodecapeptide sequence (residues 214-225) forms the binding site for LSD2, a flavin-dependent lysine-specific histone demethylase. This stretch of residues binds on the surface of LSD2 and facilitates the capture and processing of the H3 tail in the nucleosome context, thus promoting the H3K4me1/2 epigenetic mark removal. LSD2 is associated with other two chromatin modifiers, G9a and NSD3. The LSD2-G9a-NSD3 complex modifies the pattern of the post translational modifications deposited on histones, thus converting the relaxed chromatin into a transcriptionally refractory state after the RNA polymerase passage. NPAC is a scaffolding factor that organizes and coordinates the epigenetic activities required for optimal transcription elongation.
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Affiliation(s)
- Jonatan Caroli
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy
| | - Andrea Mattevi
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy.
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3
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Wang Q, Liu S, Li K, Xing R, Chen X, Li P. A Computational Biology Study on the Structure and Dynamics Determinants of Thermal Stability of the Chitosanase from Aspergillus fumigatus. Int J Mol Sci 2023; 24:ijms24076671. [PMID: 37047643 PMCID: PMC10095384 DOI: 10.3390/ijms24076671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 04/14/2023] Open
Abstract
Environmentally friendly and efficient biodegradation with chitosanase for degrading chitosan to oligosaccharide has been gaining more importance. Here, we studied a chitosanase from Aspergillus fumigatus with potential for production, but does not have the ideal thermal stability. The structure predicted by the Alphafold2 model, especially the binding site and two catalytic residues, has been found to have a high similarity with the experimental structure of the chitosanase V-CSN from the same family. The effects of temperature on structure and function were studied by dynamic simulation and the results showed that the binding site had high flexibility. After heating up from 300 K to 350 K, the RMSD and RMSF of the binding site increased significantly, in particular, the downward shift of loop6 closed the binding site, resulting in the spatial hindrance of binding. The time proportions of important hydrogen bonds at the binding site decreased sharply, indicating that serious disruption of hydrogen bonds should be the main interaction factor for conformational changes. The residues contributing energetically to binding were also revealed to be in the highly flexible region, which inevitably leads to the decrease in the activity stability at high temperature. These findings provide directions for the modification of thermal stability and perspectives on the research of proteins without experimental structures.
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Affiliation(s)
- Qian Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Song Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Kecheng Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Ronge Xing
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Xiaolin Chen
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Pengcheng Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
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4
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Capelli R, Serapian SA, Colombo G. Computational Epitope Prediction and Design for Antibody Development and Detection. Methods Mol Biol 2023; 2552:255-266. [PMID: 36346596 DOI: 10.1007/978-1-0716-2609-2_13] [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] [Indexed: 06/16/2023]
Abstract
The design of optimized protein antigens is a fundamental step in the development of new vaccine candidates and in the detection of therapeutic antibodies. A fundamental prerequisite is the identification of antigenic regions that are most prone to interact with antibodies, namely, B-cell epitopes. Here, we describe an efficient structure-based computational method for epitope prediction, called MLCE. In this approach, all that is required is the 3D structure of the antigen of interest. MLCE can be applied to glycosylated proteins, facilitating the identification of immunoreactive versus immune-shielding carbohydrates.
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Affiliation(s)
- Riccardo Capelli
- SCITEC-CNR, Milan, Italy
- Politecnico di Torino, Department of Applied Science and Technology, Torino, Italy
| | | | - Giorgio Colombo
- SCITEC-CNR, Milan, Italy.
- Università di Pavia, Dipartimento di Chimica, Pavia, Italy.
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5
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Verma AK, Ahmed SF, Hossain MS, Bhojiya AA, Upadhyay SK, Srivastava AK, Singh N, Harina H, Rahaman MM, Bahadur NM. Unlocking SGK1 inhibitor potential of bis-[1-N,7-N, pyrazolo tetraethoxyphthalimido{-4-(3,5-Dimethyl-4-(spiro-3-methylpyazolo)-1,7-dihydro-1H-dipyrazolo[3,4-b;4',3'-e]pyridin-8-yl)}]p-disubstituted phenyl compounds: a computational study. J Biomol Struct Dyn 2022; 40:13412-13431. [PMID: 34696688 DOI: 10.1080/07391102.2021.1988711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
SGK1 (Serum and Glucocorticoid Regulated Kinase 1), a serine/threonine kinase that is activated by various stimuli, including serum and glucocorticoids. It controls inflammation, apoptosis, hormone release, neuro-excitability and cell proliferation, all of which play an important role in cancer progression and metastasis. SGK1 was recently proposed as a potential drug target for cancer, diabetes, and neurodegenerative diseases. In this study, molecular docking, physiochemical, toxicological properties and molecular dynamic simulation of the Bis-[1-N,7-N, Pyrazolo tetraethoxyphthalimido{-4-(3,5-Dimethyl-4-(spiro-3-methylpyazolo)-1,7-dihydro-1H-dipyrazolo[3,4-b;4',3'-e]pyridin-8-yl)}]p-disubstituted phenyl compoundsand reference EMD638683 against new SGK1 target protein. Compared to the reference inhibitor EMD638683, we choose the best compounds (series 2-6) based on the binding energy (in the range from -11.0 to -10.6 kcal/mol). With the exception of compounds 2 and 6, none of the compounds posed a risk for AMES toxicity or carcinogenicity due to their toxicological properties. 100 ns MD simulation accompanied by MM/PBSA energy calculations and PCA. According to MD simulation results, the binding of compounds 3, 4 and 5 stabilizes the SGK1 structure and causes febrile conformational changes compared to EMD638683. As a result of this research, the final selected compounds 3, 4 and 5 can be used as scaffolds to develop promising SGK1 inhibitors for the treatment of related diseases such as cancer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abhishek Kumar Verma
- Department of Life Sciences, Faculty of Science and Technology, Mewar University, Gangrar, Chittorgarh, Rajasthan, India
| | - Sk Faisal Ahmed
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Sonapur, Noakhali, Bangladesh
| | - Md Shahadat Hossain
