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Day K, Schneible JD, Young AT, Pozdin VA, Van Den Driessche G, Gaffney LA, Prodromou R, Freytes DO, Fourches D, Daniele M, Menegatti S. Photoinduced reconfiguration to control the protein-binding affinity of azobenzene-cyclized peptides. J Mater Chem B 2021; 8:7413-7427. [PMID: 32661544 DOI: 10.1039/d0tb01189d] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The impact of next-generation biorecognition elements (ligands) will be determined by the ability to remotely control their binding activity for a target biomolecule in complex environments. Compared to conventional mechanisms for regulating binding affinity (pH, ionic strength, or chaotropic agents), light provides higher accuracy and rapidity, and is particularly suited for labile targets. In this study, we demonstrate a general method to develop azobenzene-cyclized peptide ligands with light-controlled affinity for target proteins. Light triggers a cis/trans isomerization of the azobenzene, which results in a major structural rearrangement of the cyclic peptide from a non-binding to a binding configuration. Critical to this goal are the ability to achieve efficient photo-isomerization under low light dosage and the temporal stability of both cis and trans isomers. We demonstrated our method by designing photo-switchable peptides targeting vascular cell adhesion marker 1 (VCAM1), a cell marker implicated in stem cell function. Starting from a known VCAM1-binding linear peptide, an ensemble of azobenzene-cyclized variants with selective light-controlled binding were identified by combining in silico design with experimental characterization via spectroscopy and surface plasmon resonance. Variant cycloAZOB[G-VHAKQHRN-K] featured rapid, light-controlled binding of VCAM1 (KD,trans/KD,cis ∼ 130). Biotin-cycloAZOB[G-VHAKQHRN-K] was utilized to label brain microvascular endothelial cells (BMECs), showing co-localization with anti-VCAM1 antibodies in cis configuration and negligible binding in trans configuration.
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Affiliation(s)
- Kevin Day
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, North Carolina, USA.
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2
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Chu W, Prodromou R, Day KN, Schneible JD, Bacon KB, Bowen JD, Kilgore RE, Catella CM, Moore BD, Mabe MD, Alashoor K, Xu Y, Xiao Y, Menegatti S. Peptides and pseudopeptide ligands: a powerful toolbox for the affinity purification of current and next-generation biotherapeutics. J Chromatogr A 2020; 1635:461632. [PMID: 33333349 DOI: 10.1016/j.chroma.2020.461632] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 02/08/2023]
Abstract
Following the consolidation of therapeutic proteins in the fight against cancer, autoimmune, and neurodegenerative diseases, recent advancements in biochemistry and biotechnology have introduced a host of next-generation biotherapeutics, such as CRISPR-Cas nucleases, stem and car-T cells, and viral vectors for gene therapy. With these drugs entering the clinical pipeline, a new challenge lies ahead: how to manufacture large quantities of high-purity biotherapeutics that meet the growing demand by clinics and biotech companies worldwide. The protein ligands employed by the industry are inadequate to confront this challenge: while featuring high binding affinity and selectivity, these ligands require laborious engineering and expensive manufacturing, are prone to biochemical degradation, and pose safety concerns related to their bacterial origin. Peptides and pseudopeptides make excellent candidates to form a new cohort of ligands for the purification of next-generation biotherapeutics. Peptide-based ligands feature excellent target biorecognition, low or no toxicity and immunogenicity, and can be manufactured affordably at large scale. This work presents a comprehensive and systematic review of the literature on peptide-based ligands and their use in the affinity purification of established and upcoming biological drugs. A comparative analysis is first presented on peptide engineering principles, the development of ligands targeting different biomolecular targets, and the promises and challenges connected to the industrial implementation of peptide ligands. The reviewed literature is organized in (i) conventional (α-)peptides targeting antibodies and other therapeutic proteins, gene therapy products, and therapeutic cells; (ii) cyclic peptides and pseudo-peptides for protein purification and capture of viral and bacterial pathogens; and (iii) the forefront of peptide mimetics, such as β-/γ-peptides, peptoids, foldamers, and stimuli-responsive peptides for advanced processing of biologics.
