1
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Sampson JM, Cannon DA, Duan J, Epstein JCK, Sergeeva AP, Katsamba PS, Mannepalli SM, Bahna FA, Adihou H, Guéret SM, Gopalakrishnan R, Geschwindner S, Rees DG, Sigurdardottir A, Wilkinson T, Dodd RB, De Maria L, Mobarec JC, Shapiro L, Honig B, Buchanan A, Friesner RA, Wang L. Robust Prediction of Relative Binding Energies for Protein-Protein Complex Mutations Using Free Energy Perturbation Calculations. J Mol Biol 2024; 436:168640. [PMID: 38844044 DOI: 10.1016/j.jmb.2024.168640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 05/31/2024] [Indexed: 06/18/2024]
Abstract
Computational free energy-based methods have the potential to significantly improve throughput and decrease costs of protein design efforts. Such methods must reach a high level of reliability, accuracy, and automation to be effectively deployed in practical industrial settings in a way that impacts protein design projects. Here, we present a benchmark study for the calculation of relative changes in protein-protein binding affinity for single point mutations across a variety of systems from the literature, using free energy perturbation (FEP+) calculations. We describe a method for robust treatment of alternate protonation states for titratable amino acids, which yields improved correlation with and reduced error compared to experimental binding free energies. Following careful analysis of the largest outlier cases in our dataset, we assess limitations of the default FEP+ protocols and introduce an automated script which identifies probable outlier cases that may require additional scrutiny and calculates an empirical correction for a subset of charge-related outliers. Through a series of three additional case study systems, we discuss how Protein FEP+ can be applied to real-world protein design projects, and suggest areas of further study.
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Affiliation(s)
- Jared M Sampson
- Schrödinger, Inc., Life Sciences Software, New York, NY, USA
| | - Daniel A Cannon
- Schrödinger, GmbH, Life Sciences Software, Mannheim, Germany
| | - Jianxin Duan
- Schrödinger, GmbH, Life Sciences Software, Mannheim, Germany
| | | | - Alina P Sergeeva
- Columbia University, Department of Systems Biology, New York, NY, USA
| | | | - Seetha M Mannepalli
- Columbia University, Zuckerman Mind Brain Behavior Institute, New York, NY, USA
| | - Fabiana A Bahna
- Columbia University, Zuckerman Mind Brain Behavior Institute, New York, NY, USA
| | - Hélène Adihou
- AstraZeneca, Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, Gothenburg, Sweden; Max Planck Institute of Molecular Physiology, AstraZeneca-MPI Satellite Unit, Dortmund, Germany
| | - Stéphanie M Guéret
- AstraZeneca, Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, Gothenburg, Sweden; Max Planck Institute of Molecular Physiology, AstraZeneca-MPI Satellite Unit, Dortmund, Germany
| | - Ranganath Gopalakrishnan
- AstraZeneca, Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, Gothenburg, Sweden; Max Planck Institute of Molecular Physiology, AstraZeneca-MPI Satellite Unit, Dortmund, Germany
| | - Stefan Geschwindner
- AstraZeneca, Mechanistic and Structural Biology, Discovery Sciences, R&D, Gothenburg, Sweden
| | - D Gareth Rees
- AstraZeneca, Biologics Engineering, R&D, Cambridge, UK
| | | | | | - Roger B Dodd
- AstraZeneca, Biologics Engineering, R&D, Cambridge, UK
| | - Leonardo De Maria
- AstraZeneca, Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, Gothenburg, Sweden
| | - Juan Carlos Mobarec
- AstraZeneca, Mechanistic and Structural Biology, Discovery Sciences, R&D, Cambridge, UK
| | - Lawrence Shapiro
- Columbia University, Zuckerman Mind Brain Behavior Institute, New York, NY, USA; Columbia University, Department of Biochemistry and Molecular Biophysics, New York, NY, USA
| | - Barry Honig
- Columbia University, Department of Systems Biology, New York, NY, USA; Columbia University, Zuckerman Mind Brain Behavior Institute, New York, NY, USA; Columbia University, Department of Biochemistry and Molecular Biophysics, New York, NY, USA; Columbia University, Department of Medicine, New York, NY, USA
| | | | | | - Lingle Wang
- Schrödinger, Inc., Life Sciences Software, New York, NY, USA.