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Sonapur, Noakhali, Bangladesh
| | - Ali Asger Bhojiya
- Faculty of Agriculture and Veterinary Sciences, Mewar University, Gangrar, Chittorgarh, Rajasthan, India
| | - Sudhir K Upadhyay
- Department of Environmental Science, V.B.S. Purvanchal University, Jaunpur, Uttar Pradesh, India
| | | | - Nripendra Singh
- Department of Pharmacy, V.B.S, Purvanchal University, Jaunpur, Uttar Pradesh, India
| | - Harina Harina
- Department of Life Sciences, Faculty of Science and Technology, Mewar University, Gangrar, Chittorgarh, Rajasthan, India
| | | | - Newaz Mohammed Bahadur
- Department of Applied Chemistry and Chemical Engineering, Noakhali Science and Technology University, Sonapur, Noakhali, Bangladesh
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6
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Halder P, Mitra P. Human prion protein: exploring the thermodynamic stability and structural dynamics of its pathogenic mutants. J Biomol Struct Dyn 2022; 40:11274-11290. [PMID: 34338141 DOI: 10.1080/07391102.2021.1957715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
Human familial prion diseases are known to be associated with different single-point mutants of the gene coding for prion protein with a primary focus at several locations of the globular domain. We have identified 12 different single-point pathogenic mutants of human prion protein (HuPrP) with the help of extensive perturbations/mutation technique at multiple locations of HuPrP sequence related to potentiality towards conformational disorders. Among these, some of the mutants include pathogenic variants that corroborate well with the literature reported proteins while majority include some unique single-point mutants that are either not explicitly studied early or studied for variants with different residues at the specific position. Primarily, our study sheds light on the unfolding mechanism of the above mentioned mutants in depth. Besides, we could identify some mutants under investigation that demonstrates not only unfolding of the helical structures but also extension and generation of the β-sheet structures and or simultaneously have highly exposed hydrophobic surface which is assumed to be linked with the production of aggregate/fibril structures of the prion protein. Among the identified mutants, Q212E needs special attention due to its maximum exposure of hydrophobic core towards solvent and E200Q is found to be important due to its maximum extent of β-content. We are also able to identify different respective structural conformations of the proteins according to their degree of structural unfolding and those conformations can be extracted and further studied in detail. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Puspita Halder
- Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Pralay Mitra
- Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
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7
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Joshi A, Ito T, Picard D, Neckers L. The Mitochondrial HSP90 Paralog TRAP1: Structural Dynamics, Interactome, Role in Metabolic Regulation, and Inhibitors. Biomolecules 2022; 12:biom12070880. [PMID: 35883436 PMCID: PMC9312948 DOI: 10.3390/biom12070880] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 02/04/2023] Open
Abstract
The HSP90 paralog TRAP1 was discovered more than 20 years ago; yet, a detailed understanding of the function of this mitochondrial molecular chaperone remains elusive. The dispensable nature of TRAP1 in vitro and in vivo further complicates an understanding of its role in mitochondrial biology. TRAP1 is more homologous to the bacterial HSP90, HtpG, than to eukaryotic HSP90. Lacking co-chaperones, the unique structural features of TRAP1 likely regulate its temperature-sensitive ATPase activity and shed light on the alternative mechanisms driving the chaperone’s nucleotide-dependent cycle in a defined environment whose physiological temperature approaches 50 °C. TRAP1 appears to be an important bioregulator of mitochondrial respiration, mediating the balance between oxidative phosphorylation and glycolysis, while at the same time promoting mitochondrial homeostasis and displaying cytoprotective activity. Inactivation/loss of TRAP1 has been observed in several neurodegenerative diseases while TRAP1 expression is reported to be elevated in multiple cancers and, as with HSP90, evidence of addiction to TRAP1 has been observed. In this review, we summarize what is currently known about this unique HSP90 paralog and why a better understanding of TRAP1 structure, function, and regulation is likely to enhance our understanding of the mechanistic basis of mitochondrial homeostasis.
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Affiliation(s)
- Abhinav Joshi
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, MD 20892, USA; (A.J.); (T.I.)
| | - Takeshi Ito
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, MD 20892, USA; (A.J.); (T.I.)
| | - Didier Picard
- Department of Molecular and Cellular Biology, Université de Genève, Sciences III, 30 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland;
| | - Len Neckers
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, MD 20892, USA; (A.J.); (T.I.)
- Correspondence: ; Tel.: +1-240-858-3918
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8
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Verma AK, Hossain MS, Ahmed SF, Hussain N, Ashid M, Upadhyay SK, Vishvakarma NK, Bhojiya AA, Srivastava SK. " In silico identification of ethoxy phthalimide pyrazole derivatives as IL-17A and IL-18 targeted gouty arthritis agents". J Biomol Struct Dyn 2022:1-15. [PMID: 35532103 DOI: 10.1080/07391102.2022.2071338] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Two proinflammatory cytokines, IL17A and IL18, are observed to be elevated in the serum of gout patients and they play a crucial role in the development and worsening of inflammation, which has severe effects. In present study, we have combined molecular docking, molecular dynamics studies and MM-PBSA analysis to study the effectiveness of ethoxy phthalimide pyrazole derivatives (series 3a to 3e) as potential inhibitors against cytokines IL17A and IL18 as a druggable targets. The binding energy of the docked series ranges from -13.5 to -10.0 kcal/mol and extensively interacts with the amino acids in the active pocket of IL17A and IL18. Compound 3e had the lowest binding energy with IL17A at -12.6 kcal/mol compared to control allopurinol (3.32 kcal/mol). With IL18, compound 3a seems to have the lowest binding energy of -9.6 kcal/mol compared to control allopurinol (3.18 kcal/mol). In MD simulation studies, compound 3a forms a stable and energetically stabilized complex with the target protein. Depending on properties of the bound IL17A-3a and IL18-3a complexes was compared by means of MM-PBSA analysis. These derivatives can be used as a scaffold to develop promising IL17A and IL18 inhibitors to assess their potential for gouty arthritis and other related diseases.
