Alpha-synuclein’ in PreNAC(46-56) Fibril Bölütünün Moleküler Dinamik Simülasyon Yöntemi ile Konformasyonel Değerlendirmesi

Hakan Alıcı

doi:10.18016/ksutarimdoga.vi.737200

Araştırma Makalesi

Alpha-synuclein’ in PreNAC(46-56) Fibril Bölütünün Moleküler Dinamik Simülasyon Yöntemi ile Konformasyonel Değerlendirmesi

Yıl 2021, Cilt: 24 Sayı: 1, 11 - 21, 28.02.2021

Hakan Alıcı

https://doi.org/10.18016/ksutarimdoga.vi.737200

Cited By: 1

Öz

Bu araştırmada, Parkinson hastalığı ile ilişkilendirilen apha-synuclein (AS)’ in PreNAC(46-56) fibril bölütü Moleküler Dinamik Simülasyon yöntemi kullanılarak incelenmiştir. Çalışmadaki, ilk amaç PreNAC üzerine gelecekte yapılması muhtemel çalışmalar için en uygun kuvvet alanının belirlenmesidir. Literatürde biyomoleküllerin simülasyonlarında sıklıkla kullanılan yedi kuvvet alanı üzerinden yapılan değerlendirmede, başta CHARMM27 ve GROMOS53A6 olmak üzere AMBER99SB ve AMBER99SB-ILDN kuvvet alanlarının ileriki çalışmalarda ele alınmasının uygun olacağı tespit edilmiştir. Çalışmanın diğer amacı ise PreNAC arayüz için konformasyonel özelliklerin moleküler seviyede aydınlatılmasıdır. Bu kapsamda gözlemlenen önemli bulgulardan biri His50 amino asidinin en fazla konformasyonel değişim gösteren amino asit olmasıdır. Ayrıca literatürde birden fazla ailesel mutasyon içerdiği tespit edilen 53. konumdaki Thr amino asidinin yüksek konformasyonel kararlılığa sahip olduğu gözlemlenmiştir. Bunlara ilaveten, ele alınan PreNAC arayüz için tabakalar arası elektrostatik etkileşimlerin ara yüzün kararlılığı için başlıca etkileşim tipleri olduğu tespit edilmiştir. Sonuç olarak, elde edilen bulguların AS’ nin PreNAC ve benzeri fibril bölütlerinin gelecek çalışmalarına ışık tutması beklenilmektedir.