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2
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Duan Y, Cao Y, Qi L, Shaojia W, Gao W. Revealing the mechanism of the lutein protective function of epicatechin-fructan glycosylated soybean protein isolate. Curr Res Food Sci 2024; 8:100750. [PMID: 38764979 PMCID: PMC11101747 DOI: 10.1016/j.crfs.2024.100750] [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: 01/13/2024] [Revised: 04/17/2024] [Accepted: 04/22/2024] [Indexed: 05/21/2024] Open
Abstract
Lutein possesses various physiological activities but is susceptible to light degradation, thermal degradation, and oxidative degradation. As such, protecting the activity of lutein-based products using natural extracts has become a current research. In this study, lutein was protected by complexing inulin-type fructan (ITF), soybean protein isolate (SPI), and epicatechin (EC), and the protection mechanism of epicatechin-fructan glycosylated soybean protein isolate (EC-GSPI) toward lutein was elucidated comprehensively. The results showed that the addition of EC delayed the degradation of lutein. The results of light stability experiments showed that increased EC significantly enhanced the storage time of the GSPI-Lutein system from 4 to 13 days. Additionally, the effect of EC on glycosylated soybean 7S globulin (G7S) and glycosylated soybean 11S globulin (G11S) was assessed. The light stability of G11S-Lutein and G7S-Lutein after the addition of EC was from G11S > G7S → G7S > G11S. Furthermore, the proteins purified from SPI interacted differently with EC and ITF, with soybean 7S globulin (7S) mainly interacting with EC and soybean 11S globulin (11S) mainly interacting with ITF. EC-GSPI-Lutein exhibited a good protective effect, probably due to the occurrence of hygrothermal Maillard between ITF and 11S, providing a porous structure for lutein storage. At the same time, the binding of EC to 7S significantly enhanced the antioxidant property of the solution and the stability of the protein secondary structure, thereby prolonging the storage time of lutein.
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Affiliation(s)
- Yunhan Duan
- Beijing Advanced Innovation Center for Food Nutrition and Human Health (BTBU), School of Food and Health, Beijing Higher Institution Engineering Research Center of Food Additives and Ingredients, Beijing Technology and Business University, Beijing, 100048, China
| | - Yanping Cao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health (BTBU), School of Food and Health, Beijing Higher Institution Engineering Research Center of Food Additives and Ingredients, Beijing Technology and Business University, Beijing, 100048, China
| | - Lijun Qi
- Chenguang Biotech Group Limited Co., Ltd, Handan, 057250, China
| | - Wang Shaojia
- Beijing Advanced Innovation Center for Food Nutrition and Human Health (BTBU), School of Food and Health, Beijing Higher Institution Engineering Research Center of Food Additives and Ingredients, Beijing Technology and Business University, Beijing, 100048, China
| | - Wei Gao
- Chenguang Biotech Group Limited Co., Ltd, Handan, 057250, China
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3
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Sampson JM, Cannon DA, Duan J, Epstein JCK, Sergeeva AP, Katsamba PS, Mannepalli SM, Bahna FA, Adihou H, Guéret SM, Gopalakrishnan R, Geschwindner S, Rees DG, Sigurdardottir A, Wilkinson T, Dodd RB, De Maria L, Mobarec JC, Shapiro L, Honig B, Buchanan A, Friesner RA, Wang L. Robust prediction of relative binding energies for protein-protein complex mutations using free energy perturbation calculations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.22.590325. [PMID: 38712280 PMCID: PMC11071377 DOI: 10.1101/2024.04.22.590325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Computational free energy-based methods have the potential to significantly improve throughput and decrease costs of protein design efforts. Such methods must reach a high level of reliability, accuracy, and automation to be effectively deployed in practical industrial settings in a way that impacts protein design projects. Here, we present a benchmark study for the calculation of relative changes in protein-protein binding affinity for single point mutations across a variety of systems from the literature, using free energy perturbation (FEP+) calculations. We describe a method for robust treatment of alternate protonation states for titratable amino acids, which yields improved correlation with and reduced error compared to experimental binding free energies. Following careful analysis of the largest outlier cases in our dataset, we assess limitations of the default FEP+ protocols and introduce an automated script which identifies probable outlier cases that may require additional scrutiny and calculates an empirical correction for a subset of charge-related outliers. Through a series of three additional case study systems, we discuss how protein FEP+ can be applied to real-world protein design projects, and suggest areas of further study.