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Affiliation(s)
- Abhishek Kumar Verma
- Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Off Jaipur-Ajmer Expressway, Jaipur, Rajasthan, India
| | - Md Shahadat Hossain
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Sonapur, Noakhali, Bangladesh
| | - Sk Faisal Ahmed
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Sonapur, Noakhali, Bangladesh
| | - Nasir Hussain
- Department of Chemistry, Faculty of Science and Technology, Mewar University, Chittorgarh, Rajasthan, India
| | - Mohammad Ashid
- Department of Chemistry, Faculty of Science and Technology, Mewar University, Chittorgarh, Rajasthan, India
| | - Sudhir K Upadhyay
- Department of Environmental Science, V.B.S. Purvanchal University, Jaunpur, Uttar Pradesh, India
| | | | - Ali Asger Bhojiya
- Department of Science, U.S. Ostwal Science, Arts & Commerce College, Chittorgarh, India
| | - Sandeep Kumar Srivastava
- Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Off Jaipur-Ajmer Expressway, Jaipur, Rajasthan, India
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9
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Gonzalez-Teran B, Pittman M, Felix F, Thomas R, Richmond-Buccola D, Hüttenhain R, Choudhary K, Moroni E, Costa MW, Huang Y, Padmanabhan A, Alexanian M, Lee CY, Maven BEJ, Samse-Knapp K, Morton SU, McGregor M, Gifford CA, Seidman JG, Seidman CE, Gelb BD, Colombo G, Conklin BR, Black BL, Bruneau BG, Krogan NJ, Pollard KS, Srivastava D. Transcription factor protein interactomes reveal genetic determinants in heart disease. Cell 2022; 185:794-814.e30. [PMID: 35182466 PMCID: PMC8923057 DOI: 10.1016/j.cell.2022.01.021] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 08/20/2021] [Accepted: 01/25/2022] [Indexed: 02/08/2023]
Abstract
Congenital heart disease (CHD) is present in 1% of live births, yet identification of causal mutations remains challenging. We hypothesized that genetic determinants for CHDs may lie in the protein interactomes of transcription factors whose mutations cause CHDs. Defining the interactomes of two transcription factors haplo-insufficient in CHD, GATA4 and TBX5, within human cardiac progenitors, and integrating the results with nearly 9,000 exomes from proband-parent trios revealed an enrichment of de novo missense variants associated with CHD within the interactomes. Scoring variants of interactome members based on residue, gene, and proband features identified likely CHD-causing genes, including the epigenetic reader GLYR1. GLYR1 and GATA4 widely co-occupied and co-activated cardiac developmental genes, and the identified GLYR1 missense variant disrupted interaction with GATA4, impairing in vitro and in vivo function in mice. This integrative proteomic and genetic approach provides a framework for prioritizing and interrogating genetic variants in heart disease.
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Affiliation(s)
- Barbara Gonzalez-Teran
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Maureen Pittman
- Gladstone Institutes, San Francisco, CA, USA; Department of Epidemiology & Biostatistics, Institute for Computational Health Sciences, and Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Franco Felix
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | | | - Desmond Richmond-Buccola
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Ruth Hüttenhain
- Gladstone Institutes, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
| | | | | | - Mauro W Costa
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Yu Huang
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Arun Padmanabhan
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA; Division of Cardiology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Michael Alexanian
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Clara Youngna Lee
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Bonnie E J Maven
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA; Developmental and Stem Cell Biology Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Kaitlen Samse-Knapp
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Sarah U Morton
- Division of Newborn Medicine, Department of Medicine, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Michael McGregor
- Gladstone Institutes, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
| | - Casey A Gifford
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - J G Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA; Cardiovascular Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Bruce D Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Bruce R Conklin
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Brian L Black
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Benoit G Bruneau
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA; Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA; Division of Cardiology, Department of Pediatrics, UCSF School of Medicine, San Francisco, CA, USA
| | - Nevan J Krogan
- Gladstone Institutes, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
| | - Katherine S Pollard
- Gladstone Institutes, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA; Department of Epidemiology & Biostatistics, Institute for Computational Health Sciences, and Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
| | - Deepak Srivastava
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA; Division of Cardiology, Department of Pediatrics, UCSF School of Medicine, San Francisco, CA, USA; Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
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10
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Zhang Q, Chen Y, Ni D, Huang Z, Wei J, Feng L, Su JC, Wei Y, Ning S, Yang X, Zhao M, Qiu Y, Song K, Yu Z, Xu J, Li X, Lin H, Lu S, Zhang J. Targeting a cryptic allosteric site of SIRT6 with small-molecule inhibitors that inhibit the migration of pancreatic cancer cells. Acta Pharm Sin B 2022; 12:876-889. [PMID: 35256952 PMCID: PMC8897208 DOI: 10.1016/j.apsb.2021.06.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/17/2021] [Accepted: 06/23/2021] [Indexed: 02/07/2023] Open
Abstract
SIRT6 belongs to the conserved NAD+-dependent deacetylase superfamily and mediates multiple biological and pathological processes. Targeting SIRT6 by allosteric modulators represents a novel direction for therapeutics, which can overcome the selectivity problem caused by the structural similarity of orthosteric sites among deacetylases. Here, developing a reversed allosteric strategy AlloReverse, we identified a cryptic allosteric site, Pocket Z, which was only induced by the bi-directional allosteric signal triggered upon orthosteric binding of NAD+. Based on Pocket Z, we discovered an SIRT6 allosteric inhibitor named JYQ-42. JYQ-42 selectively targets SIRT6 among other histone deacetylases and effectively inhibits SIRT6 deacetylation, with an IC50 of 2.33 μmol/L. JYQ-42 significantly suppresses SIRT6-mediated cancer cell migration and pro-inflammatory cytokine production. JYQ-42, to our knowledge, is the most potent and selective allosteric SIRT6 inhibitor. This study provides a novel strategy for allosteric drug design and will help in the challenging development of therapeutic agents that can selectively bind SIRT6.
