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Pradhan SS, R SS, Kanikaram SP, V M DD, Pargaonkar A, Dandamudi RB, Sivaramakrishnan V. Metabolic deregulation associated with aging modulates protein aggregation in the yeast model of Huntington's disease. J Biomol Struct Dyn 2023:1-18. [PMID: 37732342 DOI: 10.1080/07391102.2023.2257322] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 09/05/2023] [Indexed: 09/22/2023]
Abstract
Huntington's disease is associated with increased CAG repeat resulting in an expanded polyglutamine tract in the protein Huntingtin (HTT) leading to its aggregation resulting in neurodegeneration. Previous studies have shown that N-terminal HTT with 46Q aggregated in the stationary phase but not the logarithmic phase in the yeast model of HD. We carried out a metabolomic analysis of logarithmic and stationary phase yeast model of HD expressing different polyQ lengths attached to N-terminal HTT tagged with enhanced green fluorescent protein (EGFP). The results show significant changes in the metabolic profile and deregulated pathways in stationary phase cells compared to logarithmic phase cells. Comparison of metabolic pathways obtained from logarithmic phase 46Q versus 25Q with those obtained for presymptomatic HD patients from our previous study and drosophila model of HD showed considerable overlap. The arginine biosynthesis pathway emerged as one of the key pathways that is common in stationary phase yeast compared to logarithmic phase and HD patients. Treatment of yeast with arginine led to a significant decrease, while transfer to arginine drop-out media led to a significant increase in the size of protein aggregates in both logarithmic and stationary phase yeast model of HD. Knockout of arginine transporters in the endoplasmic reticulum and vacuole led to a significant decrease in mutant HTT aggregation. Overall our results highlight arginine as a critical metabolite that modulates the aggregation of mutant HTT and disease progression in HD.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sai Sanwid Pradhan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
| | - Sai Swaroop R
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
| | - Sai Phalguna Kanikaram
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
| | - Datta Darshan V M
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
| | - Ashish Pargaonkar
- Application Division, Agilent Technologies Ltd., Bengaluru, Karnataka, India
| | | | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
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2
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Stolzke T, Brandenbusch C. Simplified choice of suitable excipients within biologics formulation design using protein-protein interaction- and water activity-maps. Eur J Pharm Biopharm 2022; 176:153-167. [DOI: 10.1016/j.ejpb.2022.05.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/16/2022] [Accepted: 05/23/2022] [Indexed: 01/17/2023]
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3
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Mamsa SSA, Meloni BP. Arginine and Arginine-Rich Peptides as Modulators of Protein Aggregation and Cytotoxicity Associated With Alzheimer's Disease. Front Mol Neurosci 2021; 14:759729. [PMID: 34776866 PMCID: PMC8581540 DOI: 10.3389/fnmol.2021.759729] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/29/2021] [Indexed: 01/10/2023] Open
Abstract
A substantial body of evidence indicates cationic, arginine-rich peptides (CARPs) are effective therapeutic compounds for a range of neurodegenerative pathologies, with beneficial effects including the reduction of excitotoxic cell death and mitochondrial dysfunction. CARPs, therefore, represent an emergent class of promising neurotherapeutics with multimodal mechanisms of action. Arginine itself is a known chaotrope, able to prevent misfolding and aggregation of proteins. The putative role of proteopathies in chronic neurodegenerative diseases such as Alzheimer's disease (AD) warrants investigation into whether CARPs could also prevent the aggregation and cytotoxicity of amyloidogenic proteins, particularly amyloid-beta and tau. While monomeric arginine is well-established as an inhibitor of protein aggregation in solution, no studies have comprehensively discussed the anti-aggregatory properties of arginine and CARPs on proteins associated with neurodegenerative disease. Here, we review the structural, physicochemical, and self-associative properties of arginine and the guanidinium moiety, to explore the mechanisms underlying the modulation of protein aggregation by monomeric and multimeric arginine molecules. Arginine-rich peptide-based inhibitors of amyloid-beta and tau aggregation are discussed, as well as further modulatory roles which could reduce proteopathic cytotoxicity, in the context of therapeutic development for AD.
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Affiliation(s)
- Somayra S A Mamsa
- School of Molecular Sciences, Faculty of Science, The University of Western Australia, Perth, WA, Australia.,Perron Institute for Neurological and Translational Science, QEII Medical Centre, Perth, WA, Australia
| | - Bruno P Meloni
- Perron Institute for Neurological and Translational Science, QEII Medical Centre, Perth, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Crawley, WA, Australia.,Department of Neurology, Sir Charles Gairdner Hospital, QEII Medical Centre, Perth, WA, Australia
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4
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Marforio TD, Calza A, Mattioli EJ, Zerbetto F, Calvaresi M. Dissecting the Supramolecular Dispersion of Fullerenes by Proteins/Peptides: Amino Acid Ranking and Driving Forces for Binding to C 60. Int J Mol Sci 2021; 22:ijms222111567. [PMID: 34768997 PMCID: PMC8583719 DOI: 10.3390/ijms222111567] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 01/05/2023] Open
Abstract
Molecular dynamics simulations were used to quantitatively investigate the interactions between the twenty proteinogenic amino acids and C60. The conserved amino acid backbone gave a constant energetic interaction ~5.4 kcal mol−1, while the contribution to the binding due to the amino acid side chains was found to be up to ~5 kcal mol−1 for tryptophan but lower, to a point where it was slightly destabilizing, for glutamic acid. The effects of the interplay between van der Waals, hydrophobic, and polar solvation interactions on the various aspects of the binding of the amino acids, which were grouped as aromatic, charged, polar and hydrophobic, are discussed. Although π–π interactions were dominant, surfactant-like and hydrophobic effects were also observed. In the molecular dynamics simulations, the interacting residues displayed a tendency to visit configurations (i.e., regions of the Ramachandran plot) that were absent when C60 was not present. The amino acid backbone assumed a “tepee-like” geometrical structure to maximize interactions with the fullerene cage. Well-defined conformations of the most interactive amino acids (Trp, Arg, Met) side chains were identified upon C60 binding.