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Affiliation(s)
| | | | - Jianxin Duan
- Schrödinger, GmbH, Life Sciences Software, Mannheim, Germany
| | | | - Alina P. Sergeeva
- Columbia University, Department of Systems Biology, New York, NY, USA
| | | | - Seetha M. Mannepalli
- Columbia University, Zuckerman Mind Brain Behavior Institute, New York, NY, USA, 10027
| | - Fabiana A. Bahna
- Columbia University, Zuckerman Mind Brain Behavior Institute, New York, NY, USA, 10027
| | - Hélène Adihou
- AstraZeneca, Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, Gothenburg, Sweden
- Max Planck Institute of Molecular Physiology, AstraZeneca-MPI Satellite Unit, Dortmund, Germany
| | - Stéphanie M. Guéret
- AstraZeneca, Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, Gothenburg, Sweden
- Max Planck Institute of Molecular Physiology, AstraZeneca-MPI Satellite Unit, Dortmund, Germany
| | - Ranganath Gopalakrishnan
- AstraZeneca, Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, Gothenburg, Sweden
- Max Planck Institute of Molecular Physiology, AstraZeneca-MPI Satellite Unit, Dortmund, Germany
| | - Stefan Geschwindner
- AstraZeneca, Mechanistic and Structural Biology, Discovery Sciences, R&D, Cambridge, UK
| | | | | | | | - Roger B. Dodd
- AstraZeneca, Biologics Engineering, R&D, Cambridge, UK
| | - Leonardo De Maria
- AstraZeneca, Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, Gothenburg, Sweden
| | - Juan Carlos Mobarec
- AstraZeneca, Mechanistic and Structural Biology, Discovery Sciences, R&D, Cambridge, UK
| | - Lawrence Shapiro
- Columbia University, Zuckerman Mind Brain Behavior Institute, New York, NY, USA, 10027
- Columbia University, Department of Biochemistry and Molecular Biophysics, New York, NY, USA
| | - Barry Honig
- Columbia University, Department of Systems Biology, New York, NY, USA
- Columbia University, Zuckerman Mind Brain Behavior Institute, New York, NY, USA, 10027
- Columbia University, Department of Biochemistry and Molecular Biophysics, New York, NY, USA
- Columbia University, Department of Medicine, New York, NY, USA
| | | | | | - Lingle Wang
- Schrödinger, Inc., Life Sciences Software, New York, NY, USA
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4
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Dey P, Biswas P. Aggregation propensities of proteins with varying degrees of disorder. J Comput Chem 2023; 44:874-886. [PMID: 36468418 DOI: 10.1002/jcc.27049] [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: 08/06/2022] [Revised: 11/10/2022] [Accepted: 11/15/2022] [Indexed: 12/10/2022]
Abstract
The hydration thermodynamics of a globular protein (AcP), three intrinsically disordered protein regions (1CD3, 1MVF, 1F0R) and a fully disordered protein (α-synuclein) is studied by an approach that combines an all-atom explicit water molecular dynamics simulations and three-dimensional reference interaction site model (3D-RISM) theory. The variation in hydration free energy with percentage disorder of the selected proteins is investigated through its nonelectrostatic and electrostatic components. A decrease in hydration free energy is observed with an increase in percentage disorder, indicating favorable interactions of the disordered proteins with the solvent. This confirms the role of percentage disorder in determining the aggregation propensity of proteins which is measured in terms of the hydration free energy in addition to their respective mean net charge and mean hydrophobicity. The hydration free energy is decoupled into energetic and entropic terms. A residue-wise decomposition analysis of the hydration free energy for the selected proteins is evaluated. The decomposition shows that the disordered regions contribute more than the ordered ones for the intrinsically disordered protein regions. The dominant role of electrostatic interactions is confirmed from the residue-wise decomposition of the hydration free energy. The results depict that the negatively charged residues contribute more to the total hydration free energy for the proteins with negative mean net charge, while the positively charged residues contribute more for proteins with positive mean net charge.
