1
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Alici H, Uversky VN, Kang DE, Woo JA, Coskuner-Weber O. The impacts of the mitochondrial myopathy-associated G58R mutation on the dynamic structural properties of CHCHD10. J Biomol Struct Dyn 2024; 42:5607-5616. [PMID: 37349880 DOI: 10.1080/07391102.2023.2227713] [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: 12/16/2022] [Accepted: 06/14/2023] [Indexed: 06/24/2023]
Abstract
The mitochondria are responsible for producing energy within the cell, and in mitochondrial myopathy, there is a defect in the energy production process. The CHCHD10 gene codes for a protein called coiled-coil-helix-coiled-coil-helix domain-containing protein 10 (CHCHD10), which is found in the mitochondria and is involved in the regulation of mitochondrial function. G58R mutation has been shown to disrupt the normal function of CHCHD10, leading to mitochondrial dysfunction and ultimately to the development of mitochondrial myopathy. The structures of G58R mutant CHCHD10 and how G58R mutation impacts the wild-type CHCHD10 protein at the monomeric level are unknown. To address this problem, we conducted homology modeling, multiple run molecular dynamics simulations and bioinformatics calculations. We represent herein the structural ensemble properties of the G58R mutant CHCHD10 (CHCHD10G58R) in aqueous solution. Moreover, we describe the impacts of G58R mutation on the structural ensembles of wild-type CHCHD10 (CHCHD10WT) in aqueous solution. The dynamics properties as well as structural properties of CHCHD10WT are impacted by the mitochondrial myopathy-related G58R mutation. Specifically, the secondary and tertiary structure properties, root mean square fluctuations, Ramachandran diagrams and results from principal component analysis demonstrate that the CHCHD10WT and CHCHD10G58R proteins possess different structural ensemble characteristics and describe the impacts of G58R mutation on CHCHD10WT. These findings may be helpful for designing new treatments for mitochondrial myopathy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hakan Alici
- Faculty of Sciences, Department of Physics, Zonguldak Bulent Ecevit University, Zonguldak, Turkey
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - David E Kang
- School of Medicine, Department of Pathology, Case Western Reserve University, Cleveland, USA
- Louis Stokes Cleveland VA Medical Center, Cleveland, USA
| | - Junga Alexa Woo
- School of Medicine, Department of Pathology, Case Western Reserve University, Cleveland, USA
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2
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Bakker M, Sørensen HV, Skepö M. Exploring the Role of Globular Domain Locations on an Intrinsically Disordered Region of p53: A Molecular Dynamics Investigation. J Chem Theory Comput 2024; 20:1423-1433. [PMID: 38230670 PMCID: PMC10867847 DOI: 10.1021/acs.jctc.3c00971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/18/2024]
Abstract
The pre-tetramerization loop (PTL) of the human tumor suppressor protein p53 is an intrinsically disordered region (IDR) necessary for the tetramerization process, and its flexibility contributes to the essential conformational changes needed. Although the IDR can be accurately simulated in the traditional manner of molecular dynamics (MD) with the end-to-end distance (EEdist) unhindered, we sought to explore the effects of restraining the EEdist to the values predicted by electron microscopy (EM) and other distances. Simulating the PTL trajectory with a restrained EEdist , we found an increased agreement of nuclear magnetic resonance (NMR) chemical shifts with experiments. Additionally, we observed a plethora of secondary structures and contacts that only appear when the trajectory is restrained. Our findings expand the understanding of the tetramerization of p53 and provide insight into how mutations could make the protein impotent. In particular, our findings demonstrate the importance of restraining the EEdist in studying IDRs and how their conformations change under different conditions. Our results provide a better understanding of the PTL and the conformational dynamics of IDRs in general, which are useful for further studies regarding mutations and their effects on the activity of p53.