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5
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Intrinsically disordered protein regions and phase separation: sequence determinants of assembly or lack thereof. Emerg Top Life Sci 2021; 4:307-329. [PMID: 33078839 DOI: 10.1042/etls20190164] [Citation(s) in RCA: 130] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/23/2020] [Accepted: 09/28/2020] [Indexed: 02/07/2023]
Abstract
Intrinsically disordered protein regions (IDRs) - regions that do not fold into a fixed three-dimensional structure but instead exist in a heterogeneous ensemble of conformations - have recently entered mainstream cell biology in the context of liquid-liquid phase separation (LLPS). IDRs are frequently found to be enriched in phase-separated compartments. Due to this observation, the presence of an IDR in a protein is frequently assumed to be diagnostic of its ability to phase separate. In this review, we clarify the role of IDRs in biological assembly and explore the physical principles through which amino acids can confer the attractive molecular interactions that underlie phase separation. While some disordered regions will robustly drive phase separation, many others will not. We emphasize that rather than 'disorder' driving phase separation, multivalency drives phase separation. As such, whether or not a disordered region is capable of driving phase separation will depend on the physical chemistry encoded within its amino acid sequence. Consequently, an in-depth understanding of that physical chemistry is a prerequisite to make informed inferences on how and why an IDR may be involved in phase separation or, more generally, in protein-mediated intermolecular interactions.
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6
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Cloutier TK, Sudrik C, Mody N, Hasige SA, Trout BL. Molecular computations of preferential interactions of proline, arginine.HCl, and NaCl with IgG1 antibodies and their impact on aggregation and viscosity. MAbs 2021; 12:1816312. [PMID: 32938318 PMCID: PMC7531574 DOI: 10.1080/19420862.2020.1816312] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Preferential interactions of excipients with the antibody surface govern their effect on the stability of antibodies in solution. We probed the preferential interactions of proline, arginine.HCl (Arg.HCl), and NaCl with three therapeutically relevant IgG1 antibodies via experiment and simulation. With simulations, we examined how excipients interacted with different types of surface patches in the variable region (Fv). For example, proline interacted most strongly with aromatic surfaces, Arg.HCl was included near negative residues, and NaCl was excluded from negative residues and certain hydrophobic regions. The differences in interaction of different excipients with the same surface patch on an antibody may be responsible for variations in the antibody's aggregation, viscosity, and self-association behaviors in each excipient. Proline reduced self-association for all three antibodies and reduced aggregation for the antibody with an association-limited aggregation mechanism. The effects of Arg.HCl and NaCl on aggregation and viscosity were highly dependent on the surface charge distribution and the extent of exclusion from highly hydrophobic patches. At pH 5.5, both tended to increase the aggregation of an antibody with a strongly positive charge on the Fv, while only NaCl reduced the aggregation of the antibody with a large negative charge patch on the Fv. Arg.HCl reduced the viscosities of antibodies with either a hydrophobicity-driven mechanism or a charge-driven mechanism. Analysis of this data presents a framework for understanding how amino acid and ionic excipients interact with different protein surfaces, and how these interactions translate to the observed stability behavior.
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Affiliation(s)
- Theresa K Cloutier
- Department of Chemical Engineering, Massachusetts Institute of Technology , Cambridge, Maryland, USA
| | - Chaitanya Sudrik
- Department of Chemical Engineering, Massachusetts Institute of Technology , Cambridge, Maryland, USA
| | - Neil Mody
- Dosage Form Design and Development, AstraZeneca , Gaithersburg, Maryland, USA
| | - Sathish A Hasige
- Dosage Form Design and Development, AstraZeneca , Gaithersburg, Maryland, USA
| | - Bernhardt L Trout
- Department of Chemical Engineering, Massachusetts Institute of Technology , Cambridge, Maryland, USA
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7
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Ye Y, Huo X, Yin Z. Protein-protein interactions at high concentrations: Effects of ArgHCl and NaCl on the stability, viscosity and aggregation mechanisms of protein solution. Int J Pharm 2021; 601:120535. [PMID: 33811966 DOI: 10.1016/j.ijpharm.2021.120535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/10/2021] [Accepted: 03/22/2021] [Indexed: 10/21/2022]
Abstract
The aim of this work was to use the diffusion coefficient ration (Dm/Dline) as a parameter to characterize the stability of protein at high concentration, to compare the effects of ArgHCl and NaCl on the interaction of highly concentrated proteins under different pH conditions, and to explore the correlation with protein stability. For this purpose, a high-concentration bovine serum albumin solution (BSA) was selected as the model system, and the diffusion coefficient, aggregation degree, conformational stability, and solution viscosity of the protein were studied by dynamic light scattering (DLS) and spectral detection techniques. The result showed that there was a significant correlation between the Dm/Dline and the protein aggregation. The Dm/Dline of the protein was minimum at pH 7.4, which corresponded to the maximum degree of aggregation and the highest solution viscosity. At pH 7.4, the hydrophobic interactions and the increased conformational stability of ArgHCl maximized the stability of the protein and reduced the viscosity of the solution by 69.3%. At pH 3.0, the strong charge shielding effect of ArgHCl and NaCl and the decreased conformational stability induced protein aggregation and the gel formation. These findings provided valuable insights into the mechanism of protein aggregation and the diffusion coefficient ration (Dm/Dline) could be a potential tool for the pre-formulation studies.
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Affiliation(s)
- Yalin Ye
- Key Laboratory of Drug Targeting and Novel Drug Delivery System Ministry of Education, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China
| | - Xingli Huo
- Key Laboratory of Drug Targeting and Novel Drug Delivery System Ministry of Education, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China
| | - Zongning Yin
- Key Laboratory of Drug Targeting and Novel Drug Delivery System Ministry of Education, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China.