Anahtar Kelimeler

PreNAC, Parkinson, Moleküler dinamik, Simülasyon, Kuvvet alanı

Destekleyen Kurum

zonguldak bülent ecevit üniversitesi

Proje Numarası

2015-22794455-03 nolu Altyapı Projesi

Kaynakça

Alιcι H 2020. Structural Analyses and Force Fields Comparison for NACore (68–78) and SubNACore (69–77) Fibril Segments of Parkinson’s Disease. Journal of Molecular Modeling, 26: 132.
Appel‐Cresswell S, Vilarino‐Guell C, Encarnacion M, Sherman H, Yu I, Shah B, Weir D, Thompson C, Szu‐Tu C, Trinh J 2013. Alpha‐Synuclein P. H50q, a Novel Pathogenic Mutation for Parkinson's Disease. Movement Disorders, 28 (6): 811-813.
Berendsen HJ, Postma JP, van Gunsteren WF, Hermans J 1981. Interaction Models for Water in Relation to Protein Hydration. In: Intermolecular Forces, Springer, Dordrecht, pp. 331-342.
Berhanu WM, Hansmann UH 2012. Side‐Chain Hydrophobicity and the Stability of Aβ16–22 Aggregates. Protein Science, 21 (12): 1837-1848.
Berhanu WM, Masunov AE 2012. Unique Example of Amyloid Aggregates Stabilized by Main Chain H-Bond Instead of the Steric Zipper: Molecular Dynamics Study of the Amyloidogenic Segment of Amylin Wild-Type and Mutants. Journal of Molecular Modeling, 18 (3): 891-903.
Best RB, Zhu X, Shim J, Lopes PE, Mittal J, Feig M, MacKerell AD Jr. 2012. Optimization of the Additive Charmm All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, Ψ and Side-Chain Χ1 and Χ2 Dihedral Angles. Journal of Chemical Theory andCcomputation, 8 (9): 3257-3273.
Bussi G, Donadio D, Parrinello M 2007. Canonical Sampling through Velocity Rescaling. The Journal of Chemical Physics, 126 (1): 014101.
Carballo‐Pacheco M, Strodel B 2017. Comparison of Force Fields for Alzheimer's A: A Case Study for Intrinsically Disordered Proteins. Protein Science, 26 (2): 174-185.
Çınar E, Çakmaklı GY, Tel BC, 2019. Parkinson Hastalığında Nöroprotektif Tedaviler. Turkish Journal of Neurology, 25: 189-197.
Darden T, York D, Pedersen L 1993. Particle Mesh Ewald: An N⋅ Log (N) Method for Ewald Sums in Large Systems. The Journal of Chemical Physics, 98 (12): 10089-10092.
De Lau LM, Breteler MMB, 2006. Epidemiology of Parkinson's Disease. The Lancet Neurology, 5 (6): 525-535. DeLano WL 2002. The PyMOL Molecular Graphics System, http://www. pymol. org.
Demir K, Alıcı H, Yaşar F 2018. Conformational Stability of the Tetrameric De Novo Designed Hexcoil-Ala Helical Bundle. Chinese Journal of Physics, 56(1): 46-57.
Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T 2003. A Point‐Charge Force Field for Molecular Mechanics Simulations of Proteins Based on Condensed‐Phase Quantum Mechanical Calculations. Journal of Computational Chemistry, 24 (16): 1999-2012.
Glenner GG, Wong CW 1984. Alzheimer's Disease: Initial Report of the Purification and Characterization of a Novel Cerebrovascular Amyloid Protein. Biochemical and Biophysical Research Communications, 120 (3): 885-890.
Goedert M, Spillantini MG, Del Tredici K, Braak H 2013. 100 Years of Lewy Pathology. Nature Reviews Neurology, 9 (1): 13.
Hess B, Bekker H, Berendsen HJ, Fraaije JG 1997. Lincs: A Linear Constraint Solver for Molecular Simulations. Journal of Computational Chemistry, 18 (12): 1463-1472.
Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C 2006. Comparison of Multiple Amber Force Fields and Development of Improved Protein Backbone Parameters. Proteins: Structure, Function, and Bioinformatics, 65 (3): 712-725.
Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML 1983. Comparison of Simple Potential Functions for Simulating Liquid Water. The Journal of Chemical Physics, 79 (2): 926-935.
Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL 2001. Evaluation and Reparametrization of the Opls-Aa Force Field for Proteins Via Comparison with Accurate Quantum Chemical Calculations on Peptides. The Journal of Physical Chemistry B, 105 (28): 6474-6487.