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Affiliation(s)
- Priya Dey
- Department of Chemistry, University of Delhi, Delhi, India
| | - Parbati Biswas
- Department of Chemistry, University of Delhi, Delhi, India
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5
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Lv Y, Dong F, Cui J, Hao J, Luo R, Wang S, Rodas-Gonzalez A, Liu S. Fusion of Spectral and Textural Data of Hyperspectral Imaging for Glycine Content Prediction in Beef Using SFCN Algorithms. FOOD ANAL METHOD 2022. [DOI: 10.1007/s12161-022-02425-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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6
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Dong F, Bi Y, Hao J, Liu S, Lv Y, Cui J, Wang S, Han Y, Rodas-González A. A Combination of Near-Infrared Hyperspectral Imaging with Two-Dimensional Correlation Analysis for Monitoring the Content of Alanine in Beef. BIOSENSORS 2022; 12:bios12111043. [PMID: 36421161 PMCID: PMC9688476 DOI: 10.3390/bios12111043] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/15/2022] [Accepted: 11/15/2022] [Indexed: 05/31/2023]
Abstract
Alanine (Ala), as the most important free amino acid, plays a significant role in food taste characteristics and human health regulation. The feasibility of using near-infrared hyperspectral imaging (NIR-HSI) combined with two-dimensional correlation spectroscopy (2D-COS) analysis to predict beef Ala content quickly and nondestructively is first proposed in this study. With Ala content as the external disturbance condition, the sequence of chemical bond changes caused by synchronous and asynchronous correlation spectrum changes in 2D-COS was analyzed, and local sensitive variables closely related to Ala content were obtained. On this basis, the simplified linear, nonlinear, and artificial neural network models developed by the weighted coefficient based on the feature wavelength extraction method were compared. The results show that with the change in Ala content in beef, the double-frequency absorption of the C-H bond of CH2 in the chemical bond sequence occurred prior to the third vibration of the C=O bond and the first stretching of O-H in COOH. Furthermore, the wavelength within the 1136-1478 nm spectrum range was obtained as the local study area of Ala content. The linear partial least squares regression (PLSR) model based on effective wavelengths was selected by competitive adaptive reweighted sampling (CARS) from 2D-COS analysis, and provided excellent results (R2C of 0.8141, R2P of 0.8458, and RPDp of 2.54). Finally, the visual distribution of Ala content in beef was produced by the optimal simplified combination model. The results show that 2D-COS combined with NIR-HSI could be used as an effective method to monitor Ala content in beef.
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Affiliation(s)
- Fujia Dong
- School of Food and Wine, Ningxia University, Yinchuan 750021, China
| | - Yongzhao Bi
- School of Food and Wine, Ningxia University, Yinchuan 750021, China
| | - Jie Hao
- School of Food and Wine, Ningxia University, Yinchuan 750021, China
| | - Sijia Liu
- School of Food and Wine, Ningxia University, Yinchuan 750021, China
| | - Yu Lv
- School of Food and Wine, Ningxia University, Yinchuan 750021, China
| | - Jiarui Cui
- School of Food and Wine, Ningxia University, Yinchuan 750021, China
| | - Songlei Wang
- School of Food and Wine, Ningxia University, Yinchuan 750021, China
| | - Yafang Han
- School of Food and Wine, Ningxia University, Yinchuan 750021, China
| | - Argenis Rodas-González
- Department of Animal Science, Faculty of Agricultural and Food Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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7
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Kim D, Chong SH, Shin S, Ham S. Mutation effects on FAS1 domain 4 based on structure and solubility. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140746. [PMID: 34942360 DOI: 10.1016/j.bbapap.2021.140746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 12/07/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Mutations in the fasciclin 1 domain 4 (FAS1-4) of transforming growth factor β-induced protein (TGFBIp) are associated with insoluble extracellular deposits and corneal dystrophies (CDs). The decrease in solubility upon mutation has been implicated in CD; however, the exact molecular mechanisms are not well understood. Here, we performed molecular dynamics simulations followed by solvation thermodynamic analyses of the FAS1-4 domain and its three mutants-R555W, R555Q, and A546T-linked to granular corneal dystrophy type 1, Thiel-Behnke corneal dystrophy and lattice corneal dystrophy, respectively. We found that both R555W and R555Q mutants have less affinity toward solvent water relative to the wild-type protein. In the R555W mutant, a remarkable increase in solvation free energy was observed because of the structural changes near the mutation site. The mutation site W555 is buried in other hydrophobic residues, and R557 simultaneously forms salt bridges with E554 and D561. In the R555Q mutant, the increase in solvation free energy is caused by structural rearrangements far from the mutation site. R558 separately forms salt bridges with D575, E576, and E598. Thus, we thus identified the relationship between the decrease in solubility and conformational changes caused by mutations, which may be useful in designing potential therapeutics and in blocking FAS1 aggregation related to CD.
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Affiliation(s)
- DongGun Kim
- Department of Chemistry, The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa-ro 47-gil 100, Yongsan-gu, Seoul 04310, Republic of Korea; Department of Chemistry, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Song-Ho Chong
- Department of Chemistry, The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa-ro 47-gil 100, Yongsan-gu, Seoul 04310, Republic of Korea
| | - Seokmin Shin
- Department of Chemistry, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 08826, Republic of Korea.
| | - Sihyun Ham
- Department of Chemistry, The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa-ro 47-gil 100, Yongsan-gu, Seoul 04310, Republic of Korea.