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8
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Park H, Jin Seo H, Hong SH, Ha ES, Lee S, Kim JS, Baek IH, Kim MS, Hwang SJ. Characterization and therapeutic efficacy evaluation of glimepiride and L-arginine co-amorphous formulation prepared by supercritical antisolvent process: Influence of molar ratio and preparation methods. Int J Pharm 2020; 581:119232. [PMID: 32240805 DOI: 10.1016/j.ijpharm.2020.119232] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/27/2020] [Accepted: 03/14/2020] [Indexed: 11/30/2022]
Abstract
The glimepiride/L-arginine (GA) binary systems were prepared at various molar ratios by using a supercritical antisolvent (SAS) process. For comparison, the GA system was also prepared by physical mixing (PM), melt quenching (MQ), and solvent evaporation (SE) methods. Analyses by DSC and PXRD showed that only the GA binary mixture at 1:1 M ratio prepared by the SAS process was a pure co-amorphous mixture with an excellent content uniformity. On the other hand, GA mixture prepared by PM and SE were not pure co-amorphous systems and contained crystalline eutectic mixture, and MQ method at 170 °C induced the decrease in drug content due to decomposition of glimepiride. The positive deviation of experimentally measured glass transition temperature (Tg) compared to predicted Tg by the Gordon Taylor equation suggests specific molecular interactions between glimepiride and L-arginine in solid-state GA co-amorphous (GACA) mixture. The intermolecular interactions between glimepiride and L-arginine in GACA system were characterized by FT-IR and solid-state NMR analyses. Improved glimepiride dissolution rate of GACA formulation were confirmed using the solubility test, contact angle measurement, and dissolution test. Furthermore, the evaluation of pharmacodynamic hypoglycemic effect demonstrated that GACA prepared by the SAS process significantly improved the therapeutic efficacy of glimepiride.
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Affiliation(s)
- Heejun Park
- College of Pharmacy, Pusan National University, 63 Busandaehak-ro, Geumjeong-gu, Busan 46241, Republic of Korea
| | - Hye Jin Seo
- Yonsei Institute of Pharmaceutical Sciences & College of Pharmacy, Yonsei University, 85 Songdogwahak-ro, Yeonsu-gu, Incheon 21983, Republic of Korea
| | - Seung-Hyeon Hong
- Yonsei Institute of Pharmaceutical Sciences & College of Pharmacy, Yonsei University, 85 Songdogwahak-ro, Yeonsu-gu, Incheon 21983, Republic of Korea
| | - Eun-Sol Ha
- College of Pharmacy, Pusan National University, 63 Busandaehak-ro, Geumjeong-gu, Busan 46241, Republic of Korea
| | - Sibeum Lee
- Advanced Drug Delivery Pharma, 25 Tapsil-ro 35 beon-gil, Giheung-gu, Yongin, Gyeonggi 17084, Republic of Korea
| | - Jeong-Soo Kim
- Dong-A ST Co. Ltd., 21 Geumhwa-ro 105 beon-gil, Giheung-gu, Yongin, Gyeonggi 17073, Republic of Korea
| | - In-Hwan Baek
- College of Pharmacy, Kyungsung University, 309, Suyeong-ro, Nam-gu, Busan 48434, Republic of Korea
| | - Min-Soo Kim
- College of Pharmacy, Pusan National University, 63 Busandaehak-ro, Geumjeong-gu, Busan 46241, Republic of Korea.
| | - Sung-Joo Hwang
- Yonsei Institute of Pharmaceutical Sciences & College of Pharmacy, Yonsei University, 85 Songdogwahak-ro, Yeonsu-gu, Incheon 21983, Republic of Korea.
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9
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Antimicrobial peptide ROAD-1 triggers phase change in local membrane environment to execute its activity. J Mol Model 2019; 25:281. [PMID: 31468141 DOI: 10.1007/s00894-019-4163-8] [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: 02/27/2019] [Accepted: 08/15/2019] [Indexed: 10/26/2022]
Abstract
Emergence of antibiotic-resistant pathogens has paved way for development of newer class of drugs that would not be susceptible to resistance. Antimicrobial peptides such as defensins that target the microbial membrane are promising candidates. ROAD-1 is an alpha-defensin present in the oral cavity of rhesus macaque and shares very high sequence similarity to human enteric defensin 5. In this study we have performed microsecond long all atom molecular dynamic simulations to understand the mechanism of action of ROAD-1. We find that ROAD-1 is able to adopt an energetically stable conformation predominantly stabilized by electrostatic interactions only in presence of bacterial membranes. In mammalian membrane even though it gets absorbed onto the bilayer, it is unable to adopt an equilibrium conformation. Binding of ROAD-1 to bilayer induces clustering of POPG molecules up to 15 Å around the peptide. POPG molecules show higher order parameters than the neighboring POPE implying coexistence of different phases. Analysis of binding free energy of ROAD-1-membrane complex indicates Arg1, Arg2, Arg7, and Arg25 to play key role in its antimicrobial activity. Unlike its homolog HD5, ROAD-1 is not observed to form a dimer. Our study gives insight into the membrane-bound conformation of ROAD-1 and its mechanism of action that can aid in designing defensin-based therapeutics. Graphical abstract Antimicrobial peptide ROAD-1 adopts a different membrane-bound conformation as compared with HD5 even though they belong to the same family implying a different mechanism of action.
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10
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Austerberry JI, Thistlethwaite A, Fisher K, Golovanov AP, Pluen A, Esfandiary R, van der Walle CF, Warwicker J, Derrick JP, Curtis R. Arginine to Lysine Mutations Increase the Aggregation Stability of a Single-Chain Variable Fragment through Unfolded-State Interactions. Biochemistry 2019; 58:3413-3421. [DOI: 10.1021/acs.biochem.9b00367] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- James I. Austerberry
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Angela Thistlethwaite
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Karl Fisher
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Alexander P. Golovanov
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, United Kingdom
- School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Alain Pluen
- Manchester Pharmacy School, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Reza Esfandiary
- Dosage Form Design & Development, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | | | - Jim Warwicker
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, United Kingdom
- School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Jeremy P. Derrick
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Robin Curtis
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, United Kingdom
- School of Chemical Engineering and Analytical Science, University of Manchester, Manchester M1 7DN, United Kingdom
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11
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Hirano A, Shiraki K, Kameda T. Effects of Arginine on Multimodal Chromatography: Experiments and Simulations. Curr Protein Pept Sci 2018; 20:40-48. [DOI: 10.2174/1389203718666171024115407] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/01/2017] [Accepted: 09/09/2017] [Indexed: 11/22/2022]
Abstract
Multimodal or mixed-mode chromatography can be used to separate various proteins, including
antibodies. The separation quality and efficiency have been improved by the addition of solutes, especially
arginine. This review summarizes the mechanism underlying the effects of arginine on protein
elution in multimodal chromatography with neutral, anionic or cationic resin ligands; the mechanism has
been investigated using experiments and molecular dynamics simulations. Arginine is effective in facilitating
protein elution compared to salts and protein denaturants such as guanidine and urea. The unique
elution effect of arginine can be explained by the interplay among arginine, proteins and the resin
ligands. Arginine exhibits multiple binding modes for the ligands and further affinity for protein aromatic
residues through its guanidinium group. These properties make arginine versatile for protein elution
in multimodal chromatography. Taking into account that arginine is an aggregation suppressor for
proteins but not a protein denaturant, arginine is a promising protein-eluting reagent for multimodal
chromatography.