Kumari R, Kumar R, Consortium OSDD, Lynn A 2014. G_Mmpbsa a Gromacs Tool for High-Throughput Mm-Pbsa Calculations. Journal of Chemical Information and Modeling, 54 (7): 1951-1962.
Lang AE, Lozano AM 1998. Parkinson's Disease. New England Journal of Medicine-Unbound Volume, 339 (16): 1130-1143.
Lesage S, Anheim M, Letournel F, Bousset L, Honoré A, Rozas N, Pieri L, Madiona K, Dürr A, Melki R 2013. G51d Α‐Synuclein Mutation Causes a Novel Parkinsonian–Pyramidal Syndrome. Annals of Neurology, 73 (4): 459-471.
Lindorff‐Larsen K, Piana S, Palmo K, Maragakis P, Klepeis JL, Dror RO, Shaw DE 2010. Improved Side‐Chain Torsion Potentials for the Amber Ff99sb Protein Force Field. Proteins: Structure, Function, and Bioinformatics, 78 (8): 1950-1958.
Lobanov MY, Bogatyreva NS, Galzitskaya OV 2008. Radius of Gyration as an Indicator of Protein Structure Compactness. Molecular Biology, 42 (4): 623-628.
MacKerell Jr AD, Bashford D, Bellott M, Dunbrack Jr RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S 1998. All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins. The Journal of Physical Chemistry B, 102 (18): 3586-3616.
Miyamoto S, Kollman PA 1992. Settle: An Analytical Version of the Shake and Rattle Algorithm for Rigid Water Models. Journal of Computational Chemistry, 13 (8): 952-962.
Oostenbrink C, Villa A, Mark AE, Van Gunsteren WF 2004. A Biomolecular Force Field Based on the Free Enthalpy of Hydration and Solvation: The Gromos Force‐Field Parameter Sets 53a5 and 53a6. Journal of Computational Chemistry, 25 (13): 1656-1676.
Parrinello M, Rahman A 1981. Polymorphic Transitions in Single Crystals: A New Molecular Dynamics Method. Journal of Applied Physics, 52 (12): 7182-7190.
Pasanen P, Myllykangas L, Siitonen M, Raunio A, Kaakkola S, Lyytinen J, Tienari PJ, Pöyhönen M, Paetau A 2014. A Novel Α-Synuclein Mutation A53e Associated with Atypical Multiple System Atrophy and Parkinson's Disease-Type Pathology. Neurobiology of Aging, 35 (9): 2180-e1.
Polymeropoulos MH, Lavedan C, Leroy E, Ide SE, Dehejia A, Dutra A, Pike B, Root H, Rubenstein, J Boyer R 1997. Mutation in the Α-Synuclein Gene Identified in Families with Parkinson's Disease. Sciece, 276 (5321): 2045-2047.
Pronk S, Páll S, Schulz R, Larsson P, Bjelkmar P, Apostolov R, Shirts MR, Smith JC, Kasson PM, van der Spoel D 2013. Gromacs 4.5: A High-Throughput and Highly Parallel Open Source Molecular Simulation Toolkit. Bioinformatics, 29 (7): 845-854.
Rodriguez JA, Ivanova MI, Sawaya MR, Cascio D, Reyes FE, Shi D, Sangwan S, Guenther EL, Johnson LM, Zhang M 2015. Structure of the Toxic Core of Α-Synuclein from Invisible Crystals. Nature, 525 (7570): 486-490.
Schmid N, Eichenberger AP, Choutko A, Riniker S, Winger M, Mark AE, van Gunsteren WF 2011. Definition and Testing of the Gromos Force-Field Versions 54a7 and 54b7. European Biophysics Journal, 40 (7): 843.
Spillantini MG, Schmidt ML, Lee VM-Y, Trojanowski JQ, Jakes R, Goedert M 1997. Α-Synuclein in Lewy Bodies. Nature, 388 (6645): 839-840.
Ulmer TS, Bax A, Cole NB, Nussbaum RL 2005. Structure and Dynamics of Micelle-Bound Human Α-Synuclein. Journal of Biological Chemistry, 280 (10): 9595-9603.
Xi W, Vanderford EK, Hansmann UH, 2018 Out-of-Register Aβ42 Assemblies as Models for Neurotoxic Oligomers and Fibrils. Journal of Chemical Theory and Computation, 14 (2): 1099-1110.
Verlet L 1967. Computer" Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules. Physical Review, 159 (1): 98.
Yoshino H, Hirano M, Stoessl AJ, Imamichi Y, Ikeda A, Li Y, Funayama M, Yamada I, Nakamura, YSossi V 2017. Homozygous Alpha-Synuclein P. A53v in Familial Parkinson's Disease. Neurobiology of Aging, 57: 248-e7.
Yu,H, Yan Y, Zhang C, Dalby PA 2017. Two Strategies to Engineer Flexible Loops for Improved Enzyme Thermostability. Scientific Reports, 7: 41212.
Zheng J, Ma B, Tsai C-J, Nussinov R 2006. Structural Stability and Dynamics of an Amyloid-Forming Peptide Gnnqqny from the Yeast Prion Sup-35. Biophysical Journal, 91 (3): 824-833.