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Key Words
- ADPr, ADP-ribose
- Allosteric inhibitor
- BSA, bull serum albumin
- CCK-8, Cell Counting Kit-8
- Cell migration
- Cytokine production
- DMSO, dimethyl sulfoxide
- FBS, fetal bovine serum
- FDL, Fluor de Lys
- H3K18, histone 3 lysine 18
- H3K56, histone 3 lysine 56
- H3K9, histone 3 lysine 9
- HDAC, histone deacetylase
- HPLC, high-performance liquid chromatography
- IC50, half-maximum inhibitory concentration
- IPTG, isopropyl-β-d-thiogalactoside
- MD, molecular dynamics
- Molecular dynamics simulations
- NAD+, nicotinamide adenine dinucleotide
- NAM, nicotinamide
- PBS, phosphate buffer saline
- PMA, phorbol 12-myristate 13-acetate
- PMSF, phenylmethanesulfonyl fluoride
- Pancreatic cancer
- RMSD, root-mean-square deviation
- RT-qPCR, real-time quantitative PCR
- Reversed allostery
- SDS-PAGE, SDS-polyacrylamide gel electrophoresis
- SIRT6
- SIRT6, sirtuin 6
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11
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Elucidating the 3D Structure of a Surface Membrane Antigen from Trypanosoma cruzi as a Serodiagnostic Biomarker of Chagas Disease. Vaccines (Basel) 2022; 10:vaccines10010071. [PMID: 35062732 PMCID: PMC8781870 DOI: 10.3390/vaccines10010071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/28/2021] [Accepted: 12/29/2021] [Indexed: 11/16/2022] Open
Abstract
Chagas disease (CD) is a vector-borne parasitosis, caused by the protozoan parasite Trypanosoma cruzi, that affects millions of people worldwide. Although endemic in South America, CD is emerging throughout the world due to climate change and increased immigratory flux of infected people to non-endemic regions. Containing of the diffusion of CD is challenged by the asymptomatic nature of the disease in early infection stages and by the lack of a rapid and effective diagnostic test. With the aim of designing new serodiagnostic molecules to be implemented in a microarray-based diagnostic set-up for early screening of CD, herein, we report the recombinant production of the extracellular domain of a surface membrane antigen from T. cruzi (TcSMP) and confirm its ability to detect plasma antibodies from infected patients. Moreover, we describe its high-resolution (1.62 Å) crystal structure, to which in silico epitope predictions were applied in order to locate the most immunoreactive regions of TcSMP in order to guide the design of epitopes that may be used as an alternative to the full-length antigen for CD diagnosis. Two putative, linear epitopes, belonging to the same immunogenic region, were synthesized as free peptides, and their immunological properties were tested in vitro. Although both peptides were shown to adopt a structural conformation that allowed their recognition by polyclonal antibodies raised against the recombinant protein, they were not serodiagnostic for T. cruzi infections. Nevertheless, they represent good starting points for further iterative structure-based (re)design cycles.
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12
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Structure-function relationships of the disease-linked A218T oxytocin receptor variant. Mol Psychiatry 2022; 27:907-917. [PMID: 34980886 PMCID: PMC9054668 DOI: 10.1038/s41380-021-01241-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/24/2021] [Accepted: 07/15/2021] [Indexed: 12/20/2022]
Abstract
Various single nucleotide polymorphisms (SNPs) in the oxytocin receptor (OXTR) gene have been associated with behavioral traits, autism spectrum disorder (ASD) and other diseases. The non-synonymous SNP rs4686302 results in the OXTR variant A218T and has been linked to core characteristics of ASD, trait empathy and preterm birth. However, the molecular and intracellular mechanisms underlying those associations are still elusive. Here, we uncovered the molecular and intracellular consequences of this mutation that may affect the psychological or behavioral outcome of oxytocin (OXT)-treatment regimens in clinical studies, and provide a mechanistic explanation for an altered receptor function. We created two monoclonal HEK293 cell lines, stably expressing either the wild-type or A218T OXTR. We detected an increased OXTR protein stability, accompanied by a shift in Ca2+ dynamics and reduced MAPK pathway activation in the A218T cells. Combined whole-genome and RNA sequencing analyses in OXT-treated cells revealed 7823 differentially regulated genes in A218T compared to wild-type cells, including 429 genes being associated with ASD. Furthermore, computational modeling provided a molecular basis for the observed change in OXTR stability suggesting that the OXTR mutation affects downstream events by altering receptor activation and signaling, in agreement with our in vitro results. In summary, our study provides the cellular mechanism that links the OXTR rs4686302 SNP with genetic dysregulations associated with aspects of ASD.
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13
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Khalid H, Shahid S, Tariq S, Ijaz B, Ashfaq UA, Ahmad M. Discovery of Novel HCV NS5B polymerase inhibitor, 2-(3,4-dimethyl-5,5-dioxidobenzo[e]pyrazolo[4,3-c][1,2]thiazin-2(4H)-yl)-N-(2-fluorobenzyl)acetamide via molecular docking and experimental approach. Clin Exp Pharmacol Physiol 2021; 48:1653-1661. [PMID: 34386985 DOI: 10.1111/1440-1681.13571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/13/2021] [Accepted: 08/08/2021] [Indexed: 11/27/2022]
Abstract
Hepatitis C Virus (HCV) is a viral infection posing a severe global threat that left untreated progresses to end-stage liver disease, including cirrhosis and hepatocellular carcinoma (HCC). Moreover, no prophylactic approach exists so far enabling its prevention. The NS5B polymerase holds special significance as the target of intervention against HCV infection. The current study kindles benzothiazine derivatives against HCV NS5B polymerase through in silico and experimental approaches. Following docking, the compound 2-(3,4-dimethyl-5,5-dioxidobenzo[e]pyrazolo[4,3-c][1,2]thiazin-2(4H)-yl)-N-(2-fluorobenzyl)acetamide was revealed to form effective binding interaction in the proposed site of HCV NS5B with a score of -10 kcal/mol and subsequently was deciphered through molecular dynamics (MD) simulation study which indicated interaction of residues TYR_382, VAL_381 and HIS_467 through hydrophobic interaction and two residues such as GLU_202 and LYS_209 contributed in the formation of water bridges. The subsequent in silico pharmacological analysis revealed its safe drug profile. The cytotoxicity activity of compound 6c indicated to be non-toxic in HepG2 cells at concentration ranges from 0.001-1.0 µmol/L with >80% cell viability and diminished expression of the HCV NS5B to 98% at the dose of 1.0 µmol/L and 90% at 0.5µmol/L. Thus the hit compound 6c might be a potent NS5B polymerase inhibitor required to be validated further through in vivo and preclinical studies.