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Affiliation(s)
- Atsushi Hirano
- Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8565, Japan
| | - Kentaro Shiraki
- Institute of Applied Physics, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Koto, Tokyo 135-0064, Japan
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12
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Arginine refolds, stabilizes, and restores function of mutant pVHL proteins in animal model of the VHL cancer syndrome. Oncogene 2018; 38:1038-1049. [PMID: 30194449 DOI: 10.1038/s41388-018-0491-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 05/09/2018] [Accepted: 08/15/2018] [Indexed: 01/01/2023]
Abstract
The von Hippel-Lindau (VHL) syndrome is a rare inherited cancer, caused by mutations in the VHL gene, many of which render the VHL protein (pVHL) unstable. pVHL is a tumor-suppressor protein implicated in a variety of cellular processes, most notably in response to changes in oxygen availability, due to its role as part of an E3-ligase complex which targets the hypoxia-inducible factor (HIF) for degradation. Previously we reported, using in silico and in vitro analyses, that common oncogenic VHL mutations render pVHL less stable than the wild-type protein, distort its core domain and as a result reduce the ability of the protein to bind its target HIF-1α. Among various chemical chaperones tested, arginine was the most effective in refolding mutant of pVHL. Here we examined the consequences of administering L- or D-arginine to a Drosophila VHL model and to human renal carcinoma cells, both expressing misfolded versions of human pVHL. Arginine treatment increased pVHL solubility in both models and increased the half-life of the mutant pVHL proteins in the cell culture. In both models, L- as well as D-arginine enhanced the ability of wild-type pVHL and certain misfolded mutant versions of pVHL to bind ODD, the HIF-derived target peptide, reflecting restoration of pVHL function. Moreover, continuous feeding of Drosophila expressing misfolded versions of pVHL either L- or D-arginine rich diet rescued their lethal phenotype. Collectively, these in vivo results suggest that arginine supplementation should be examined as a potential novel treatment for VHL cancer syndrome.
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13
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Salt-dependent elution of uncharged aromatic solutes in ion-exchange chromatography. J Chromatogr A 2018; 1546:46-55. [DOI: 10.1016/j.chroma.2018.02.049] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 02/15/2018] [Accepted: 02/23/2018] [Indexed: 01/22/2023]
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14
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Hong T, Iwashita K, Shiraki K. Viscosity Control of Protein Solution by Small Solutes: A Review. Curr Protein Pept Sci 2018; 19:746-758. [PMID: 29237380 PMCID: PMC6182935 DOI: 10.2174/1389203719666171213114919] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 12/01/2017] [Accepted: 12/02/2017] [Indexed: 12/22/2022]
Abstract
Viscosity of protein solution is one of the most troublesome issues for the high-concentration formulation of protein drugs. In this review, we summarize the practical methods that suppress the viscosity of protein solution using small molecular additives. The small amount of salts decreases the viscosity that results from electrostatic repulsion and attraction. The chaotrope suppresses the hydrophobic attraction and cluster formation, which can lower the solution viscosity. Arginine hydrochloride (ArgHCl) also suppresses the solution viscosity due to the hydrophobic and aromatic interactions between protein molecules. The small molecular additives are the simplest resolution of the high viscosity of protein solution as well as understanding of the primary cause in complex phenomena of protein interactions.
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Affiliation(s)
- Taehun Hong
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki305-8573, Japan
| | - Kazuki Iwashita
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki305-8573, Japan
| | - Kentaro Shiraki
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki305-8573, Japan
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15
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Cui PF, Zhuang WR, Hu X, Xing L, Yu RY, Qiao JB, He YJ, Li F, Ling D, Jiang HL. A new strategy for hydrophobic drug delivery using a hydrophilic polymer equipped with stacking units. Chem Commun (Camb) 2018; 54:8218-8221. [DOI: 10.1039/c8cc04363a] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A highly hydrophilic polymer was used to deliver aromatic ring-containing hydrophobic agent doxorubicin (DOX) via π–π interaction.
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16
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Charge state of arginine as an additive on heat-induced protein aggregation. Int J Biol Macromol 2016; 87:563-9. [DOI: 10.1016/j.ijbiomac.2016.03.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/08/2016] [Accepted: 03/09/2016] [Indexed: 01/28/2023]
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17
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Kyriakou PK, Ekblad B, Kristiansen PE, Kaznessis YN. Interactions of a class IIb bacteriocin with a model lipid bilayer, investigated through molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:824-35. [PMID: 26774214 DOI: 10.1016/j.bbamem.2016.01.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 01/06/2016] [Accepted: 01/12/2016] [Indexed: 01/15/2023]
Abstract
The emergence of antibiotic resistant microorganisms poses an alarming threat to global health. Antimicrobial peptides (AMPs) are considered a possible effective alternative to conventional antibiotic therapies. An understanding of the mechanism of action of AMPs is needed in order to better control and optimize their bactericidal activity. Plantaricin EF is a heterodimeric AMP, consisting of two peptides Plantaricin E (PlnE) and Plantaricin F (PlnF). We studied the behavior of these peptides on the surface of a model lipid bilayer. We identified the residues that facilitate peptide-peptide interactions. We also identified residues that mediate interactions of the dimer with the membrane. PlnE interacts with the membrane through amino acids at both its termini, while only the N terminus of PlnF approaches the membrane. By comparing the activity of single-site mutants of the two-peptide bacteriocin and the simulations of the bacteriocin on the surface of a model lipid bilayer, structure activity relationships are proposed. These studies allow us to generate hypotheses that relate biophysical interactions observed in simulations with the experimentally measured activity. We find that single-site amino acid substitutions result in markedly stronger antimicrobial activity when they strengthen the interactions between the two peptides, while, concomitantly, they weaken peptide-membrane association. This effect is more pronounced in the case of the PlnE mutant (G20A), which interacts the strongest with PlnF and the weakest with the membrane while displaying the highest activity.