A Conformational Evaluation for PreNAC(46-56) Fibril Segment of Alpha-synuclein using Molecular Dynamic Simulation Method

Yıl 2021, Cilt: 24 Sayı: 1, 11 - 21, 28.02.2021

Hakan Alıcı

https://doi.org/10.18016/ksutarimdoga.vi.737200

Cited By: 1

Öz

In this study, the PreNAC (46-56) fibril segment of Alpha-Synuclein (AS) associated with Parkinson's disease was examined using the molecular dynamic simulation method. The first goal of the study was to determine the most suitable force field for future studies on PreNAC. In this regard, we covered seven force fields that were widely used in biomolecule simulations, and it was determined that it is appropriate to treat the AMBER99SB and AMBER99SB-ILDN force fields, mainly CHARMM27 and GROMOS53A6, for future studies. Another goal of the study was to illuminate the conformational properties of the PreNAC interface at the molecular level. One of the most important discoveries observed in this context was that His50 was the most unstable amino acid. In addition, it was observed that amino acid 53, which is known to contain more than one family mutation, sustained high conformational stability. In addition, inter-sheet electrostatic interactions were the dominant interaction type for the stability of PreNAC interface. As a result, the findings in this study are expected to shed light on future studies of PreNAC of AS and its similar fibril segments.