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Affiliation(s)
- Hina Khalid
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Sana Shahid
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Somayya Tariq
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Bushra Ijaz
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Matloob Ahmad
- Department of Chemistry, Government College University, Faisalabad, Pakistan
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14
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Bonet LFS, Loureiro JP, Pereira GRC, Da Silva ANR, De Mesquita JF. Molecular dynamics and protein frustration analysis of human fused in Sarcoma protein variants in Amyotrophic Lateral Sclerosis type 6: An In Silico approach. PLoS One 2021; 16:e0258061. [PMID: 34587215 PMCID: PMC8480726 DOI: 10.1371/journal.pone.0258061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/16/2021] [Indexed: 11/18/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is the most frequent adult-onset motor neuron disorder. The disease is characterized by degeneration of upper and lower motor neurons, leading to death usually within five years after the onset of symptoms. While most cases are sporadic, 5%-10% of cases can be associated with familial inheritance, including ALS type 6, which is associated with mutations in the Fused in Sarcoma (FUS) gene. This work aimed to evaluate how the most frequent ALS-related mutations in FUS, R521C, R521H, and P525L affect the protein structure and function. We used prediction algorithms to analyze the effects of the non-synonymous single nucleotide polymorphisms and performed evolutionary conservation analysis, protein frustration analysis, and molecular dynamics simulations. Most of the prediction algorithms classified the three mutations as deleterious. All three mutations were predicted to reduce protein stability, especially the mutation R521C, which was also predicted to increase chaperone binding tendency. The protein frustration analysis showed an increase in frustration in the interactions involving the mutated residue 521C. Evolutionary conservation analysis showed that residues 521 and 525 of human FUS are highly conserved sites. The molecular dynamics results indicate that protein stability could be compromised in all three mutations. They also affected the exposed surface area and protein compactness. The analyzed mutations also displayed high flexibility in most residues in all variants, most notably in the interaction site with the nuclear import protein of FUS.
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Affiliation(s)
- L. F. S. Bonet
- Department of Genetics and Molecular Biology, Laboratory of Bioinformatics and Computational Biology, Federal University of the State of Rio de Janeiro, Rio de Janeiro, Brazil
| | - J. P. Loureiro
- Department of Genetics and Molecular Biology, Laboratory of Bioinformatics and Computational Biology, Federal University of the State of Rio de Janeiro, Rio de Janeiro, Brazil
| | - G. R. C. Pereira
- Department of Genetics and Molecular Biology, Laboratory of Bioinformatics and Computational Biology, Federal University of the State of Rio de Janeiro, Rio de Janeiro, Brazil
| | - A. N. R. Da Silva
- Department of Genetics and Molecular Biology, Laboratory of Bioinformatics and Computational Biology, Federal University of the State of Rio de Janeiro, Rio de Janeiro, Brazil
| | - J. F. De Mesquita
- Department of Genetics and Molecular Biology, Laboratory of Bioinformatics and Computational Biology, Federal University of the State of Rio de Janeiro, Rio de Janeiro, Brazil
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15
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Masgras I, Laquatra C, Cannino G, Serapian SA, Colombo G, Rasola A. The molecular chaperone TRAP1 in cancer: From the basics of biology to pharmacological targeting. Semin Cancer Biol 2021; 76:45-53. [PMID: 34242740 DOI: 10.1016/j.semcancer.2021.07.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/25/2021] [Accepted: 07/02/2021] [Indexed: 12/22/2022]
Abstract
TRAP1, the mitochondrial component of the Hsp90 family of molecular chaperones, displays important bioenergetic and proteostatic functions. In tumor cells, TRAP1 contributes to shape metabolism, dynamically tuning it with the changing environmental conditions, and to shield from noxious insults. Hence, TRAP1 activity has profound effects on the capability of neoplastic cells to evolve towards more malignant phenotypes. Here, we discuss our knowledge on the biochemical functions of TRAP1 in the context of a growing tumor mass, and we analyze the possibility of targeting its chaperone functions for developing novel anti-neoplastic approaches.
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Affiliation(s)
- Ionica Masgras
- Dipartimento di Scienze Biomediche, Università di Padova, Padova, Italy; Istituto di Neuroscienze, Consiglio Nazionale Delle Ricerche (CNR), Padova, Italy
| | - Claudio Laquatra
- Dipartimento di Scienze Biomediche, Università di Padova, Padova, Italy
| | - Giuseppe Cannino
- Dipartimento di Scienze Biomediche, Università di Padova, Padova, Italy
| | | | | | - Andrea Rasola
- Dipartimento di Scienze Biomediche, Università di Padova, Padova, Italy.
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16
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Moghadam B, Ashouri M, Roohi H, Karimi-Jafari MH. Computational evidence of new putative allosteric sites in the acetylcholinesterase receptor. J Mol Graph Model 2021; 107:107981. [PMID: 34246109 DOI: 10.1016/j.jmgm.2021.107981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/27/2021] [Accepted: 06/29/2021] [Indexed: 10/21/2022]
Abstract
Acetylcholinesterase (AChE), with a rigid structure and buried active site at the end of a deep narrow gorge, is interesting enough to solve the paradox between high catalytic activity and unavailability of the active site in treatment of Alzheimer's disease (AD). In this way, the blind docking process is performed on an ensemble of AChE structures created with molecular dynamics (MD) simulations to survey the whole space of AChE to find multiple access pathways to the active site and ranking them based on their affinity scores. Our results show that there are other allosteric binding sites in the protein structure whose inhibition, can affect protein function by disrupting the release of the Acetylcholine (AC) degradation products. In this study, inhibitory activities of Hybride14 and two natural compounds (Papaverine and Palmatine) were evaluated for all possible allosteric sites via docking method. The results confirmed the non-competitive inhibition mechanism. The best binding mode for these inhibitors and efficacy of hydrogen bonds and hydrophobic interactions on inhibitory activities of ligands were also disclosed. Furthermore, our studies provide significant molecular insight for AChE inhibition that could aid in the development of new drugs for AD's treatment.