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Affiliation(s)
- Michael
J. Bakker
- Faculty
of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
- Division
of Computational Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Henrik V. Sørensen
- Division
of Computational Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
- MAX
IV Laboratory, Lund Institute of Advanced
Neutron and X-ray Science, Scheelevägen 19, SE-223 770 Lund, Sweden
| | - Marie Skepö
- Division
of Computational Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
- LINXS
- Institute of Advanced Neutron and X-ray Science, Scheelevägen 19, SE-233 70 Lund, Sweden
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3
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Pan Z, Mu J, Chen HF. Balanced Three-Point Water Model OPC3-B for Intrinsically Disordered and Ordered Proteins. J Chem Theory Comput 2023; 19:4837-4850. [PMID: 37452752 DOI: 10.1021/acs.jctc.3c00297] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Intrinsically disordered proteins (IDPs) play a critical role in many biological processes. Due to the inherent structural flexibility of IDPs, experimental methods present significant challenges for sampling their conformational information at the atomic level. Therefore, molecular dynamics (MD) simulations have emerged as the primary tools for modeling IDPs whose accuracy depend on force field and water model. To enhance the accuracy of physical modeling of IDPs, several force fields have been developed. However, current water models lack precision and underestimate the interaction between water molecules and proteins. Here, we used Monte-Carlo re-weighting method to re-parameterize a three-point water model based on OPC3 for IDPs (named OPC3-B). We benchmarked the performance of OPC3-B compared with nine different water models for 10 IDPs and three ordered proteins. The results indicate that the performance of OPC3-B is better than other water models for both IDPs and ordered proteins. At the same time, OPC3-B possess the power of transferability with other force field to simulate IDPs. This newly developed water model can be used to insight into the research of sequence-disordered-function paradigm for IDPs.
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Affiliation(s)
- Zhengsong Pan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- 4+4 Medical Doctor Program, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Junxi Mu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Center for Bioinformation Technology, Shanghai 200235, China
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4
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Das D, Mattaparthi VSK. Conformational dynamics of A30G α-synuclein that causes familial Parkinson disease. J Biomol Struct Dyn 2023; 41:14702-14714. [PMID: 36961209 DOI: 10.1080/07391102.2023.2193997] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 02/25/2023] [Indexed: 03/25/2023]
Abstract
The first gene shown to be responsible for autosomal-dominant Parkinson's disease (PD) is the SNCA gene, which encodes for alpha synuclein (α-Syn). Recently, a novel heterozygous A30G mutation of the SNCA gene associated with familial PD has been reported. However, little research has been done on how the A30G mutation affects the structure of α-Syn. So, using atomistic molecular dynamics (MD) simulation, we demonstrate here the key structural characteristics of A30G α-Syn in the free monomer form and membrane associated state. From the MD trajectory analysis, the structure of A30G α-Syn was noticed to exhibit rapid conformational change, increase in backbone flexibility near the site of mutation and decrease in α-helical propensity. The typical torsion angles in residues (Val26 and Glu28) near the mutation site were observed to deviate significantly in A30G α-Syn. In the case of membrane bound A30G α-Syn, the regions that were submerged in the lipid bilayer (N-helix (3-37) and turn region (38-44)) found to contain higher helical content than the elevated region above the lipid surface. The bending angle in the helix-N and helix-C regions were noticed to be relatively higher in the free form of A30G α-Syn (38.50) than in the membrane bound form (370). The A30G mutation in α-Syn was predicted to have an impact on the stability and function of the protein based on ΔΔG values obtained from the online servers. Our results demonstrate that the A30G mutation in α-Syn altered the protein's α-helical structure and slightly altered the membrane binding.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dorothy Das
- Molecular Modelling and Simulation Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