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8
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Chatterjee P, Le T, Bui HTD, Cho MK, Ham S. Atomic Level Investigations of Early Aggregation of Tau43 in Water I. Conformational Propensity of Monomeric Tau43. B KOREAN CHEM SOC 2021. [DOI: 10.1002/bkcs.12338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Prathit Chatterjee
- Department of Chemistry The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa‐ro 47‐Gil 100, Yongsan‐Ku Seoul 04310 Korea
| | - Thi‐Diem Le
- Department of Chemistry The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa‐ro 47‐Gil 100, Yongsan‐Ku Seoul 04310 Korea
| | - Huong T. D. Bui
- Department of Chemistry The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa‐ro 47‐Gil 100, Yongsan‐Ku Seoul 04310 Korea
| | - Myung Keun Cho
- Department of Chemistry The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa‐ro 47‐Gil 100, Yongsan‐Ku Seoul 04310 Korea
- Department of Chemistry College of Natural Sciences, Seoul National University, Gwanak‐ro 1, Gwanak‐ku Seoul 08826 Korea
| | - Sihyun Ham
- Department of Chemistry The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa‐ro 47‐Gil 100, Yongsan‐Ku Seoul 04310 Korea
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9
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Luwang JW, Nair AR, Natesh R. Stability of p53 oligomers: Tetramerization of p53 impinges on its stability. Biochimie 2021; 189:99-107. [PMID: 34197865 DOI: 10.1016/j.biochi.2021.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 06/21/2021] [Accepted: 06/24/2021] [Indexed: 10/21/2022]
Abstract
The p53 protein has been known to exist structurally in three different forms inside the cells. Earlier studies have reported the predominance of the lower oligomeric forms of p53 over its tetrameric form inside the cells, although only the tetrameric p53 contributes to its transcriptional activity. However, it remains unclear the functional relevance of the existence of other p53 oligomers inside the cells. In this study, we characterize the stability and conformational state of tetrameric, dimeric and monomeric p53 that spans both DNA Binding Domain (DBD) and Tetramerization Domain (TD) of human p53 (94-360 amino acid residues). Intriguingly, our studies reveal an unexpected drastic reduction in tetrameric p53 thermal stability in comparison to its dimeric and monomeric form with a higher propensity to aggregate at physiological temperature. Our EMSA study suggests that tetrameric p53, not their lower oligomeric counterpart, exhibit rapid loss of binding to their consensus DNA elements at the physiological temperature. This detrimental effect of destabilization is imparted due to the tetramerization of p53 that drives the DBDs to misfold at a faster pace when compared to its lower oligomeric form. This crosstalk between DBDs is achieved when it exists as a tetramer but not as dimer or monomer. Our findings throw light on the plausible reason for the predominant existence of p53 in dimer and monomer forms inside the cells with a lesser population of tetramer form. Therefore, the transient disruption of tetramerization between TDs could be a potential cue for the stabilization of p53 inside the cells.
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Affiliation(s)
- Johnson Wahengbam Luwang
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram, 695551, Kerala, India
| | - Aadithye R Nair
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram, 695551, Kerala, India
| | - Ramanathan Natesh
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram, 695551, Kerala, India.
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10
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Aggarwal L, Biswas P. Hydration Thermodynamics of the N-Terminal FAD Mutants of Amyloid-β. J Chem Inf Model 2021; 61:298-310. [PMID: 33440932 DOI: 10.1021/acs.jcim.0c01286] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The hydration thermodynamics of amyloid-β (Aβ) and its pathogenic familial Alzheimer's disease (FAD) mutants such as A2V, Taiwan (D7H), Tottori (D7N), and English (H6R) and the protective A2T mutant is investigated by a combination of all-atom, explicit water molecular dynamics (MD) simulations and the three-dimensional reference interaction site model (3D-RISM) theory. The change in the hydration free energy on mutation is decomposed into the energetic and entropic components, which comprise electrostatic and nonelectrostatic contributions. An increase in the hydration free energy is observed for A2V, D7H, D7N, and H6R mutations that increase the aggregation propensity of Aβ and lead to an early onset of Alzheimer's disease, while a reverse trend is noted for the protective A2T mutation. An antiphase correlation is found between the change in the hydration energy and the internal energy of Aβ upon mutation. A residue-wise decomposition analysis shows that the change in the hydration free energy of Aβ on mutation is primarily due to the hydration/dehydration of the side-chain atoms of the negatively charged residues. The decrease in the hydration of the negatively charged residues on mutation may decrease the solubility of the mutant, which increases the observed aggregation propensity of the FAD mutants. Results obtained from the theory show an excellent match with the experimentally reported data.
