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Song X, Bu Y. Electric field controlled uphill electron migration along α-helical oligopeptides. Phys Chem Chem Phys 2021; 23:1464-1474. [PMID: 33399139 DOI: 10.1039/d0cp05085g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A systematic study on applied electric field effects (Eapp) on electron transfer along the peptides is very important for the regulation of electron transfer behaviors so as to realize the functions of proteins. In this work, we computationally investigated the uphill migration behaviors of excess electrons along the peptide chains under Eapp using the density functional theory method. We examined the electronic property changes of the model α-helical oligopeptides, the dynamics behavior of an excess electron along the peptide chains under Eapp opposite to the internal dipole field of peptides. We found that Eapp of different intensities can effectively modulate the electron-binding abilities, Frontier molecular orbital (FMO) energies and distributions, dipole moments and other corresponding properties with different degrees. The electron-binding abilities of α-helical oligopeptides revealed by vertical electron affinity and FMO energies decrease in weak Eapp and then increase greatly in high Eapp, while the dipole moments change mildly in weak Eapp and increase significantly until a threshold and then become gentle in high Eapp. Analysis of FMO and electron distributions indicates that an excess electron can migrate uphill from the N-terminus to the C-terminus of the α-helical peptides in an irregular jump mode as Eapp linearly increases. Another interesting finding is that α-helical peptides with diverse chain lengths have different sensitivities to Eapp. The longer the peptide is, the more obvious the effects of Eapp are. Additionally, compared to the Eapp effect on linear oligopeptides, we summarized the systematic rule about the Eapp effect on excess electron migration uphill along the peptide chains. Clearly, this work not only enriches the information of the Eapp effect on electronic properties and electron transfers in the helical peptides, but also provides a new perspective for modulating electron migration behaviors in protein electronics engineering.
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Affiliation(s)
- Xiufang Song
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China.
| | - Yuxiang Bu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China.
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Inayathullah M, Tan A, Jeyaraj R, Lam J, Cho NJ, Liu CW, Manoukian MAC, Ashkan K, Mahmoudi M, Rajadas J. Self-assembly and sequence length dependence on nanofibrils of polyglutamine peptides. Neuropeptides 2016; 57:71-83. [PMID: 26874369 DOI: 10.1016/j.npep.2016.01.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 01/11/2016] [Accepted: 01/31/2016] [Indexed: 10/22/2022]
Abstract
Huntington's disease (HD) is recognized as a currently incurable, inherited neurodegenerative disorder caused by the accumulation of misfolded polyglutamine (polyQ) peptide aggregates in neuronal cells. Yet, the mechanism by which newly formed polyQ chains interact and assemble into toxic oligomeric structures remains a critical, unresolved issue. In order to shed further light on the matter, our group elected to investigate the folding of polyQ peptides - examining glutamine repeat lengths ranging from 3 to 44 residues. To characterize these aggregates we employed a diverse array of technologies, including: nuclear magnetic resonance; circular dichroism; Fourier transform infrared spectroscopy; fluorescence resonance energy transfer (FRET), and atomic force microscopy. The data we obtained suggest that an increase in the number of glutamine repeats above 14 residues results in disordered loop structures, with different repeat lengths demonstrating unique folding characteristics. This differential folding manifests in the formation of distinct nano-sized fibrils, and on this basis, we postulate the idea of 14 polyQ repeats representing a critical loop length for neurotoxicity - a property that we hope may prove amenable to future therapeutic intervention. Furthermore, FRET measurements on aged assemblages indicate an increase in the end-to-end distance of the peptide with time, most probably due to the intermixing of individual peptide strands within the nanofibril. Further insight into this apparent time-dependent reorganization of aggregated polyQ peptides may influence future disease modeling of polyQ-related proteinopathies, in addition to directing novel clinical innovations.