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Affiliation(s)
- Behnaz Moghadam
- Department of Chemistry, Faculty of Science, University of Guilan, Iran
| | - Mitra Ashouri
- Department of Physical Chemistry, School of Chemistry, College of Science, University of Tehran, Tehran, Iran.
| | - Hossein Roohi
- Department of Chemistry, Faculty of Science, University of Guilan, Iran.
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17
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La Sala G, Gunnarsson A, Edman K, Tyrchan C, Hogner A, Frolov AI. Unraveling the Allosteric Cross-Talk between the Coactivator Peptide and the Ligand-Binding Site in the Glucocorticoid Receptor. J Chem Inf Model 2021; 61:3667-3680. [PMID: 34156843 DOI: 10.1021/acs.jcim.1c00323] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The glucocorticoid receptor (GR) is a nuclear receptor that controls critical biological processes by regulating the transcription of specific genes. There is a known allosteric cross-talk between the ligand and coregulator binding sites within the GR ligand-binding domain that is crucial for the control of the functional response. However, the molecular mechanisms underlying such an allosteric control remain elusive. Here, molecular dynamics (MD) simulations, bioinformatic analysis, and biophysical measurements are integrated to capture the structural and dynamic features of the allosteric cross-talk within the GR. We identified a network of evolutionarily conserved residues that enables the allosteric signal transduction, in agreement with experimental data. MD simulations clarify how such a network is dynamically interconnected and offer a mechanistic explanation of how different peptides affect the intensity of the allosteric signal. This study provides useful insights to elucidate the GR allosteric regulation, ultimately providing a foundation for designing novel drugs.
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Affiliation(s)
- Giuseppina La Sala
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Anders Gunnarsson
- Discovery Science, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Karl Edman
- Discovery Science, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Christian Tyrchan
- Medicinal Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Anders Hogner
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Andrey I Frolov
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
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18
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Vucinic J, Novikov G, Montanier CY, Dumon C, Schiex T, Barbe S. A Comparative Study to Decipher the Structural and Dynamics Determinants Underlying the Activity and Thermal Stability of GH-11 Xylanases. Int J Mol Sci 2021; 22:ijms22115961. [PMID: 34073139 PMCID: PMC8199483 DOI: 10.3390/ijms22115961] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 11/23/2022] Open
Abstract
With the growing need for renewable sources of energy, the interest for enzymes capable of biomass degradation has been increasing. In this paper, we consider two different xylanases from the GH-11 family: the particularly active GH-11 xylanase from Neocallimastix patriciarum, NpXyn11A, and the hyper-thermostable mutant of the environmentally isolated GH-11 xylanase, EvXyn11TS. Our aim is to identify the molecular determinants underlying the enhanced capacities of these two enzymes to ultimately graft the abilities of one on the other. Molecular dynamics simulations of the respective free-enzymes and enzyme–xylohexaose complexes were carried out at temperatures of 300, 340, and 500 K. An in-depth analysis of these MD simulations showed how differences in dynamics influence the activity and stability of these two enzymes and allowed us to study and understand in greater depth the molecular and structural basis of these two systems. In light of the results presented in this paper, the thumb region and the larger substrate binding cleft of NpXyn11A seem to play a major role on the activity of this enzyme. Its lower thermal stability may instead be caused by the higher flexibility of certain regions located further from the active site. Regions such as the N-ter, the loops located in the fingers region, the palm loop, and the helix loop seem to be less stable than in the hyper-thermostable EvXyn11TS. By identifying molecular regions that are critical for the stability of these enzymes, this study allowed us to identify promising targets for engineering GH-11 xylanases. Eventually, we identify NpXyn11A as the ideal host for grafting the thermostabilizing traits of EvXyn11TS.
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Affiliation(s)
- Jelena Vucinic
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, ANITI, 31400 Toulouse, France; (J.V.); (G.N.); (C.Y.M.); (C.D.)
- Université Fédérale de Toulouse, ANITI, INRAE, UR 875, 31326 Toulouse, France;
| | - Gleb Novikov
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, ANITI, 31400 Toulouse, France; (J.V.); (G.N.); (C.Y.M.); (C.D.)
| | - Cédric Y. Montanier
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, ANITI, 31400 Toulouse, France; (J.V.); (G.N.); (C.Y.M.); (C.D.)
| | - Claire Dumon
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, ANITI, 31400 Toulouse, France; (J.V.); (G.N.); (C.Y.M.); (C.D.)
| | - Thomas Schiex
- Université Fédérale de Toulouse, ANITI, INRAE, UR 875, 31326 Toulouse, France;
| | - Sophie Barbe
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, ANITI, 31400 Toulouse, France; (J.V.); (G.N.); (C.Y.M.); (C.D.)
- Correspondence:
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19
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Wang L, Zhang Q, You Q. Targeting the HSP90-CDC37-kinase chaperone cycle: A promising therapeutic strategy for cancer. Med Res Rev 2021; 42:156-182. [PMID: 33846988 DOI: 10.1002/med.21807] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 03/19/2021] [Accepted: 03/31/2021] [Indexed: 12/25/2022]
Abstract
Heat shock protein 90 (HSP90) is an indispensable molecular chaperone that facilitates the maturation of numerous oncoproteins in cancer cells, including protein kinases, ribonucleoproteins, steroid hormone receptors, and transcription factors. Although over 30 HSP90 inhibitors have steadily entered clinical trials, further clinical advancement has been restricted by their limited efficacy, inevitable heat shock response, and multiple side-effects, likely induced via an ATP inhibition mechanism. Since both ATP and various co-chaperones play essential roles in the HSP90 chaperone cycle to achieve integrated function, optimal therapeutics require an understanding of the dynamic interactions among HSP90, ATP, and cochaperones. To date, continuous research has promoted the exploration of the cochaperone cell division cycle 37 (CDC37) as a kinase-specific recognizer and has shown that the HSP90-CDC37-kinase complex is particularly relevant in cancers. Indeed, disrupting the HSP90-CDC37-kinase complex, rather than totally blocking the ATP function of HSP90, is emerging as an alternative way to avoid the limitations of current inhibitors. In this review, we first briefly introduce the HSP90-CDC37-kinase cycle and present the currently available approaches for inhibitor development targeting this cycle and provide insights into selective regulation of the kinase clients of HSP90 by more directional ways.