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Affiliation(s)
- Leena Aggarwal
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Parbati Biswas
- Department of Chemistry, University of Delhi, Delhi 110007, India
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11
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Local environment effects on charged mutations for developing aggregation-resistant monoclonal antibodies. Sci Rep 2020; 10:21191. [PMID: 33273506 PMCID: PMC7713239 DOI: 10.1038/s41598-020-78136-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 11/11/2020] [Indexed: 11/10/2022] Open
Abstract
Protein aggregation is a major concern in biotherapeutic applications of monoclonal antibodies. Introducing charged mutations is among the promising strategies to improve aggregation resistance. However, the impact of such mutations on solubilizing activity depends largely on the inserting location, whose mechanism is still not well understood. Here, we address this issue from a solvation viewpoint, and this is done by analyzing how the change in solvation free energy upon charged mutation is composed of individual contributions from constituent residues. To this end, we perform molecular dynamics simulations for a number of antibody mutants and carry out the residue-wise decomposition of the solvation free energy. We find that, in addition to the previously identified “global” principle emphasizing the key role played by the protein total net charge, a local net charge within \documentclass[12pt]{minimal}
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\begin{document}$$\sim$$\end{document}∼15 Å from the mutation site exerts significant effects. For example, when the net charge of an antibody is positive, the global principle states that introducing a positively charged mutation will lead to more favorable solvation. Our finding further adds that an even more optimal mutation can be done at the site around which more positively charged residues and fewer negatively charged residues are present. Such a “local” design principle accounts for the location dependence of charged mutations, and will be useful in producing aggregation-resistant antibodies.
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12
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Maruyama Y, Takano H, Mitsutake A. Analysis of molecular dynamics simulations of 10-residue peptide, chignolin, using statistical mechanics: Relaxation mode analysis and three-dimensional reference interaction site model theory. Biophys Physicobiol 2019; 16:407-429. [PMID: 31984194 PMCID: PMC6975981 DOI: 10.2142/biophysico.16.0_407] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 08/29/2019] [Indexed: 01/03/2023] Open
Abstract
Molecular dynamics simulation is a fruitful tool for investigating the structural stability, dynamics, and functions of biopolymers at an atomic level. In recent years, simulations can be performed on time scales of the order of milliseconds using special purpose systems. Since the most stable structure, as well as meta-stable structures and intermediate structures, is included in trajectories in long simulations, it is necessary to develop analysis methods for extracting them from trajectories of simulations. For these structures, methods for evaluating the stabilities, including the solvent effect, are also needed. We have developed relaxation mode analysis to investigate dynamics and kinetics of simulations based on statistical mechanics. We have also applied the three-dimensional reference interaction site model theory to investigate stabilities with solvent effects. In this paper, we review the results for designing amino-acid substitution of the 10-residue peptide, chignolin, to stabilize the misfolded structure using these developed analysis methods.
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Affiliation(s)
- Yutaka Maruyama
- Architecture Development Team, FLAGSHIP 2020 Project, RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Hiroshi Takano
- Department of Physics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Ayori Mitsutake
- Department of Physics, School of Science and Technology, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
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13
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Chong SH, Ham S. Folding Free Energy Landscape of Ordered and Intrinsically Disordered Proteins. Sci Rep 2019; 9:14927. [PMID: 31624293 PMCID: PMC6797787 DOI: 10.1038/s41598-019-50825-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/19/2019] [Indexed: 01/05/2023] Open
Abstract
Folding funnel is the essential concept of the free energy landscape for ordered proteins. How does this concept apply to intrinsically disordered proteins (IDPs)? Here, we address this fundamental question through the explicit characterization of the free energy landscapes of the representative α-helical (HP-35) and β-sheet (WW domain) proteins and of an IDP (pKID) that folds upon binding to its partner (KIX). We demonstrate that HP-35 and WW domain indeed exhibit the steep folding funnel: the landscape slope for these proteins is ca. −50 kcal/mol, meaning that the free energy decreases by ~5 kcal/mol upon the formation of 10% native contacts. On the other hand, the landscape of pKID is funneled but considerably shallower (slope of −24 kcal/mol), which explains why pKID is disordered in free environments. Upon binding to KIX, the landscape of pKID now becomes significantly steep (slope of −54 kcal/mol), which enables otherwise disordered pKID to fold. We also show that it is the pKID–KIX intermolecular interactions originating from hydrophobic residues that mainly confer the steep folding funnel. The present work not only provides the quantitative characterization of the protein folding free energy landscape, but also establishes the usefulness of the folding funnel concept to IDPs.
