1
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Petkowski JJ, Seager MD, Bains W, Seager S. General instability of dipeptides in concentrated sulfuric acid as relevant for the Venus cloud habitability. Sci Rep 2024; 14:17083. [PMID: 39048621 PMCID: PMC11269616 DOI: 10.1038/s41598-024-67342-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 07/10/2024] [Indexed: 07/27/2024] Open
Abstract
Recent renewed interest in the possibility of life in the acidic clouds of Venus has led to new studies on organic chemistry in concentrated sulfuric acid. We have previously found that the majority of amino acids are stable in the range of Venus' cloud sulfuric acid concentrations (81% and 98% w/w, the rest being water). The natural next question is whether dipeptides, as precursors to larger peptides and proteins, could be stable in this environment. We investigated the reactivity of the peptide bond using 20 homodipeptides and find that the majority of them undergo solvolysis within a few weeks, at both sulfuric acid concentrations. Notably, a few exceptions exist. HH and GG dipeptides are stable in 98% w/w sulfuric acid for at least 4 months, while II, LL, VV, PP, RR and KK resist hydrolysis in 81% w/w sulfuric acid for at least 5 weeks. Moreover, the breakdown process of the dipeptides studied in 98% w/w concentrated sulfuric acid is different from the standard acid-catalyzed hydrolysis that releases monomeric amino acids. Despite a few exceptions at a single concentration, no homodipeptides have demonstrated stability across both acid concentrations studied. This indicates that any hypothetical life on Venus would likely require a functional substitute for the peptide bond that can maintain stability throughout the range of sulfuric acid concentrations present.
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Affiliation(s)
- Janusz J Petkowski
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
- Faculty of Environmental Engineering, Wroclaw University of Science and Technology, 50-370, Wroclaw, Poland.
- JJ Scientific, 02-792, Mazowieckie, Warsaw, Poland.
| | - Maxwell D Seager
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
- Nanoplanet Consulting, Concord, MA, 01742, USA
| | - William Bains
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- School of Physics and Astronomy, Cardiff University, 4 The Parade, Cardiff, CF24 3AA, UK
- Rufus Scientific, Melbourn, Herts, SG8 6ED, UK
| | - Sara Seager
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Nanoplanet Consulting, Concord, MA, 01742, USA
- Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Department of Aeronautics and Astronautics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
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2
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Yogeshwar SM, Muñiz-Castrillo S, Sabater L, Peris-Sempere V, Mallajosyula V, Luo G, Yan H, Yu E, Zhang J, Lin L, Fagundes Bueno F, Ji X, Picard G, Rogemond V, Pinto AL, Heidbreder A, Höftberger R, Graus F, Dalmau J, Santamaria J, Iranzo A, Schreiner B, Giannoccaro MP, Liguori R, Shimohata T, Kimura A, Ono Y, Binks S, Mariotto S, Dinoto A, Bonello M, Hartmann CJ, Tambasco N, Nigro P, Prüss H, McKeon A, Davis MM, Irani SR, Honnorat J, Gaig C, Finke C, Mignot E. HLA-DQB1*05 subtypes and not DRB1*10:01 mediates risk in anti-IgLON5 disease. Brain 2024; 147:2579-2592. [PMID: 38425314 PMCID: PMC11224611 DOI: 10.1093/brain/awae048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 10/09/2023] [Accepted: 01/21/2024] [Indexed: 03/02/2024] Open
Abstract
Anti-IgLON5 disease is a rare and likely underdiagnosed subtype of autoimmune encephalitis. The disease displays a heterogeneous phenotype that includes sleep, movement and bulbar-associated dysfunction. The presence of IgLON5-antibodies in CSF/serum, together with a strong association with HLA-DRB1*10:01∼DQB1*05:01, supports an autoimmune basis. In this study, a multicentric human leukocyte antigen (HLA) study of 87 anti-IgLON5 patients revealed a stronger association with HLA-DQ than HLA-DR. Specifically, we identified a predisposing rank-wise association with HLA-DQA1*01:05∼DQB1*05:01, HLA-DQA1*01:01∼DQB1*05:01 and HLA-DQA1*01:04∼DQB1*05:03 in 85% of patients. HLA sequences and binding cores for these three DQ heterodimers were similar, unlike those of linked DRB1 alleles, supporting a causal link to HLA-DQ. This association was further reflected in an increasingly later age of onset across each genotype group, with a delay of up to 11 years, while HLA-DQ-dosage dependent effects were also suggested by reduced risk in the presence of non-predisposing DQ1 alleles. The functional relevance of the observed HLA-DQ molecules was studied with competition binding assays. These proof-of-concept experiments revealed preferential binding of IgLON5 in a post-translationally modified, but not native, state to all three risk-associated HLA-DQ receptors. Further, a deamidated peptide from the Ig2-domain of IgLON5 activated T cells in two patients, compared with one control carrying HLA-DQA1*01:05∼DQB1*05:01. Taken together, these data support a HLA-DQ-mediated T-cell response to IgLON5 as a potentially key step in the initiation of autoimmunity in this disease.