Anahtar Kelimeler

Force field, Molecular dynamic, Parkinson’s disease, PreNAC, Simulation

Proje Numarası

2015-22794455-03 nolu Altyapı Projesi

Kaynakça

Alιcι H 2020. Structural Analyses and Force Fields Comparison for NACore (68–78) and SubNACore (69–77) Fibril Segments of Parkinson’s Disease. Journal of Molecular Modeling, 26: 132.
Appel‐Cresswell S, Vilarino‐Guell C, Encarnacion M, Sherman H, Yu I, Shah B, Weir D, Thompson C, Szu‐Tu C, Trinh J 2013. Alpha‐Synuclein P. H50q, a Novel Pathogenic Mutation for Parkinson's Disease. Movement Disorders, 28 (6): 811-813.
Berendsen HJ, Postma JP, van Gunsteren WF, Hermans J 1981. Interaction Models for Water in Relation to Protein Hydration. In: Intermolecular Forces, Springer, Dordrecht, pp. 331-342.
Berhanu WM, Hansmann UH 2012. Side‐Chain Hydrophobicity and the Stability of Aβ16–22 Aggregates. Protein Science, 21 (12): 1837-1848.
Berhanu WM, Masunov AE 2012. Unique Example of Amyloid Aggregates Stabilized by Main Chain H-Bond Instead of the Steric Zipper: Molecular Dynamics Study of the Amyloidogenic Segment of Amylin Wild-Type and Mutants. Journal of Molecular Modeling, 18 (3): 891-903.
Best RB, Zhu X, Shim J, Lopes PE, Mittal J, Feig M, MacKerell AD Jr. 2012. Optimization of the Additive Charmm All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, Ψ and Side-Chain Χ1 and Χ2 Dihedral Angles. Journal of Chemical Theory andCcomputation, 8 (9): 3257-3273.
Bussi G, Donadio D, Parrinello M 2007. Canonical Sampling through Velocity Rescaling. The Journal of Chemical Physics, 126 (1): 014101.
Carballo‐Pacheco M, Strodel B 2017. Comparison of Force Fields for Alzheimer's A: A Case Study for Intrinsically Disordered Proteins. Protein Science, 26 (2): 174-185.
Çınar E, Çakmaklı GY, Tel BC, 2019. Parkinson Hastalığında Nöroprotektif Tedaviler. Turkish Journal of Neurology, 25: 189-197.
Darden T, York D, Pedersen L 1993. Particle Mesh Ewald: An N⋅ Log (N) Method for Ewald Sums in Large Systems. The Journal of Chemical Physics, 98 (12): 10089-10092.
De Lau LM, Breteler MMB, 2006. Epidemiology of Parkinson's Disease. The Lancet Neurology, 5 (6): 525-535. DeLano WL 2002. The PyMOL Molecular Graphics System, http://www. pymol. org.
Demir K, Alıcı H, Yaşar F 2018. Conformational Stability of the Tetrameric De Novo Designed Hexcoil-Ala Helical Bundle. Chinese Journal of Physics, 56(1): 46-57.
Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T 2003. A Point‐Charge Force Field for Molecular Mechanics Simulations of Proteins Based on Condensed‐Phase Quantum Mechanical Calculations. Journal of Computational Chemistry, 24 (16): 1999-2012.
Glenner GG, Wong CW 1984. Alzheimer's Disease: Initial Report of the Purification and Characterization of a Novel Cerebrovascular Amyloid Protein. Biochemical and Biophysical Research Communications, 120 (3): 885-890.
Goedert M, Spillantini MG, Del Tredici K, Braak H 2013. 100 Years of Lewy Pathology. Nature Reviews Neurology, 9 (1): 13.
Hess B, Bekker H, Berendsen HJ, Fraaije JG 1997. Lincs: A Linear Constraint Solver for Molecular Simulations. Journal of Computational Chemistry, 18 (12): 1463-1472.
Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C 2006. Comparison of Multiple Amber Force Fields and Development of Improved Protein Backbone Parameters. Proteins: Structure, Function, and Bioinformatics, 65 (3): 712-725.
Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML 1983. Comparison of Simple Potential Functions for Simulating Liquid Water. The Journal of Chemical Physics, 79 (2): 926-935.
Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL 2001. Evaluation and Reparametrization of the Opls-Aa Force Field for Proteins Via Comparison with Accurate Quantum Chemical Calculations on Peptides. The Journal of Physical Chemistry B, 105 (28): 6474-6487.
Kumari R, Kumar R, Consortium OSDD, Lynn A 2014. G_Mmpbsa a Gromacs Tool for High-Throughput Mm-Pbsa Calculations. Journal of Chemical Information and Modeling, 54 (7): 1951-1962.
Lang AE, Lozano AM 1998. Parkinson's Disease. New England Journal of Medicine-Unbound Volume, 339 (16): 1130-1143.
Lesage S, Anheim M, Letournel F, Bousset L, Honoré A, Rozas N, Pieri L, Madiona K, Dürr A, Melki R 2013. G51d Α‐Synuclein Mutation Causes a Novel Parkinsonian–Pyramidal Syndrome. Annals of Neurology, 73 (4): 459-471.