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Affiliation(s)
- Song-Ho Chong
- Department of Chemistry, The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa-ro 47-gil 100, Yongsan-Ku, Seoul, 04310, Korea
| | - Sihyun Ham
- Department of Chemistry, The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa-ro 47-gil 100, Yongsan-Ku, Seoul, 04310, Korea.
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14
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Choi TS, Han JY, Heo CE, Lee SW, Kim HI. Electrostatic and hydrophobic interactions of lipid-associated α-synuclein: The role of a water-limited interfaces in amyloid fibrillation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1854-1862. [DOI: 10.1016/j.bbamem.2018.02.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 02/05/2018] [Accepted: 02/05/2018] [Indexed: 12/22/2022]
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15
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Mancini O, Wellbrock T, Rolinski OJ, Kubiak-Ossowska K, Mulheran PA. Probing beta amyloid aggregation using fluorescence anisotropy: experiments and simulation. Phys Chem Chem Phys 2018; 20:4216-4225. [DOI: 10.1039/c7cp08217g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Simulated fluorescence anisotropy from Tyr residues distinguishes a beta amyloid monomer (black) from oligomers (coloured).
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Affiliation(s)
- Onorio Mancini
- Department of Chemical Engineering and Process Engineering
- University of Strathclyde
- Glasgow
- UK
| | | | | | | | - Paul A. Mulheran
- Department of Chemical Engineering and Process Engineering
- University of Strathclyde
- Glasgow
- UK
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16
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Kuhn AB, Kube S, Karow-Zwick AR, Seeliger D, Garidel P, Blech M, Schäfer LV. Improved Solution-State Properties of Monoclonal Antibodies by Targeted Mutations. J Phys Chem B 2017; 121:10818-10827. [DOI: 10.1021/acs.jpcb.7b09126] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Alexander B. Kuhn
- Theoretical
Chemistry, Ruhr-University Bochum, D-44780 Bochum, Germany
| | | | | | | | | | | | - Lars V. Schäfer
- Theoretical
Chemistry, Ruhr-University Bochum, D-44780 Bochum, Germany
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17
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Abidin RS, Lua LHL, Middelberg APJ, Sainsbury F. Insert engineering and solubility screening improves recovery of virus-like particle subunits displaying hydrophobic epitopes. Protein Sci 2015; 24:1820-8. [PMID: 26401641 DOI: 10.1002/pro.2775] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 08/20/2015] [Indexed: 11/09/2022]
Abstract
The Polyomavirus coat protein, VP1 has been developed as an epitope presentation system able to provoke humoral immunity against a variety of pathogens, such as Influenza and Group A Streptococcus. The ability of the system to carry cytotoxic T cell epitopes on a surface-exposed loop and the impact on protein solubility has not been examined. Four variations of three selected epitopes were cloned into surface-exposed loops of VP1, and expressed in Escherichia coli. VP1 pentamers, also known as capsomeres, were purified via a glutathione-S-transferase tag. Size exclusion chromatography indicated severe aggregation of the recombinant VP1 during enzymatic tag removal resulting from the introduction the hydrophobic epitopes. Inserts were modified to possess double aspartic acid residues at each end of the hydrophobic epitopes and a high-throughput buffer condition screen was implemented with protein aggregation monitored during tag removal by spectrophotometry and dynamic light scattering. These analyses showed that the insertion of charged residues at the extremities of epitopes could improve solubility of capsomeres and revealed multiple windows of opportunity for further condition optimization. A combination of epitope design, pH optimization, and the additive l-arginine permitted the recovery of soluble VP1 pentamers presenting hydrophobic epitopes and their subsequent assembly into virus-like particles.