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Affiliation(s)
- Panagiota K Kyriakou
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, United States
| | - Bie Ekblad
- Department of Biosciences, University of Oslo, Post box 1041 Blindern, 0316 Oslo, Norway
| | - Per Eugen Kristiansen
- Department of Biosciences, University of Oslo, Post box 1041 Blindern, 0316 Oslo, Norway
| | - Yiannis N Kaznessis
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, United States.
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Hirano A, Arakawa T, Kameda T. Effects of arginine on multimodal anion exchange chromatography. Protein Expr Purif 2015. [DOI: 10.1016/j.pep.2015.07.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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19
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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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20
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21
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Shah D, Shaikh AR. Interaction of arginine, lysine, and guanidine with surface residues of lysozyme: implication to protein stability. J Biomol Struct Dyn 2015; 34:104-14. [PMID: 25730443 DOI: 10.1080/07391102.2015.1013158] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Additives are widely used to suppress aggregation of therapeutic proteins. However, the molecular mechanisms of effect of additives to stabilize proteins are still unclear. To understand this, we herein perform molecular dynamics simulations of lysozyme in the presence of three commonly used additives: arginine, lysine, and guanidine. These additives have different effects on stability of proteins and have different structures with some similarities; arginine and lysine have aliphatic side chain, while arginine has a guanidinium group. We analyze atomic contact frequencies to study the interactions of the additives with individual residues of lysozyme. Contact coefficient, quantified from contact frequencies, is helpful in analyzing the interactions with the guanidine groups as well as aliphatic side chains of arginine and lysine. Strong preference for contacts to the additives (over water) is seen for the acidic followed by polar and the aromatic residues. Further analysis suggests that the hydration layer around the protein surface is depleted more in the presence of arginine, followed by lysine and guanidine. Molecular dynamics simulations also reveal that the internal dynamics of protein, as indicated by the lifetimes of the hydrogen bonds within the protein, changes depending on the additives. Particularly, we note that the side-chain hydrogen-bonding patterns within the protein differ with the additives, with several side-chain hydrogen bonds missing in the presence of guanidine. These results collectively indicate that the aliphatic chain of arginine and lysine plays a critical role in the stabilization of the protein.
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Affiliation(s)
- Dhawal Shah
- a Petroleum and Chemical Engineering Department , Sultan Qaboos University , Muscat , Oman
| | - Abdul Rajjak Shaikh
- b Department of Chemical Sciences and Engineering , Kobe University , Kobe , Japan
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22
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Nuhu MM, Curtis R. Arginine dipeptides affect insulin aggregation in a pH- and ionic strength-dependent manner. Biotechnol J 2015; 10:404-16. [PMID: 25611817 DOI: 10.1002/biot.201400190] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 12/17/2014] [Accepted: 01/20/2015] [Indexed: 12/29/2022]
Abstract
Solutions containing arginine or mixtures of arginine and other amino acids are commonly used for protein liquid formulations to overcome problems such as high viscosities, aggregation, and phase separation. The aim of this work is to examine whether the stabilizing properties of arginine can be improved by incorporating the amino acid into a dipeptide. A series of arginine-containing dipeptides have been tested for their ability to suppress insulin aggregation over a range of pH and ionic strength. The aggregation is monitored at room temperature using a combination of turbidimetry and light scattering for solutions at pH 5.5 or 3.7, whereas thermal-induced aggregation is measured at pH 7.5. In addition, intrinsic fluorescence has been used to quantify additive binding to insulin. The dipeptide diArg is the most effective additive in solutions at pH 5.5 and 3.7, whereas the dipeptide Arg-Phe almost completely eliminates thermally-induced aggregation of insulin at pH 7.5 up to temperature of 90°C. Insulin has been chosen as a model system because the molecular forces controlling its aggregation are well known. From this understanding, we are able to provide a molecular basis for how the various dipeptides affect insulin aggregation.
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Affiliation(s)
- Mariam M Nuhu
- School of Chemical Engineering and Analytical Sciences, The University of Manchester, Manchester, United Kingdom
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23
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Shah D, Mjalli FS. Effect of water on the thermo-physical properties of Reline: An experimental and molecular simulation based approach. Phys Chem Chem Phys 2014; 16:23900-7. [DOI: 10.1039/c4cp02600d] [Citation(s) in RCA: 213] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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24
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Hirano A, Tanaka T, Kataura H, Kameda T. Arginine Side Chains as a Dispersant for Individual Single-Wall Carbon Nanotubes. Chemistry 2014; 20:4922-30. [DOI: 10.1002/chem.201400003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Indexed: 12/11/2022]
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25
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Hirano A, Arakawa T, Kameda T. Interaction of arginine with Capto MMC in multimodal chromatography. J Chromatogr A 2014; 1338:58-66. [DOI: 10.1016/j.chroma.2014.02.053] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 02/18/2014] [Accepted: 02/18/2014] [Indexed: 12/01/2022]
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Calvaresi M, Zerbetto F. The devil and holy water: protein and carbon nanotube hybrids. Acc Chem Res 2013; 46:2454-63. [PMID: 23826731 DOI: 10.1021/ar300347d] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Integrating carbon nanotubes (CNTs) with biological systems to form hybrid functional assemblies is an innovative research area with great promise for medical, nanotechnology, and materials science applications. The specifics of molecular recognition and catalytic activity of proteins combined with the mechanical and electronic properties of CNTs provides opportunities for physicists, chemists, biologists, and materials scientists to understand and develop new nanomachines, sensors, or any of a number of other molecular assemblies. Researchers know relatively little about the structure, function, and spatial orientation of proteins noncovalently adsorbed on CNTs, yet because the interaction of CNTs with proteins depends strongly on the tridimensional structure of the proteins, many of these questions can be answered in simple terms. In this Account, we describe recent research investigating the properties of CNT/protein hybrids. Proteins act to solvate CNTs and may sort them according to diameter or chirality. In turn, CNTs can support and immobilize enzymes, creating functional materials. Additional applications include proteins that assemble ordered hierarchical objects containing CNTs, and CNTs that act as protein carriers for vaccines, for example. Protein/CNT hybrids can form bioscaffolds and can serve as therapeutic and imaging materials. Proteins can detect CNTs or coat them to make them biocompatible. One of the more challenging applications for protein/CNT hybrids is to make CNT substrates for cell growth and neural interfacing applications. The challenge arises from the structures' interactions with living cells, which poses questions surrounding the (nano)toxicology of CNTs and whether and how CNTs can detect biological processes or sense them as they occur. The surface chemistry of CNTs and proteins, including interactions such as π-π stacking interactions, hydrophobic interactions, surfactant-like interactions, and charge-π interactions, governs the wealth of structures, processes, and functions that appear when such different types of molecules interact. Each residue stars in one of two main roles, and understanding which residues are best suited for which type of interaction can lead to the design of new hybrids. Nonlocally, the peptide or protein primary, secondary, and tertiary structures govern the binding of proteins by CNTs. The conjugation of proteins with CNTs presents some serious difficulties both experimentally and culturally (such as bridging the "jargon barrier" across disciplines). The intersection of these fields lies between communities characterized by distinctly different approaches and methodologies. However, the examples of this Account illustrate that when this barrier is overcome, the exploitation of hybrid CNT-protein systems offers great potential.