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Affiliation(s)
- Lei Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, China.,Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, China
| | - Qiuyue Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, China.,Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, China.,Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, China
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20
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Serapian SA, Triveri A, Marchetti F, Castelli M, Colombo G. Exploiting Folding and Degradation Machineries To Target Undruggable Proteins: What Can a Computational Approach Tell Us? ChemMedChem 2021; 16:1593-1599. [PMID: 33443306 DOI: 10.1002/cmdc.202000960] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Indexed: 01/03/2023]
Abstract
Advances in genomics and proteomics have unveiled an ever-growing number of key proteins and provided mechanistic insights into the genesis of pathologies. This wealth of data showed that changes in expression levels of specific proteins, mutations, and post-translational modifications can result in (often subtle) perturbations of functional protein-protein interaction networks, which ultimately determine disease phenotypes. Although many such validated pathogenic proteins have emerged as ideal drug targets, there are also several that escape traditional pharmacological regulation; these proteins have thus been labeled "undruggable". The challenges posed by undruggable targets call for new sorts of molecular intervention. One fascinating solution is to perturb a pathogenic protein's expression levels, rather than blocking its activities. In this Concept paper, we shall discuss chemical interventions aimed at recruiting undruggable proteins to the ubiquitin proteasome system, or aimed at disrupting protein-protein interactions in the chaperone-mediated cellular folding machinery: both kinds of intervention lead to a decrease in the amount of active pathogenic protein expressed. Specifically, we shall discuss the role of computational strategies in understanding the molecular determinants characterizing the function of synthetic molecules typically designed for either type of intervention. Finally, we shall provide our perspectives and views on the current limitations and possibilities to expand the scope of rational approaches to the design of chemical regulators of protein levels.
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Affiliation(s)
- Stefano A Serapian
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100, Pavia, Italy
| | - Alice Triveri
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100, Pavia, Italy
| | - Filippo Marchetti
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100, Pavia, Italy
| | - Matteo Castelli
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100, Pavia, Italy
| | - Giorgio Colombo
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100, Pavia, Italy
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21
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Saha A, Arantes PR, Hsu RV, Narkhede YB, Jinek M, Palermo G. Molecular Dynamics Reveals a DNA-Induced Dynamic Switch Triggering Activation of CRISPR-Cas12a. J Chem Inf Model 2020; 60:6427-6437. [PMID: 33107304 PMCID: PMC7605327 DOI: 10.1021/acs.jcim.0c00929] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Indexed: 02/06/2023]
Abstract
CRISPR-Cas12a is a genome-editing system, recently also harnessed for nucleic acid detection, which is promising for the diagnosis of the SARS-CoV-2 coronavirus through the DETECTR technology. Here, a collective ensemble of multimicrosecond molecular dynamics characterizes the key dynamic determinants allowing nucleic acid processing in CRISPR-Cas12a. We show that DNA binding induces a switch in the conformational dynamics of Cas12a, which results in the activation of the peripheral REC2 and Nuc domains to enable cleavage of nucleic acids. The simulations reveal that large-amplitude motions of the Nuc domain could favor the conformational activation of the system toward DNA cleavages. In this process, the REC lobe plays a critical role. Accordingly, the joint dynamics of REC and Nuc shows the tendency to prime the conformational transition of the DNA target strand toward the catalytic site. Most notably, the highly coupled dynamics of the REC2 region and Nuc domain suggests that REC2 could act as a regulator of the Nuc function, similar to what was observed previously for the HNH domain in the CRISPR-associated nuclease Cas9. These mutual domain dynamics could be critical for the nonspecific binding of DNA and thereby for the underlying mechanistic functioning of the DETECTR technology. Considering that REC is a key determinant in the system's specificity, our findings provide a rational basis for future biophysical studies aimed at characterizing its function in CRISPR-Cas12a. Overall, our outcomes advance our mechanistic understanding of CRISPR-Cas12a and provide grounds for novel engineering efforts to improve genome editing and viral detection.