| | - Venkata Satish Kumar Mattaparthi
- Molecular Modelling and Simulation Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
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5
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Man VH, He X, Gao J, Wang J. Phosphorylation of Tau R2 Repeat Destabilizes Its Binding to Microtubules: A Molecular Dynamics Simulation Study. ACS Chem Neurosci 2023; 14:458-467. [PMID: 36669127 PMCID: PMC10032563 DOI: 10.1021/acschemneuro.2c00611] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 01/05/2023] [Indexed: 01/22/2023] Open
Abstract
Phosphorylation, the most popular post-translational modification of tau protein, plays an important role in regulating tau physiological functions. However, aberrant phosphorylation attenuates the binding affinity of tau to a microtubule (MT), resulting in MT destabilization followed by accumulation of neurofibrillary tangles in the brain. There are in total 85 potential phosphorylation sites in a full-length tau protein, and about half of them are abnormal as they occur in tau of Alzheimer's disease (AD) brain only. In this work, we investigated the impact of abnormal Ser289, Ser293, and Ser289/Ser293 phosphorylation on tau R2-MT binding and the conformation of tau R2 using molecular dynamics simulation. We found that the phosphorylation significantly affected R2-MT interaction and reduced the binding affinity of tau R2 peptides to MTs. Free energy decomposition analysis suggested that the post-translational modified residues themselves made a significant contribution to destabilize tau repeat R2-MT binding. Therefore, the phosphorylation may attenuate the binding affinity of tau to MTs. Additionally, the phosphorylation also enhanced helix-coil transition of monomeric R2 peptides, which may result in the acceleration of tau aggregation. Since these phosphorylated sites have not been examined in previous experimental studies, our finding through all-atom molecular dynamics simulations and free energy analysis can inspire experimental scientists to investigate the impact of the phosphorylation on MT binding and aggregation of full-length tau and the pathological roles of the phosphorylation at those sites in AD development through in vitro/in vivo assays.
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Affiliation(s)
- Viet Hoang Man
- Department
of Pharmaceutical Sciences and Computational Chemical Genomics Screening
Center, School of Pharmacy, University of
Pittsburgh, Pittsburgh, Pennsylvania15261, United States
| | - Xibing He
- Department
of Pharmaceutical Sciences and Computational Chemical Genomics Screening
Center, School of Pharmacy, University of
Pittsburgh, Pittsburgh, Pennsylvania15261, United States
| | - Jie Gao
- Department
of Neuroscience, The Ohio State University
Wexner Medical Center, Columbus, Ohio43210, United States
| | - Junmei Wang
- Department
of Pharmaceutical Sciences and Computational Chemical Genomics Screening
Center, School of Pharmacy, University of
Pittsburgh, Pittsburgh, Pennsylvania15261, United States
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6
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Alici H, Uversky VN, Kang DE, Woo JA, Coskuner-Weber O. Effects of the Jokela type of spinal muscular atrophy-related G66V mutation on the structural ensemble characteristics of CHCHD10. Proteins 2023; 91:739-749. [PMID: 36625206 DOI: 10.1002/prot.26463] [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: 07/01/2022] [Revised: 12/05/2022] [Accepted: 01/03/2023] [Indexed: 01/11/2023]
Abstract
The G66V pathological variant of the coiled-coil-helix-coiled-coil-helix domain-containing protein 10 (CHCHD10), mitochondrial, plays a role in Jokela type spinal muscular atrophy. The wild-type and G66V mutant-type CHCHD10 proteins contain intrinsically disordered regions, and therefore, their structural ensemble studies have been experiencing difficulties using conventional tools. Here, we show our results regarding the first characterization of the structural ensemble characteristics of the G66V mutant form of CHCHD10 and the first comparison of these characteristics with the structural ensemble properties of wild-type CHCHD10. We find that the structural properties, potential of mean force surfaces, and principal component analysis show stark differences between these two proteins. These results are important for a better pathology, biochemistry and structural biology understanding of CHCHD10 and its G66V genetic variant and it is likely that these reported structural properties are important for designing more efficient treatments for the Jokela type of spinal muscular atrophy disease.