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Affiliation(s)
- Wenning Chu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Raphael Prodromou
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Kevin N Day
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - John D Schneible
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Kaitlyn B Bacon
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - John D Bowen
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Ryan E Kilgore
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Carly M Catella
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Brandyn D Moore
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Matthew D Mabe
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Kawthar Alashoor
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642
| | - Yiman Xu
- College of Material Science and Engineering, Donghua University, 201620 Shanghai, People's Republic of China
| | - Yuanxin Xiao
- College of Textile, Donghua University, Songjiang District, Shanghai, 201620, People's Republic of China
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606.
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3
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Bastida A, Zúñiga J, Requena A, Miguel B, Candela ME, Soler MA. Conformational Changes of Trialanine in Water Induced by Vibrational Relaxation of the Amide I Mode. J Phys Chem B 2016; 120:348-57. [PMID: 26690744 DOI: 10.1021/acs.jpcb.5b09753] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Most of the protein-based diseases are caused by anomalies in the functionality and stability of these molecules. Experimental and theoretical studies of the conformational dynamics of proteins are becoming in this respect essential to understand the origin of these anomalies. However, a description of the conformational dynamics of proteins based on mechano-energetic principles still remains elusive because of the intrinsic high flexibility of the peptide chains, the participation of weak noncovalent interactions, and the role of the ubiquitous water solvent. In this work, the conformational dynamics of trialanine dissolved in water (D2O) is investigated through Molecular Dynamics (MD) simulations combined with instantaneous normal modes (INMs) analysis both at equilibrium and after the vibrational excitation of the C-terminal amide I mode. The conformational equilibrium between α and pPII conformers is found to be altered by the intramolecular relaxation of the amide I mode as a consequence of the different relaxation pathways of each conformer which modify the amount of vibrational energy stored in the torsional motions of the tripeptide, so the α → pPII and pPII → α conversion rates are increased differently. The selectivity of the process comes from the shifts of the vibrational frequencies with the conformational changes that modify the resonance conditions driving the intramolecular energy flows.
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Affiliation(s)
- Adolfo Bastida
- Departamento de Química Física, Universidad de Murcia , 30100 Murcia, Spain
| | - José Zúñiga
- Departamento de Química Física, Universidad de Murcia , 30100 Murcia, Spain
| | - Alberto Requena
- Departamento de Química Física, Universidad de Murcia , 30100 Murcia, Spain
| | - Beatriz Miguel
- Departamento de Ingeniería Química y Ambiental, Universidad Politécnica de Cartagena , 30203 Cartagena, Spain
| | | | - Miguel Angel Soler
- Department of Medical and Biological Sciences, University of Udine , 33100 Udine, Italy
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4
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Buchenberg S, Leitner DM, Stock G. Scaling Rules for Vibrational Energy Transport in Globular Proteins. J Phys Chem Lett 2016; 7:25-30. [PMID: 26650387 DOI: 10.1021/acs.jpclett.5b02514] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Computational studies of vibrational energy flow in biomolecules have to date mapped out transport pathways on a case-by-case basis. To provide a more general approach, we derive scaling rules for vibrational energy transport in a globular protein, which are identified from extensive nonequilibrium molecular dynamics simulations of vibrational energy flow in the villin headpiece subdomain HP36. We parametrize a master equation based on inter-residue, residue-solvent, and heater-residue energy-transfer rates, which closely reproduces the results of the all-atom simulations. From that fit, two scaling rules emerge, one for energy transport along the protein backbone which relies on a diffusion model and another for energy transport between tertiary contacts, which is based on a harmonic model. Requiring only the calculation of mean and variance of relatively few atomic distances, the approach holds the potential to predict the pathways and time scales of vibrational energy flow in large proteins.