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Affiliation(s)
- Aakash Saha
- Department
of Bioengineering, University of California,
Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Pablo R. Arantes
- Department
of Bioengineering, University of California,
Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Rohaine V. Hsu
- Department
of Bioengineering, University of California,
Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Yogesh B. Narkhede
- Department
of Bioengineering, University of California,
Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Martin Jinek
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Giulia Palermo
- Department
of Bioengineering, University of California,
Riverside, 900 University Avenue, Riverside, California 92521, United States
- Department
of Chemistry, University of California,
Riverside, 900 University Avenue, Riverside, California 92521, United States
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22
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Barros EP, Demir Ö, Soto J, Cocco MJ, Amaro RE. Markov state models and NMR uncover an overlooked allosteric loop in p53. Chem Sci 2020; 12:1891-1900. [PMID: 34163952 PMCID: PMC8179107 DOI: 10.1039/d0sc05053a] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The tumor suppressor p53 is the most frequently mutated gene in human cancer, and thus reactivation of mutated p53 is a promising avenue for cancer therapy. Analysis of wildtype p53 and the Y220C cancer mutant long-timescale molecular dynamics simulations with Markov state models and validation by NMR relaxation studies has uncovered the involvement of loop L6 in the slowest motions of the protein. Due to its distant location from the DNA-binding surface, the conformational dynamics of this loop has so far remained largely unexplored. We observe mutation-induced stabilization of alternate L6 conformations, distinct from all experimentally-determined structures, in which the loop is both extended and located further away from the DNA-interacting surface. Additionally, the effect of the L6-adjacent Y220C mutation on the conformational landscape of the functionally-important loop L1 suggests an allosteric role to this dynamic loop and the inactivation mechanism of the mutation. Finally, the simulations reveal a novel Y220C cryptic pocket that can be targeted for p53 rescue efforts. Our approach exemplifies the power of the MSM methodology for uncovering intrinsic dynamic and kinetic differences among distinct protein ensembles, such as for the investigation of mutation effects on protein function. Wildtype and Y220C L1 and L6 loops conformational landscape, with MSM-identified L6 states highlighted on the right.![]()
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Affiliation(s)
- Emilia P Barros
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093 USA +1-858-534-9645 +1-858-534-9629
| | - Özlem Demir
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093 USA +1-858-534-9645 +1-858-534-9629
| | - Jenaro Soto
- Department of Pharmaceutical Sciences, University of California Irvine Irvine CA 92697 USA
| | - Melanie J Cocco
- Department of Pharmaceutical Sciences, University of California Irvine Irvine CA 92697 USA.,Department of Molecular Biology and Biochemistry, University of California Irvine Irvine 92697 CA USA
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093 USA +1-858-534-9645 +1-858-534-9629
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23
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Meli M, Morra G, Colombo G. Simple Model of Protein Energetics To Identify Ab Initio Folding Transitions from All-Atom MD Simulations of Proteins. J Chem Theory Comput 2020; 16:5960-5971. [PMID: 32693598 PMCID: PMC8009504 DOI: 10.1021/acs.jctc.0c00524] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
A fundamental
requirement to predict the native conformation, address
questions of sequence design and optimization, and gain insights into
the folding mechanisms of proteins lies in the definition of an unbiased
reaction coordinate that reports on the folding state without the
need to compare it to reference values, which might be unavailable
for new (designed) sequences. Here, we introduce such a reaction coordinate,
which does not depend on previous structural knowledge of the native
state but relies solely on the energy partition within the protein:
the spectral gap of the pair nonbonded energy matrix (ENergy Gap,
ENG). This quantity can be simply calculated along unbiased MD trajectories.
We show that upon folding the gap increases significantly, while its
fluctuations are reduced to a minimum. This is consistently observed
for a diverse set of systems and trajectories. Our approach allows
one to promptly identify residues that belong to the folding core
as well as residues involved in non-native contacts that need to be
disrupted to guide polypeptides to the folded state. The energy gap
and fluctuations criteria are then used to develop an automatic detection
system which allows us to extract and analyze folding transitions
from a generic MD trajectory. We speculate that our method can be
used to detect conformational ensembles in dynamic and intrinsically
disordered proteins, revealing potential preorganization for binding.
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Affiliation(s)
| | - Giulia Morra
- SCITEC-CNR, Via Mario Bianco 9, Milano 20131, Italy.,Weill-Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Giorgio Colombo
- SCITEC-CNR, Via Mario Bianco 9, Milano 20131, Italy.,University of Pavia, Department of Chemistry, Viale Taramelli 12, Pavia 27100, Italy
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24
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Li Y, Zhang XL, Yuan X, Hou JC, Sang P, Yang LQ. Probing intrinsic dynamics and conformational transition of HIV gp120 by molecular dynamics simulation. RSC Adv 2020; 10:30499-30507. [PMID: 35516019 PMCID: PMC9056330 DOI: 10.1039/d0ra06416e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/07/2020] [Accepted: 08/04/2020] [Indexed: 11/21/2022] Open
Abstract
The HIV envelope glycoprotein gp120 has evolved two distinct conformational states to balance viral infection and immune escape. One is a closed state resistant to most neutralization antibodies, and the other is an open state responsible for the binding of the receptor and coreceptors. Although the structures of gp120 in these two conformational states have been determined, a detailed molecular mechanism involving intrinsic dynamics and conformational transition is still elusive. In this study, μs-scale molecular dynamics simulation is performed to probe molecular dynamics and conformational transition away from the open state and approach the closed state. Our results reveal that open gp120 shows a larger structural deviation, higher conformational flexibility, and more conformational diversity than the form in the closed state, providing a structural explanation for receptor or coreceptor affinity at the open state and the neutralization resistance of closed conformation. Seven regions with greatly decreased coupled motions in the open states have been observed by dynamic cross-correlation analysis, indicating that conformational transition can be mainly attributed to the relaxation of intrinsic dynamics. Three conformations characterized by the structural orientations of the V1/V2 region and the V3 loop, suggesting gp120 is intrinsically dynamic from the open state to the closed state. Taken together, these findings shed light on the understanding of the conformational control mechanism of HIV. The HIV envelope glycoprotein gp120 has evolved two distinct conformational states to balance viral infection and immune escape.![]()
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Affiliation(s)
- Yi Li
- College of Mathematics and Computer Science
- Dali University
- Dali
- China
- Science and Education Department
| | - Xiao-Ling Zhang
- College of Mathematics and Computer Science
- Dali University
- Dali
- China
| | - Xue Yuan
- College of Mathematics and Computer Science
- Dali University
- Dali
- China
| | - Jiang-Chun Hou
- Science and Education Department
- Second People's Hospital of Yunnan Province
- Kunming
- China
| | - Peng Sang
- College of Agriculture and Biological Science
- Dali University
- Dali
- China
| | - Li-Quan Yang
- College of Agriculture and Biological Science
- Dali University
- Dali
- China
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25
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Santos de Oliveira FL, Vieira Carletti J, Azevedo FFN, Freitas de Sousa FJ, Caetano EWS, Freire VN, Zanatta G. mTOR–mLST8 interaction: hot spot identification through quantum biochemistry calculations. NEW J CHEM 2020. [DOI: 10.1039/d0nj04099a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Quantum calculation of mTOR–mLST8 interaction.
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Affiliation(s)
| | | | | | | | | | | | - Geancarlo Zanatta
- Department of Physics at Federal University of Ceará
- 60455-760 Fortaleza
- Brazil
- Postgraduate Research Program in Biochemistry at Federal University of Ceará
- Fortaleza
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