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Affiliation(s)
- Hakan Alici
- Department of Physics, Faculty of Arts and Sciences, Zonguldak Bulent Ecevit University, Zonguldak, Turkey
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - David E Kang
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.,Louis Stokes Cleveland VA Medical Center, Cleveland, Ohio, USA
| | - Junga Alexa Woo
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
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7
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Ji X, Liu H, Zhang Y, Chen J, Chen HF. Personal Precise Force Field for Intrinsically Disordered and Ordered Proteins Based on Deep Learning. J Chem Inf Model 2023; 63:362-374. [PMID: 36533639 DOI: 10.1021/acs.jcim.2c01501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Intrinsically disordered proteins (IDPs) are proteins without a fixed three-dimensional (3D) structure under physiological conditions and are associated with Parkinson's disease, Alzheimer's disease, cancer, cardiovascular disease, amyloidosis, diabetes, and other diseases. Experimental methods can hardly capture the ensemble of diverse conformations for IDPs. Molecular dynamics (MD) simulations can sample continuous conformations that might provide a valuable complement to experimental data. However, the accuracy of MD simulations depends on the quality of force field. In particular, the evolutionary conservation and coevolution of IDPs introduce that current force fields could not precisely reproduce the conformation of IDPs. In order to improve the performance of force field, deep learning and reweighting methods were used to automatically generate personal force field parameters for intrinsically disordered and ordered proteins. At first, the deep learning method predicted more accuracy φ/ψ dihedral of residue than the previous method. Then, reweighting optimized the personal force field parameters for each residue. Finally, typical representative systems such as IDPs, structure protein, and fast-folding protein were used to evaluate this force field. The results indicate that two personal force field parameters (named PPFF1 and PPFF1_af2) could better reproduce the experimental observables than ff03CMAP force field. In summary, this strategy will provide feasibility for the development of precise personal force fields.
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Affiliation(s)
- Xiaoyue Ji
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai200240, China
| | - Hao Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai200240, China
| | - Yangpeng Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai200240, China
| | - Jun Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai200240, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai200240, China.,Shanghai Center for Bioinformation Technology, Shanghai200235, China
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8
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Jheng CP, Lee CI. Combination of structure-based virtual screening, molecular docking and molecular dynamics approaches for the discovery of anti-prion fibril flavonoids. Front Mol Biosci 2023; 9:1088733. [PMID: 36685276 PMCID: PMC9849400 DOI: 10.3389/fmolb.2022.1088733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/16/2022] [Indexed: 01/06/2023] Open
Abstract
Prion diseases are a group of rare neurodegenerative diseases caused by the structural conversion of cellular prion into Scrapie prion resulting aggregated fibrils. Therapy of prion diseases has been developed for several decades, especially drug designs based on the structure of prion monomers. Unfortunately, none of the designed anti-prion drugs function well clinically. To fight against prion fibrils, a drug design based on the precise structure of mammalian prion fibrils is highly required. Fortunately, based on the advantage of newly advanced cryo-electron microscopy (cryo-EM) in the deconvolution of large complexes, three prion fibril structures were resolved in the last 2 years. Based on the cryo-EM solved prion fibril structures, we are able to find some molecules fighting against prion fibrils. Quercetin, one flavonoid molecule in the polyphenol group, has been found to disaggregate the prion fibrils in vitro. In this study, we performed the molecular docking and molecular dynamics simulation on quercetin-like molecules possessing pharmacological properties to evaluate the anti-prion ability of tested molecules. As a result, four quercetin-like molecules interact with prion fibril and decrease the β-strand content by converting some β-strands into loop and helical structures to disintegrate the existing fibril structure. The results of this study are significant in the treatment of prion diseases, and the approaches used in this study are applicable to other amyloid diseases.