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Affiliation(s)
- Matteo Calvaresi
- Dipartimento di Chimica “G. Ciamician”, Università di Bologna, V. F. Selmi 2, 40126 Bologna, Italy
| | - Francesco Zerbetto
- Dipartimento di Chimica “G. Ciamician”, Università di Bologna, V. F. Selmi 2, 40126 Bologna, Italy
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27
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Lima MA, Oliveira-Neto M, Kadowaki MAS, Rosseto FR, Prates ET, Squina FM, Leme AFP, Skaf MS, Polikarpov I. Aspergillus niger β-glucosidase has a cellulase-like tadpole molecular shape: insights into glycoside hydrolase family 3 (GH3) β-glucosidase structure and function. J Biol Chem 2013; 288:32991-3005. [PMID: 24064212 DOI: 10.1074/jbc.m113.479279] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aspergillus niger is known to secrete large amounts of β-glucosidases, which have a variety of biotechnological and industrial applications. Here, we purified an A. niger β-glucosidase (AnBgl1) and conducted its biochemical and biophysical analyses. Purified enzyme with an apparent molecular mass of 116 kDa forms monomers in solution as judged by native gel electrophoresis and has a pI value of 4.55, as found for most of the fungi of β-glucosidases. Surprisingly, the small angle x-ray experiments reveal that AnBgl1 has a tadpole-like structure, with the N-terminal catalytic domain and C-terminal fibronectin III-like domain (FnIII) connected by the long linker peptide (∼100 amino acid residues) in an extended conformation. This molecular organization resembles the one adopted by other cellulases (such as cellobiohydrolases, for example) that frequently contain a catalytic domain linked to the cellulose-binding module that mediates their binding to insoluble and polymeric cellulose. The reasons why AnBgl1, which acts on the small soluble substrates, has a tadpole molecular shape are not entirely clear. However, our enzyme pulldown assays with different polymeric substrates suggest that AnBgl1 has little or no capacity to bind to and to adsorb cellulose, xylan, and starch, but it has high affinity to lignin. Molecular dynamics simulations suggested that clusters of residues located in the C-terminal FnIII domain interact strongly with lignin fragments. The simulations showed that numerous arginine residues scattered throughout the FnIII surface play an important role in the interaction with lignin by means of cation-π stacking with the lignin aromatic rings. These results indicate that the C-terminal FnIII domain could be operational for immobilization of the enzyme on the cell wall and for the prevention of unproductive binding of cellulase to the biomass lignin.
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Affiliation(s)
- Marisa A Lima
- From the Instituto de Física de São Carlos, Universidade de São Paulo, Caixa Postal 369, São Carlos 13560-970, SP
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Structure-activity relations of myxinidin, an antibacterial peptide derived from the epidermal mucus of hagfish. Antimicrob Agents Chemother 2013; 57:5665-73. [PMID: 24002100 DOI: 10.1128/aac.01341-13] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The structure-activity relations of myxinidin, a peptide derived from epidermal mucus of hagfish, Myxine glutinosa L., were investigated. Analysis of key residues allowed us to design new peptides with increased efficiency. Antimicrobial activity of native and modified peptides demonstrated the key role of uncharged residues in the sequence; the loss of these residues reduces almost entirely myxinidin antimicrobial activity, while insertion of arginine at charged and uncharged position increases antimicrobial activity compared with that of native myxinidin. Particularly, we designed a peptide capable of achieving a high inhibitory effect on bacterial growth. Experiments were conducted using both Gram-negative and Gram-positive bacteria. Nuclear magnetic resonance (NMR) studies showed that myxinidin is able to form an amphipathic α-helical structure at the N terminus and a random coil region at the C terminus.
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29
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Shmueli MD, Schnaider L, Rosenblum D, Herzog G, Gazit E, Segal D. Structural insights into the folding defects of oncogenic pVHL lead to correction of its function in vitro. PLoS One 2013; 8:e66333. [PMID: 23840444 PMCID: PMC3688787 DOI: 10.1371/journal.pone.0066333] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 05/04/2013] [Indexed: 01/22/2023] Open
Abstract
Loss of function mutations in the von Hippel-Lindau (pVHL) tumor suppressor protein are tumorigenic. In silico analysis of the structure and folding of WT pVHL identified in its core an aromatic tetrahedron, essential for stabilizing the protein. The mutations disrupt the aromatic tetrahedron, leading to misfolding of pVHL. Using biophysical methods we confirmed the in silico predictions, demonstrating that mutant pVHL proteins have lower stability than the WT, distort the core domain and as a result reduce the ability of the protein to bind its target HIF-1α. Using bacterial pVHL-EGFP based assay we screened for osmolytes capable of restoring folding of mutant pVHL. Among them, Arginine was the most effective and was verified by in vitro assays as a potent re-folder of pVHL. This resulted in functional restoration of the mutant proteins to the level of the WT.