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Affiliation(s)
- Mohammed Inayathullah
- Biomaterials & Advanced Drug Delivery Laboratory (BioADD), Stanford University School of Medicine, Stanford University, Palo Alto, CA, USA; Bioorganic and Neurochemistry Laboratory, Central Leather Research Institute, Adyar, Chennai, Tamilnadu, India; Cardiovascular Pharmacology Division, Cardiovascular Institute, Stanford University School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Aaron Tan
- Biomaterials & Advanced Drug Delivery Laboratory (BioADD), Stanford University School of Medicine, Stanford University, Palo Alto, CA, USA; UCL Medical School, University College London (UCL), London, UK; University College London Hospitals NHS Foundation Trust, London, UK.
| | - Rebecca Jeyaraj
- UCL Medical School, University College London (UCL), London, UK
| | - James Lam
- UCL Medical School, University College London (UCL), London, UK
| | - Nam-Joon Cho
- Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford University, Palo Alto, CA, USA; School of Materials Science and Engineering, Nanyang Technological University, Singapore
| | - Corey W Liu
- Stanford Magnetic Resonance Laboratory, Stanford University, Palo Alto, CA, USA
| | - Martin A C Manoukian
- Department of Dermatology, Stanford University School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Keyoumars Ashkan
- Department of Neurosurgery, King's College Hospital NHS Foundation Trust, King's College London, London, UK
| | - Morteza Mahmoudi
- Biomaterials & Advanced Drug Delivery Laboratory (BioADD), Stanford University School of Medicine, Stanford University, Palo Alto, CA, USA; Nanotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran; Cardiovascular Pharmacology Division, Cardiovascular Institute, Stanford University School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Jayakumar Rajadas
- Biomaterials & Advanced Drug Delivery Laboratory (BioADD), Stanford University School of Medicine, Stanford University, Palo Alto, CA, USA; Cardiovascular Pharmacology Division, Cardiovascular Institute, Stanford University School of Medicine, Stanford University, Palo Alto, CA, USA.
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de la Lande A, Gillet N, Chen S, Salahub DR. Progress and challenges in simulating and understanding electron transfer in proteins. Arch Biochem Biophys 2015; 582:28-41. [PMID: 26116376 DOI: 10.1016/j.abb.2015.06.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Revised: 06/15/2015] [Accepted: 06/22/2015] [Indexed: 11/19/2022]
Abstract
This Review presents an overview of the most common numerical simulation approaches for the investigation of electron transfer (ET) in proteins. We try to highlight the merits of the different approaches but also the current limitations and challenges. The article is organized into three sections. Section 2 deals with direct simulation algorithms of charge migration in proteins. Section 3 summarizes the methods for testing the applicability of the Marcus theory for ET in proteins and for evaluating key thermodynamic quantities entering the reaction rates (reorganization energies and driving force). Recent studies interrogating the validity of the theory due to the presence of non-ergodic effects or of non-linear responses are also described. Section 4 focuses on the tunneling aspects of electron transfer. How can the electronic coupling between charge transfer states be evaluated by quantum chemistry approaches and rationalized? What interesting physics regarding the impact of protein dynamics on tunneling can be addressed? We will illustrate the different sections with examples taken from the literature to show what types of system are currently manageable with current methodologies. We also take care to recall what has been learned on the biophysics of ET within proteins thanks to the advent of atomistic simulations.
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Affiliation(s)
- Aurélien de la Lande
- Laboratoire de Chimie Physique, UMR 8000, CNRS, Université Paris Sud. 15, av. Jean Perrin, 91405 Orsay, France.
| | - Natacha Gillet
- Laboratoire de Chimie Physique, UMR 8000, CNRS, Université Paris Sud. 15, av. Jean Perrin, 91405 Orsay, France
| | - Shufeng Chen
- Laboratoire de Chimie Physique, UMR 8000, CNRS, Université Paris Sud. 15, av. Jean Perrin, 91405 Orsay, France
| | - Dennis R Salahub
- Department of Chemistry, CMS - Centre for Molecular Simulation and IQST - Institute for Quantum Science and Technology, University of Calgary, 2500 University Drive N.W., Calgary, Alberta T2N 1N4, Canada.
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Parks JH, Semrouni D, Clavaguéra C, Ohanessian G. Relationship between Conformational Dynamics and Electron Transfer in a Desolvated Peptide. Part II. Temperature Dependence. J Phys Chem B 2013; 117:1756-69. [DOI: 10.1021/jp3078437] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Joel H. Parks
- Rowland Institute at Harvard, 100 Edwin H. Land Boulevard, Cambridge,
Massachusetts 02142 United
States
| | - David Semrouni
- Laboratoire
des Mécanismes Réactionnels, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
| | - Carine Clavaguéra
- Laboratoire
des Mécanismes Réactionnels, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
| | - Gilles Ohanessian
- Laboratoire
des Mécanismes Réactionnels, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
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