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Affiliation(s)
- Cheng-Ping Jheng
- Department of Biomedical Sciences, National Chung Cheng University, Chia-Yi, Taiwan
| | - Cheng-I Lee
- Department of Biomedical Sciences, National Chung Cheng University, Chia-Yi, Taiwan,Center for Nano Bio-Detections, National Chung Cheng University, Chia-Yi, Taiwan,Center for Innovative Research on Aging Society (CIRAS), National Chung Cheng University, Chia-Yi, Taiwan,*Correspondence: Cheng-I Lee,
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9
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Intrinsically Disordered Proteins: An Overview. Int J Mol Sci 2022; 23:ijms232214050. [PMID: 36430530 PMCID: PMC9693201 DOI: 10.3390/ijms232214050] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Many proteins and protein segments cannot attain a single stable three-dimensional structure under physiological conditions; instead, they adopt multiple interconverting conformational states. Such intrinsically disordered proteins or protein segments are highly abundant across proteomes, and are involved in various effector functions. This review focuses on different aspects of disordered proteins and disordered protein regions, which form the basis of the so-called "Disorder-function paradigm" of proteins. Additionally, various experimental approaches and computational tools used for characterizing disordered regions in proteins are discussed. Finally, the role of disordered proteins in diseases and their utility as potential drug targets are explored.
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10
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Intrinsically disordered proteins and proteins with intrinsically disordered regions in neurodegenerative diseases. Biophys Rev 2022; 14:679-707. [DOI: 10.1007/s12551-022-00968-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 05/28/2022] [Indexed: 12/14/2022] Open
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11
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Alici H, Uversky VN, Kang DE, Woo JA, Coskuner-Weber O. Structures of the Wild-Type and S59L Mutant CHCHD10 Proteins Important in Amyotrophic Lateral Sclerosis-Frontotemporal Dementia. ACS Chem Neurosci 2022; 13:1273-1280. [PMID: 35349255 DOI: 10.1021/acschemneuro.2c00011] [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: 12/14/2022] Open
Abstract
The S59L genetic mutation of the mitochondrial coiled-coil-helix-coiled-coil-helix domain-containing protein 10 (CHCHD10) is involved in the pathogenesis of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The wild-type and mutant forms of this protein contain intrinsically disordered regions, and their structural characterization has been facing challenges. Here, for the first time in the literature, we present the structural ensemble properties of the wild-type and S59L mutant form of CHCHD10 in an aqueous solution environment at the atomic level with dynamics. Even though available experiments suggested that the S59L mutation may not change the structure of the CHCHD10 protein, our structural analysis clearly shows that the structure of this protein is significantly affected by the S59L mutation. We present here the secondary structure components with their abundances per residue, the tertiary structure properties, the free energy surfaces based on the radius of gyration and end-to-end distance values, the Ramachandran plots, the quantity of intramolecular hydrogen bonds, and the principal component analysis results. These results may be crucial in designing more efficient treatment for ALS and FTD diseases.
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Affiliation(s)
- Hakan Alici
- Faculty of Arts and Sciences, Department of Physics, Zonguldak Bulent Ecevit University, Zonguldak 67100, Turkey
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - David E. Kang
- School of Medicine, Department of Pathology, Case Western Reserve University, 2103 Cornell Road, 5129 WRB, Cleveland, Ohio 44106, United States
- Louis Stokes Cleveland VA Medical Center, 10701 East Blvd, Cleveland, Ohio 44106, United States
| | - Junga Alexa Woo
- School of Medicine, Department of Pathology, Case Western Reserve University, 2103 Cornell Road, 5129 WRB, Cleveland, Ohio 44106, United States
| | - Orkid Coskuner-Weber
- Molecular Biotechnology, Turkish-German University, Sahinkaya Caddesi, No. 106, Beykoz, Istanbul 34820, Turkey
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12
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Uversky VN. Protein folding, misfolding, and un/non-folding: overview of the SP16 Session at the 20 th IUPAB congress, 45 th Annual Meeting of SBBf, and 50 th Annual Meeting of SBBq. Biophys Rev 2022; 13:879-882. [PMID: 35059012 DOI: 10.1007/s12551-021-00885-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 11/01/2021] [Indexed: 12/16/2022] Open
Abstract