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Affiliation(s)
- Merav D. Shmueli
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Lee Schnaider
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Daniel Rosenblum
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Gal Herzog
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Daniel Segal
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- * E-mail:
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30
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Hirano A, Kameda T, Shinozaki D, Arakawa T, Shiraki K. Molecular Dynamics Simulation of the Arginine-Assisted Solubilization of Caffeic Acid: Intervention in the Interaction. J Phys Chem B 2013; 117:7518-27. [DOI: 10.1021/jp401609p] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Atsushi Hirano
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8562, Japan
| | - Tomoshi Kameda
- Computational Biology Research
Center (CBRC), Advanced Industrial Science and Technology (AIST), Koto, Tokyo 135-0064, Japan
| | - Daisuke Shinozaki
- Institute of Applied Physics, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
| | - Tsutomu Arakawa
- Alliance Protein Laboratories, San Diego, California 92121, United States
| | - Kentaro Shiraki
- Institute of Applied Physics, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
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31
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Smirnova E, Safenkova I, Stein-Margolina B, Shubin V, Gurvits B. L-arginine induces protein aggregation and transformation of supramolecular structures of the aggregates. Amino Acids 2013; 45:845-55. [PMID: 23744402 DOI: 10.1007/s00726-013-1528-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Accepted: 05/29/2013] [Indexed: 12/14/2022]
Abstract
Protein misfolding, self-assembly, and aggregation are an essential problem in cell biology, biotechnology, and biomedicine. The protein aggregates are very different morphologically varying from soluble amorphous aggregates to highly ordered amyloid-like fibrils. The objective of this study was to elucidate the role of the amino acid L-arginine (Arg), a widely used suppressor of protein aggregation, in the regulation of transformations of soluble aggregation-prone proteins into supramolecular structures of higher order. However, a striking potential of Arg to govern the initial events in the process of protein aggregation has been revealed under environment conditions where the protein aggregation in its absence was not observed. Using dynamic light scattering we have demonstrated that Arg (10-100 mM) dramatically accelerated the dithiothreitol-induced aggregation of acidic model proteins. The inhibitory effect on the protein aggregation was revealed at higher concentrations of Arg. Using atomic force microscopy it was shown that aggregation of α-lactalbumin from bovine milk induced upon addition of Arg reached a state of formation of supramolecular structures of non-fibrillar species profoundly differing from those of the individual protein in type, size, and shape. The interaction of another positively charged amino acid L-lysine with α-lactalbumin also resulted in profound acceleration of the aggregation process and transformation of supramolecular structures of the aggregates.
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Affiliation(s)
- Ekaterina Smirnova
- A. N. Bach Institute of Biochemistry, Russian Academy of Sciences, 119071, Moscow, Russia
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32
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Li J, Lakshminarayanan R, Bai Y, Liu S, Zhou L, Pervushin K, Verma C, Beuerman RW. Molecular dynamics simulations of a new branched antimicrobial peptide: a comparison of force fields. J Chem Phys 2013; 137:215101. [PMID: 23231260 DOI: 10.1063/1.4768899] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Branched antimicrobial peptides are promising as a new class of antibiotics displaying high activity and low toxicity and appear to work through a unique mechanism of action. We explore the structural dynamics of a covalently branched 18 amino acid peptide (referred to as B2088) in aqueous and membrane mimicking environments through molecular dynamics (MD) simulations. Towards this, we carry out conventional MD simulations and supplement these with replica exchange simulations. The simulations are carried out using four different force fields that are commonly employed for simulating biomolecular systems. These force fields are GROMOS53a6, CHARMM27 with cMAP, CHARMM27 without cMAP and AMBER99sb. The force fields are benchmarked against experimental data available from circular dichroism and nuclear magnetic resonance spectroscopies, and show that CHARMM27 without cMAP correction is the most successful in reproducing the structural dynamics of B2088 both in water and in the presence of micelles. Although the four force fields predict different structures of B2088, they all show that B2088 stabilizes against the head group of the lipid through hydrogen bonding of its Lys and Arg side chains. This leads us to hypothesize that B2088 is unlikely to penetrate into the hydrophobic region of the membrane owing to the high free energy costs of transfer from water, and possibly acts by carpeting and thus disrupting the membrane.
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Affiliation(s)
- Jianguo Li
- Singapore Eye Research Institute, 11 Third Hospital Avenue, #06-00, Singapore 168751.
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33
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Vagenende V, Han AX, Mueller M, Trout BL. Protein-associated cation clusters in aqueous arginine solutions and their effects on protein stability and size. ACS Chem Biol 2013; 8:416-22. [PMID: 23138654 DOI: 10.1021/cb300440x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Arginine is one of the most prominent residues in protein interactions, and arginine hydrochloride is widely used as an additive in protein solutions because of its exceptional effects on protein association and folding. The molecular origins of arginine effects on protein processes remain, however, controversial, and little is known about the molecular interactions between arginine cations and protein surfaces in aqueous arginine solutions. In this study, we report a unique biochemical phenomenon whereby clusters of arginine cations (Arg(+)) are associated with a protein surface. The formation of protein-associated Arg(+) clusters is initiated by Arg(+) ions that associate with specific protein surface loci through cooperative interactions with protein guanidinium and carboxyl groups. Molecular dynamics simulations indicate that protein-associated Arg(+) ions subsequently attract other Arg(+) ions and form dynamic cation clusters that extend further than 10 Å from the protein surface. The effects of arginine on the thermal stability and size of lysozyme and ovalbumin are measured over a wide concentration range (0 to 2 M), and we find that the formation of protein-associated Arg(+) clusters consistently explains the complex effects of arginine on protein stability and size. This study elucidates the molecular mechanisms and implications of cluster formation of Arg(+) ions at a protein surface, and the findings of this study may be used to manipulate synthetic and biological systems through arginine-derived groups.