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Affiliation(s)
- R S Abidin
- The University of Queensland, Australian Institute for Bioengineering and Nanotechnology Centre for Biomolecular Engineering, St Lucia, Queensland, 4072, Australia
| | - L H L Lua
- Protein Expression Facility, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - A P J Middelberg
- The University of Queensland, Australian Institute for Bioengineering and Nanotechnology Centre for Biomolecular Engineering, St Lucia, Queensland, 4072, Australia
| | - F Sainsbury
- The University of Queensland, Australian Institute for Bioengineering and Nanotechnology Centre for Biomolecular Engineering, St Lucia, Queensland, 4072, Australia
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18
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Structural and Thermodynamic Characteristics of Amyloidogenic Intermediates of β-2-Microglobulin. Sci Rep 2015; 5:13631. [PMID: 26348154 PMCID: PMC4562173 DOI: 10.1038/srep13631] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 08/07/2015] [Indexed: 12/27/2022] Open
Abstract
β-2-microglobulin (β2m) self-aggregates to form amyloid fibril in renal patients taking long-term dialysis treatment. Despite the extensive structural and mutation studies carried out so far, the molecular details on the factors that dictate amyloidogenic potential of β2m remain elusive. Here we report molecular dynamics simulations followed by the solvation thermodynamic analyses on the wild-type β2m and D76N, D59P, and W60C mutants at the native (N) and so-called aggregation-prone intermediate (IT) states, which are distinguished by the native cis- and non-native trans-Pro32 backbone conformations. Three major structural and thermodynamic characteristics of the IT-state relative to the N-state in β2m protein are detected that contribute to the increased amyloidogenic potential: (i) the disruption of the edge D-strand, (ii) the increased solvent-exposed hydrophobic interface, and (iii) the increased solvation free energy (less affinity toward solvent water). Mutation effects on these three factors are shown to exhibit a good correlation with the experimentally observed distinct amyloidogenic propensity of the D76N (+), D59P (+), and W60C (−) mutants (+/− for enhanced/decreased). Our analyses thus identify the structural and thermodynamic characteristics of the amyloidogenic intermediates, which will serve to uncover molecular mechanisms and driving forces in β2m amyloid fibril formation.
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Chong SH, Ham S. Distinct role of hydration water in protein misfolding and aggregation revealed by fluctuating thermodynamics analysis. Acc Chem Res 2015; 48:956-65. [PMID: 25844814 DOI: 10.1021/acs.accounts.5b00032] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Protein aggregation in aqueous cellular environments is linked to diverse human diseases. Protein aggregation proceeds through a multistep process initiated by conformational transitions, called protein misfolding, of monomer species toward aggregation-prone structures. Various forms of aggregate species are generated through the association of misfolded monomers including soluble oligomers and amyloid fibrils. Elucidating the molecular mechanisms and driving forces involved in the misfolding and subsequent association has been a central issue for understanding and preventing protein aggregation diseases such as Alzheimer's, Parkinson's, and type II diabetes. In this Account, we provide a thermodynamic perspective of the misfolding and aggregation of the amyloid-beta (Aβ) protein implicated in Alzheimer's disease through the application of fluctuating thermodynamics. This approach "dissects" the conventional thermodynamic characterization of the end states into the one of the fluctuating processes connecting them, and enables one to analyze variations in the thermodynamic functions that occur during the course of protein conformational changes. The central quantity in this approach is the solvent-averaged effective energy, f = Eu + Gsolv, comprising the protein potential energy (Eu) and the solvation free energy (Gsolv), whose time variation reflects the protein dynamics on the free energy landscape. Protein configurational entropy is quantified by the magnitude of fluctuations in f. We find that misfolding of the Aβ monomer when released from a membrane environment to an aqueous phase is driven by favorable changes in protein potential energy and configurational entropy, but it is also accompanied by an unfavorable increase in solvation free energy. The subsequent dimerization of the misfolded Aβ monomers occurs in two steps. The first step, where two widely separated monomers come into contact distance, is driven by water-mediated attraction, that is, by a decrease in solvation free energy, harnessing the monomer solvation free energy earned during the misfolding. The second step, where a compact dimer structure is formed, is driven by direct protein-protein interactions, but again it is accompanied by an increase in solvation free energy. The increased solvation free energy of the dimer will function as the driving force to recruit another Aβ protein in the approach stage of subsequent oligomerizations. The fluctuating thermodynamics analysis of the misfolding and dimerization of the Aβ protein indicates that the interaction of the protein with surrounding water plays a critical role in protein aggregation. Such a water-centric perspective is further corroborated by demonstrating that, for a large number of Aβ mutants and mutants of other protein systems, the change in the experimental aggregation propensity upon mutation has a significant correlation with the protein solvation free energy change. We also find striking discrimination between the positively and negatively charged residues on the protein surface by surrounding water molecules, which is shown to play a crucial role in determining the protein aggregation propensity. We argue that the protein total charge dictates such striking behavior of the surrounding water molecules. Our results provide new insights for understanding and predicting the protein aggregation propensity, thereby offering novel design principles for producing aggregation-resistant proteins for biotherapeutics.
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Affiliation(s)
- Song-Ho Chong
- Department
of Chemistry, Sookmyung Women’s University, Cheongpa-ro 47-gil 100, Yongsan-Ku, Seoul 140-742, Korea
| | - Sihyun Ham
- Department
of Chemistry, Sookmyung Women’s University, Cheongpa-ro 47-gil 100, Yongsan-Ku, Seoul 140-742, Korea
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