The classical and idealistic consideration of the protein universe as a set of well-ordered proteinaceous machines with unique spatial organizations conducting unique biological functions is changed because of the recognition that proteins can fold, misfold, or be disordered to different degree. Functional repertoires of intrinsically disordered proteins complement functions of ordered proteins, whereas protein misfolding and concomitant oligomerization, aggregation, and fibrillation are related to the pathogenesis of numerous human diseases. Flexible proteins can undergo liquid-liquid phase separation, which is at the heart of the biogenesis of numerous membrane-less organelles. Many of these aspects were highlighted in four talks delivered at the SP16 Session at the 20th IUPAB congress, 45th Annual Meeting of SBBf, and 50th Annual Meeting of SBBq.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd, Tampa, FL MDC07 USA
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13
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Boopathi S, Poma AB, Garduño-Juárez R. An Overview of Several Inhibitors for Alzheimer's Disease: Characterization and Failure. Int J Mol Sci 2021; 22:10798. [PMID: 34639140 PMCID: PMC8509255 DOI: 10.3390/ijms221910798] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 10/01/2021] [Accepted: 10/03/2021] [Indexed: 01/04/2023] Open
Abstract
Amyloid beta (Aβ) oligomers are the most neurotoxic aggregates causing neuronal death and cognitive damage. A detailed elucidation of the aggregation pathways from oligomers to fibril formation is crucial to develop therapeutic strategies for Alzheimer's disease (AD). Although experimental techniques rely on the measure of time- and space-average properties, they face severe difficulties in the investigation of Aβ peptide aggregation due to their intrinsically disorder character. Computer simulation is a tool that allows tracing the molecular motion of molecules; hence it complements Aβ experiments, as it allows to explore the binding mechanism between metal ions and Aβ oligomers close to the cellular membrane at the atomic resolution. In this context, integrated studies of experiments and computer simulations can assist in mapping the complete pathways of aggregation and toxicity of Aβ peptides. Aβ oligomers are disordered proteins, and due to a rapid exploration of their intrinsic conformational space in real-time, they are challenging therapeutic targets. Therefore, no good drug candidate could have been identified for clinical use. Our previous investigations identified two small molecules, M30 (2-Octahydroisoquinolin-2(1H)-ylethanamine) and Gabapentin, capable of Aβ binding and inhibiting molecular aggregation, synaptotoxicity, intracellular calcium signaling, cellular toxicity and memory losses induced by Aβ. Thus, we recommend these molecules as novel candidates to assist anti-AD drug discovery in the near future. This review discusses the most recent research investigations about the Aβ dynamics in water, close contact with cell membranes, and several therapeutic strategies to remove plaque formation.
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Affiliation(s)
- Subramanian Boopathi
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico;
| | - Adolfo B. Poma
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research Polish Academy of Science, Pawińskiego 5B, 02-106 Warsaw, Poland
- International Center for Research on Innovative Biobased Materials (ICRI-BioM)—International Research Agenda, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland;
| | - Ramón Garduño-Juárez
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico;
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14
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Balli OI, Uversky VN, Durdagi S, Coskuner-Weber O. Challenges and limitations in the studies of glycoproteins: A computational chemist's perspective. Proteins 2021; 90:322-339. [PMID: 34549826 DOI: 10.1002/prot.26242] [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: 06/23/2021] [Revised: 08/24/2021] [Accepted: 09/07/2021] [Indexed: 11/08/2022]
Abstract
Experimenters face challenges and limitations while analyzing glycoproteins due to their high flexibility, stereochemistry, anisotropic effects, and hydration phenomena. Computational studies complement experiments and have been used in characterization of the structural properties of glycoproteins. However, recent investigations revealed that computational studies face significant challenges as well. Here, we introduce and discuss some of these challenges and weaknesses in the investigations of glycoproteins. We also present requirements of future developments in computational biochemistry and computational biology areas that could be necessary for providing more accurate structural property analyses of glycoproteins using computational tools. Further theoretical strategies that need to be and can be developed are discussed herein.