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Affiliation(s)
- Vincent Vagenende
- Bioprocessing Technology
Institute, A*STAR (Agency for Science, Technology and Research), 20 Biopolis Way #06-01 Centros, 138668 Singapore
| | - Alvin X. Han
- Bioprocessing Technology
Institute, A*STAR (Agency for Science, Technology and Research), 20 Biopolis Way #06-01 Centros, 138668 Singapore
| | - Monika Mueller
- Bioprocessing Technology
Institute, A*STAR (Agency for Science, Technology and Research), 20 Biopolis Way #06-01 Centros, 138668 Singapore
| | - Bernhardt L. Trout
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts
Avenue, Cambridge, E19-502b, Massachusetts 02139, United States
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Li J, Liu S, Lakshminarayanan R, Bai Y, Pervushin K, Verma C, Beuerman RW. Molecular simulations suggest how a branched antimicrobial peptide perturbs a bacterial membrane and enhances permeability. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1828:1112-21. [PMID: 23274275 DOI: 10.1016/j.bbamem.2012.12.015] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 12/03/2012] [Accepted: 12/18/2012] [Indexed: 11/29/2022]
Abstract
A covalently, branched antimicrobial peptide (BAMP) B2088 demonstrating enhanced antimicrobial effects and without additional toxicity when compared to its linear counterpart, has been developed. Atomistic molecular dynamics simulations have been used to investigate the mode of interaction of B2088 with model bacterial and mammalian membranes. These simulations suggest that both long-range electrostatic interactions and short-range hydrogen bonding play important roles in steering B2088 toward the negatively charged membranes. The reason why B2088 is selective towards the bacterial membrane is postulated to be the greater density of negative charges on the bacterial membrane which enables rapid accumulation of B2088 on the bacterial membrane to a high surface concentration, stabilizing it through excess hydrogen bond formation. The majority of hydrogen bonds are seen between the side chains of the basic residues (Arg or Lys) with the PO4 groups of lipids. In particular, formation of the bidentate hydrogen bonds between the guanidinium group of Arg and PO4 groups are found to be more favorable, both geometrically and energetically. Moreover, the planar gaunidinium group and its hydrophobic character enable the Arg side chains to solvate into the hydrophobic membrane. Structural perturbation of the bacterial membrane is found to be concentration dependent and is significant at higher concentrations of B2088, resulting in a large number of water translocations across the bacterial membrane. These simulations enhance our understanding of the action mechanism of a covalently branched antimicrobial peptide with model membranes and provide practical guidance for the design of new antimicrobial peptides.
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Affiliation(s)
- Jianguo Li
- Singapore Eye Research Institute, Singapore, Singapore
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35
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Bai Y, Liu S, Li J, Lakshminarayanan R, Sarawathi P, Tang C, Ho D, Verma C, Beuerman RW, Pervushin K. Progressive structuring of a branched antimicrobial peptide on the path to the inner membrane target. J Biol Chem 2012; 287:26606-17. [PMID: 22700968 DOI: 10.1074/jbc.m112.363259] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
In recent years, interest has grown in the antimicrobial properties of certain natural and non-natural peptides. The strategy of inserting a covalent branch point in a peptide can improve its antimicrobial properties while retaining host biocompatibility. However, little is known regarding possible structural transitions as the peptide moves on the access path to the presumed target, the inner membrane. Establishing the nature of the interactions with the complex bacterial outer and inner membranes is important for effective peptide design. Structure-activity relationships of an amphiphilic, branched antimicrobial peptide (B2088) are examined using environment-sensitive fluorescent probes, electron microscopy, molecular dynamics simulations, and high resolution NMR in solution and in condensed states. The peptide is reconstituted in bacterial outer membrane lipopolysaccharide extract as well as in a variety of lipid media mimicking the inner membrane of Gram-negative pathogens. Progressive structure accretion is observed for the peptide in water, LPS, and lipid environments. Despite inducing rapid aggregation of bacteria-derived lipopolysaccharides, the peptide remains highly mobile in the aggregated lattice. At the inner membranes, the peptide undergoes further structural compaction mediated by interactions with negatively charged lipids, probably causing redistribution of membrane lipids, which in turn results in increased membrane permeability and bacterial lysis. These findings suggest that peptides possessing both enhanced mobility in the bacterial outer membrane and spatial structure facilitating its interactions with the membrane-water interface may provide excellent structural motifs to develop new antimicrobials that can overcome antibiotic-resistant Gram-negative pathogens.
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Affiliation(s)
- Yang Bai
- Singapore Eye Research Institute, Singapore 168751
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Calvaresi M, Hoefinger S, Zerbetto F. Probing the Structure of Lysozyme-Carbon-Nanotube Hybrids with Molecular Dynamics. Chemistry 2012; 18:4308-13. [DOI: 10.1002/chem.201102703] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Indexed: 11/09/2022]
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Interactions of formulation excipients with proteins in solution and in the dried state. Adv Drug Deliv Rev 2011; 63:1053-73. [PMID: 21756953 DOI: 10.1016/j.addr.2011.06.011] [Citation(s) in RCA: 263] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 06/18/2011] [Accepted: 06/23/2011] [Indexed: 12/12/2022]
Abstract
A variety of excipients are used to stabilize proteins, suppress protein aggregation, reduce surface adsorption, or to simply provide physiological osmolality. The stabilizers encompass a wide variety of molecules including sugars, salts, polymers, surfactants, and amino acids, in particular arginine. The effects of these excipients on protein stability in solution are mainly caused by their interaction with the protein and the container surface, and most importantly with water. Some excipients stabilize proteins in solution by direct binding, while others use a number of fundamentally different mechanisms that involve indirect interactions. In the dry state, any effects that the excipients confer to proteins through their interactions with water are irrelevant, as water is no longer present. Rather, the excipients stabilize proteins through direct binding and their effects on the physical properties of the dried powder. This review will describe a number of mechanisms by which the excipients interact with proteins in solution and with various interfaces, and their effects on the physical properties of the dried protein structure, and explain how the various interaction forces are related to their observed effects on protein stability.
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Shah D, Li J, Shaikh AR, Rajagopalan R. Arginine-aromatic interactions and their effects on arginine-induced solubilization of aromatic solutes and suppression of protein aggregation. Biotechnol Prog 2011; 28:223-31. [DOI: 10.1002/btpr.710] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 06/21/2011] [Indexed: 11/06/2022]
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Shah D, Shaikh AR, Peng X, Rajagopalan R. Effects of arginine on heat-induced aggregation of concentrated protein solutions. Biotechnol Prog 2011; 27:513-20. [DOI: 10.1002/btpr.563] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Revised: 12/13/2010] [Indexed: 11/06/2022]
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Ariki R, Hirano A, Arakawa T, Shiraki K. Arginine increases the solubility of alkyl gallates through interaction with the aromatic ring. ACTA ACUST UNITED AC 2011; 149:389-94. [DOI: 10.1093/jb/mvr004] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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