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Affiliation(s)
- Sebastian Buchenberg
- Biomolecular Dynamics, Institute of Physics and Freiburg Institute for Advanced Studies (FRIAS), Albert Ludwigs University , 79104 Freiburg, Germany
| | - David M Leitner
- Biomolecular Dynamics, Institute of Physics and Freiburg Institute for Advanced Studies (FRIAS), Albert Ludwigs University , 79104 Freiburg, Germany
- Department of Chemistry and Chemical Physics Program, University of Nevada , Reno, Nevada 89557, United States
| | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics and Freiburg Institute for Advanced Studies (FRIAS), Albert Ludwigs University , 79104 Freiburg, Germany
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Xia SH, Cui G, Fang WH, Thiel W. How Photoisomerization Drives Peptide Folding and Unfolding: Insights from QM/MM and MM Dynamics Simulations. Angew Chem Int Ed Engl 2016; 55:2067-72. [PMID: 26836339 DOI: 10.1002/anie.201509622] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 11/17/2015] [Indexed: 12/14/2022]
Abstract
Photoswitchable azobenzene cross-linkers can control the folding and unfolding of peptides by photoisomerization and can thus regulate peptide affinities and enzyme activities. Using quantum mechanics/molecular mechanics (QM/MM) methods and classical MM force fields, we report the first molecular dynamics simulations of the photoinduced folding and unfolding processes in the azobenzene cross-linked FK-11 peptide. We find that the interactions between the peptide and the azobenzene cross-linker are crucial for controlling the evolution of the secondary structure of the peptide and responsible for accelerating the folding and unfolding events. They also modify the photoisomerization mechanism of the azobenzene cross-linker compared with the situation in vacuo or in solution.
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Affiliation(s)
- Shu-Hua Xia
- Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, China.
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany.
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6
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Xia SH, Cui G, Fang WH, Thiel W. How Photoisomerization Drives Peptide Folding and Unfolding: Insights from QM/MM and MM Dynamics Simulations. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509622] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Shu-Hua Xia
- Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education; College of Chemistry; Beijing Normal University; Beijing 100875 China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education; College of Chemistry; Beijing Normal University; Beijing 100875 China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education; College of Chemistry; Beijing Normal University; Beijing 100875 China
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
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7
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García-Iriepa C, Gueye M, Léonard J, Martínez-López D, Campos PJ, Frutos LM, Sampedro D, Marazzi M. A biomimetic molecular switch at work: coupling photoisomerization dynamics to peptide structural rearrangement. Phys Chem Chem Phys 2016; 18:6742-53. [DOI: 10.1039/c5cp07599h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A combined experimental and computational study of a peptide-linked retinal-like molecular switch shows the effects on photoreactivity and the α-helix structure.
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Affiliation(s)
- Cristina García-Iriepa
- Departamento de Química
- Centro de Investigación en Síntesis Química (CISQ)
- Universidad de La Rioja
- E-26006 Logroño
- Spain
| | - Moussa Gueye
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE
- Université de Strasbourg
- Strasbourg 67034
- France
| | - Jérémie Léonard
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE
- Université de Strasbourg
- Strasbourg 67034
- France
| | - David Martínez-López
- Departamento de Química
- Centro de Investigación en Síntesis Química (CISQ)
- Universidad de La Rioja
- E-26006 Logroño
- Spain
| | - Pedro J. Campos
- Departamento de Química
- Centro de Investigación en Síntesis Química (CISQ)
- Universidad de La Rioja
- E-26006 Logroño
- Spain
| | | | - Diego Sampedro
- Departamento de Química
- Centro de Investigación en Síntesis Química (CISQ)
- Universidad de La Rioja
- E-26006 Logroño
- Spain
| | - Marco Marazzi
- Department of Theoretical Chemical Biology
- Institute of Physical Chemistry
- KIT
- 76131 Karlsruhe
- Germany
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8
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Mori T, Saito S. Dynamic heterogeneity in the folding/unfolding transitions of FiP35. J Chem Phys 2015; 142:135101. [DOI: 10.1063/1.4916641] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Toshifumi Mori
- Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan and School of Physical Sciences, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan
| | - Shinji Saito
- Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan and School of Physical Sciences, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan
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9
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Buchenberg S, Knecht V, Walser R, Hamm P, Stock G. Long-range conformational transition of a photoswitchable allosteric protein: molecular dynamics simulation study. J Phys Chem B 2014; 118:13468-76. [PMID: 25365469 DOI: 10.1021/jp506873y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A local perturbation of a protein may lead to functional changes at some distal site. An example is the PDZ2 domain of human tyrosine phosphatase 1E, which shows an allosteric transition upon binding to a peptide ligand. Recently Buchli et al. presented a time-resolved study of this transition by covalently linking an azobenzene photoswitch across the binding groove and using a femtosecond laser pulse that triggers the cis-trans photoisomerization of azobenzene. To aid the interpretation of these experiments, in this work seven microsecond runs of all-atom molecular dynamics simulations each for the wild-type PDZ2 in the ligand-bound and -free state, as well as the photoswitchable protein (PDZ2S) in the cis and trans states of the photoswitch, in explicit water were conducted. First the theoretical model is validated by recalculating the available NMR data from the simulations. By comparing the results for PDZ2 and PDZ2S, it is analyzed to what extent the photoswitch indeed mimics the free-bound transition. A detailed description of the conformational rearrangement following the cis-trans photoisomerization of PDZ2S reveals a series of photoinduced structural changes that propagate from the anchor residues of the photoswitch via intermediate secondary structure segments to the C-terminus of PDZ2S. The changes of the conformational distribution of the C-terminal region is considered as the distal response of the isolated allosteric protein.