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Affiliation(s)
- Oyku Irem Balli
- Molecular Biotechnology, Turkish-German University, Istanbul, Turkey
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
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15
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Caliskan M, Mandaci SY, Uversky VN, Coskuner-Weber O. Secondary structure dependence of amyloid-β(1-40) on simulation techniques and force field parameters. Chem Biol Drug Des 2021; 97:1100-1108. [PMID: 33580600 DOI: 10.1111/cbdd.13830] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/21/2021] [Accepted: 02/07/2021] [Indexed: 12/21/2022]
Abstract
Our recent studies revealed that none of the selected widely used force field parameters and molecular dynamics simulation techniques yield structural properties for the intrinsically disordered α-synuclein that are in agreement with various experiments via testing different force field parameters. Here, we extend our studies on the secondary structure properties of the disordered amyloid-β(1-40) peptide in aqueous solution. For these purposes, we conducted extensive replica exchange molecular dynamics simulations and obtained extensive molecular dynamics simulation trajectories from David E. Shaw group. Specifically, these molecular dynamics simulations were conducted using various force field parameters and obtained results are compared to our replica exchange molecular dynamics simulations and experiments. In this study, we calculated the secondary structure abundances and radius of gyration values for amyloid-β(1-40) that were simulated using varying force field parameter sets and different simulation techniques. In addition, the intrinsic disorder propensity, as well as sequence-based secondary structure predisposition of amyloid-β(1-40) and compared the findings with the results obtained from molecular simulations using various force field parameters and different simulation techniques. Our studies clearly show that the epitope region identification of amyloid-β(1-40) depends on the chosen simulation technique and chosen force field parameters. Based on comparison with experiments, we find that best computational results in agreement with experiments are obtained using the a99sb*-ildn, charmm36m, and a99sb-disp parameters for the amyloid-β(1-40) peptide in molecular dynamics simulations without parallel tempering or via replica exchange molecular dynamics simulations.
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Affiliation(s)
- Murat Caliskan
- Molecular Biotechnology, Turkish-German University, Istanbul, Turkey
| | - Sunay Y Mandaci
- Molecular Biotechnology, Turkish-German University, Istanbul, Turkey
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.,Laboratory of New Methods in Biology, Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Russia
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16
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Fatafta H, Samantray S, Sayyed-Ahmad A, Coskuner-Weber O, Strodel B. Molecular simulations of IDPs: From ensemble generation to IDP interactions leading to disorder-to-order transitions. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 183:135-185. [PMID: 34656328 DOI: 10.1016/bs.pmbts.2021.06.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
Intrinsically disordered proteins (IDPs) lack a well-defined three-dimensional structure but do exhibit some dynamical and structural ordering. The structural plasticity of IDPs indicates that entropy-driven motions are crucial for their function. Many IDPs undergo function-related disorder-to-order transitions upon by their interaction with specific binding partners. Approaches that are based on both experimental and theoretical tools enable the biophysical characterization of IDPs. Molecular simulations provide insights into IDP structural ensembles and disorder-to-order transition mechanisms. However, such studies depend strongly on the chosen force field parameters and simulation techniques. In this chapter, we provide an overview of IDP characteristics, review all-atom force fields recently developed for IDPs, and present molecular dynamics-based simulation methods that allow IDP ensemble generation as well as the characterization of disorder-to-order transitions. In particular, we introduce metadynamics, replica exchange molecular dynamics simulations, and also kinetic models resulting from Markov State modeling, and provide various examples for the successful application of these simulation methods to IDPs.
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Affiliation(s)
- Hebah Fatafta
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Suman Samantray
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany; AICES Graduate School, RWTH Aachen University, Aachen, Germany
| | | | - Orkid Coskuner-Weber
- Molecular Biotechnology, Turkish-German University, Sahinkaya Caddesi, Istanbul, Turkey
| | - Birgit Strodel
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany; Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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