Lindorff‐Larsen K, Piana S, Palmo K, Maragakis P, Klepeis JL, Dror RO, Shaw DE 2010. Improved Side‐Chain Torsion Potentials for the Amber Ff99sb Protein Force Field. Proteins: Structure, Function, and Bioinformatics, 78 (8): 1950-1958.
Lobanov MY, Bogatyreva NS, Galzitskaya OV 2008. Radius of Gyration as an Indicator of Protein Structure Compactness. Molecular Biology, 42 (4): 623-628.
MacKerell Jr AD, Bashford D, Bellott M, Dunbrack Jr RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S 1998. All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins. The Journal of Physical Chemistry B, 102 (18): 3586-3616.
Miyamoto S, Kollman PA 1992. Settle: An Analytical Version of the Shake and Rattle Algorithm for Rigid Water Models. Journal of Computational Chemistry, 13 (8): 952-962.
Oostenbrink C, Villa A, Mark AE, Van Gunsteren WF 2004. A Biomolecular Force Field Based on the Free Enthalpy of Hydration and Solvation: The Gromos Force‐Field Parameter Sets 53a5 and 53a6. Journal of Computational Chemistry, 25 (13): 1656-1676.
Parrinello M, Rahman A 1981. Polymorphic Transitions in Single Crystals: A New Molecular Dynamics Method. Journal of Applied Physics, 52 (12): 7182-7190.
Pasanen P, Myllykangas L, Siitonen M, Raunio A, Kaakkola S, Lyytinen J, Tienari PJ, Pöyhönen M, Paetau A 2014. A Novel Α-Synuclein Mutation A53e Associated with Atypical Multiple System Atrophy and Parkinson's Disease-Type Pathology. Neurobiology of Aging, 35 (9): 2180-e1.
Polymeropoulos MH, Lavedan C, Leroy E, Ide SE, Dehejia A, Dutra A, Pike B, Root H, Rubenstein, J Boyer R 1997. Mutation in the Α-Synuclein Gene Identified in Families with Parkinson's Disease. Sciece, 276 (5321): 2045-2047.
Pronk S, Páll S, Schulz R, Larsson P, Bjelkmar P, Apostolov R, Shirts MR, Smith JC, Kasson PM, van der Spoel D 2013. Gromacs 4.5: A High-Throughput and Highly Parallel Open Source Molecular Simulation Toolkit. Bioinformatics, 29 (7): 845-854.
Rodriguez JA, Ivanova MI, Sawaya MR, Cascio D, Reyes FE, Shi D, Sangwan S, Guenther EL, Johnson LM, Zhang M 2015. Structure of the Toxic Core of Α-Synuclein from Invisible Crystals. Nature, 525 (7570): 486-490.
Schmid N, Eichenberger AP, Choutko A, Riniker S, Winger M, Mark AE, van Gunsteren WF 2011. Definition and Testing of the Gromos Force-Field Versions 54a7 and 54b7. European Biophysics Journal, 40 (7): 843.
Spillantini MG, Schmidt ML, Lee VM-Y, Trojanowski JQ, Jakes R, Goedert M 1997. Α-Synuclein in Lewy Bodies. Nature, 388 (6645): 839-840.
Ulmer TS, Bax A, Cole NB, Nussbaum RL 2005. Structure and Dynamics of Micelle-Bound Human Α-Synuclein. Journal of Biological Chemistry, 280 (10): 9595-9603.
Xi W, Vanderford EK, Hansmann UH, 2018 Out-of-Register Aβ42 Assemblies as Models for Neurotoxic Oligomers and Fibrils. Journal of Chemical Theory and Computation, 14 (2): 1099-1110.
Verlet L 1967. Computer" Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules. Physical Review, 159 (1): 98.
Yoshino H, Hirano M, Stoessl AJ, Imamichi Y, Ikeda A, Li Y, Funayama M, Yamada I, Nakamura, YSossi V 2017. Homozygous Alpha-Synuclein P. A53v in Familial Parkinson's Disease. Neurobiology of Aging, 57: 248-e7.
Yu,H, Yan Y, Zhang C, Dalby PA 2017. Two Strategies to Engineer Flexible Loops for Improved Enzyme Thermostability. Scientific Reports, 7: 41212.
Zheng J, Ma B, Tsai C-J, Nussinov R 2006. Structural Stability and Dynamics of an Amyloid-Forming Peptide Gnnqqny from the Yeast Prion Sup-35. Biophysical Journal, 91 (3): 824-833.

Toplam 40 adet kaynakça vardır.

Ayrıntılar

Birincil Dil	Türkçe
Bölüm	ARAŞTIRMA MAKALESİ (Research Article)
Yazarlar	Hakan Alıcı 0000-0001-5105-8331
Proje Numarası	2015-22794455-03 nolu Altyapı Projesi
Yayımlanma Tarihi	28 Şubat 2021
Gönderilme Tarihi	14 Mayıs 2020
Kabul Tarihi	3 Temmuz 2020
Yayımlandığı Sayı	Yıl 2021Cilt: 24 Sayı: 1

Kaynak Göster

APA	Alıcı, H. (2021). Alpha-synuclein’ in PreNAC(46-56) Fibril Bölütünün Moleküler Dinamik Simülasyon Yöntemi ile Konformasyonel Değerlendirmesi. Kahramanmaraş Sütçü İmam Üniversitesi Tarım Ve Doğa Dergisi, 24(1), 11-21. https://doi.org/10.18016/ksutarimdoga.vi.737200