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Affiliation(s)
- Sebastian Buchenberg
- Biomolecular Dynamics, Institute of Physics, University of Freiburg , 79104 Freiburg, Germany
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10
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Biswas M, Burghardt I. Azobenzene photoisomerization-induced destabilization of B-DNA. Biophys J 2014; 107:932-40. [PMID: 25140428 PMCID: PMC4142232 DOI: 10.1016/j.bpj.2014.06.044] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 06/20/2014] [Accepted: 06/25/2014] [Indexed: 11/24/2022] Open
Abstract
Molecular photoswitches provide a promising way for selective regulation of nanoscaled biological systems. It has been shown that conformational changes of azobenzene, one of the widely used photoswitches, can be used to reversibly control DNA duplex formation. Here, we investigate the conformational response of DNA upon azobenzene binding and isomerization, using a threoninol linker that has been experimentally investigated recently. To this end, nonequilibrium molecular dynamics simulations are carried out using a switching potential describing the photoinduced isomerization. Attachment of azobenzene leads to a distortion of the DNA helical conformation that is similar for the trans and cis forms. However, the trans form is stabilized by favorable stacking interactions whereas the cis form is found to remain flipped out of the basepair-stacked position. Multiple azobenzene attachment augments the distortion in DNA helical conformation. The distorted DNA retains nativelike pairing of bases at ambient temperatures, but shows weaker basepairing compared to native DNA at an elevated temperature.
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Affiliation(s)
- Mithun Biswas
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany.
| | - Irene Burghardt
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany.
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Böckmann M, Braun S, Doltsinis NL, Marx D. Mimicking photoisomerisation of azo-materials by a force field switch derived from nonadiabatic ab initio simulations: Application to photoswitchable helical foldamers in solution. J Chem Phys 2013; 139:084108. [DOI: 10.1063/1.4818489] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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12
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Kobus M, Lieder M, Nguyen PH, Stock G. Simulation of transient infrared spectra of a photoswitchable peptide. J Chem Phys 2012; 135:225102. [PMID: 22168727 DOI: 10.1063/1.3664747] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In transient infrared (IR) experiments, a molecular system may be photoexcited in a nonstationary conformational state, whose time evolution is monitored via IR spectroscopy with high temporal and structural resolution. As a theoretical formulation of these experiments, this work derives explicit expressions for transient one- and two-dimensional IR spectra and discusses various levels of approximation and sampling strategies. Adopting a photoswitchable octapeptide in water as a representative example, nonequilibrium molecular dynamics simulations are performed and the photoinduced conformational dynamics and associated IR spectra are discussed in detail. Interestingly, it is found that the time scales of dynamics and spectra may differ from residue to residue by up to an order of magnitude. Considering merely the cumulative spectrum of all residues, the contributions of the individual residues largely compensate each other, which may explain the surprisingly small frequency shifts and short photoproduct rise times found in experiment. Even when a localized amide I mode is probed (e.g., via isotope labeling), the vibrational frequency shift is shown to depend in a complicated way on the conformation of the entire peptide as well as on the interaction with the solvent. In this context, various issues concerning the interpretation of transient IR spectra and conformational dynamics in terms of a few exponential time scales are discussed.
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Affiliation(s)
- Maja Kobus
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, 79104 Freiburg, Germany
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