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Affiliation(s)
- Selina M Yogeshwar
- Stanford Center for Sleep Sciences and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, 10117, Berlin, Germany
- Einstein Center for Neurosciences Berlin, Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Sergio Muñiz-Castrillo
- Stanford Center for Sleep Sciences and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lidia Sabater
- Neuroimmunology Program, Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer, Caixa Research Institute, Universitat de Barcelona, 08036, Barcelona, Spain
| | - Vicente Peris-Sempere
- Stanford Center for Sleep Sciences and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Vamsee Mallajosyula
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Guo Luo
- Stanford Center for Sleep Sciences and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Han Yan
- Stanford Center for Sleep Sciences and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Eric Yu
- Stanford Center for Sleep Sciences and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jing Zhang
- Stanford Center for Sleep Sciences and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ling Lin
- Stanford Center for Sleep Sciences and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Flavia Fagundes Bueno
- Stanford Center for Sleep Sciences and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Xuhuai Ji
- Human Immune Monitoring Center, Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Géraldine Picard
- French Reference Center on Paraneoplastic Neurological Syndrome and Autoimmune Encephalitis, Hospices Civils de Lyon, 69677, Lyon, France
- Institut MeLiS INSERM U1314/CNRS UMR 5284, Université Claude Bernard Lyon 1, 69372 Lyon, France
| | - Véronique Rogemond
- French Reference Center on Paraneoplastic Neurological Syndrome and Autoimmune Encephalitis, Hospices Civils de Lyon, 69677, Lyon, France
- Institut MeLiS INSERM U1314/CNRS UMR 5284, Université Claude Bernard Lyon 1, 69372 Lyon, France
| | - Anne Laurie Pinto
- French Reference Center on Paraneoplastic Neurological Syndrome and Autoimmune Encephalitis, Hospices Civils de Lyon, 69677, Lyon, France
- Institut MeLiS INSERM U1314/CNRS UMR 5284, Université Claude Bernard Lyon 1, 69372 Lyon, France
| | - Anna Heidbreder
- Kepler University Hospital, Department of Neurology, Johannes Kepler University, 4020 Linz, Austria
| | - Romana Höftberger
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria
| | - Francesc Graus
- Neurology Service, Hospital Clínic of Barcelona, Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
| | - Josep Dalmau
- Neurology Service, Hospital Clínic of Barcelona, Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
- Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Spanish National Network for Research on Rare Diseases (CIBERER), 28029 Madrid, Spain
| | - Joan Santamaria
- Neurology Service, Hospital Clínic of Barcelona, Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
| | - Alex Iranzo
- Neurology Service, Hospital Clínic of Barcelona, Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
| | - Bettina Schreiner
- Department of Neurology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Experimental Immunology, University of Zurich, 8057 Zurich, Switzerland
| | - Maria Pia Giannoccaro
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, 40139 Bologna, Italy
- Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, 40100 Bologna, Italy
| | - Rocco Liguori
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, 40139 Bologna, Italy
- Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, 40100 Bologna, Italy
| | - Takayoshi Shimohata
- Department of Neurology, Gifu University Graduate School of Medicine, 501-1194 Gifu, Japan
| | - Akio Kimura
- Department of Neurology, Gifu University Graduate School of Medicine, 501-1194 Gifu, Japan
| | - Yoya Ono
- Department of Neurology, Gifu University Graduate School of Medicine, 501-1194 Gifu, Japan
| | - Sophie Binks
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
- Department of Neurology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Sara Mariotto
- Neurology Unit, Department of Neurosciences, Biomedicine, and Movement Sciences, University of Verona, 37124 Verona, Italy
| | - Alessandro Dinoto
- Neurology Unit, Department of Neurosciences, Biomedicine, and Movement Sciences, University of Verona, 37124 Verona, Italy
| | - Michael Bonello
- Department of Neurology, The Walton Centre NHS Foundation Trust, L9 7LJ, Liverpool, UK
| | - Christian J Hartmann
- Department of Neurology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
- Institute of Clinical Neuroscience and Medical Psychology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Nicola Tambasco
- Movement Disorders Center, Neurology Department, Perugia General Hospital and University of Perugia, 06156 Perugia, Italy
| | - Pasquale Nigro
- Movement Disorders Center, Neurology Department, Perugia General Hospital and University of Perugia, 06156 Perugia, Italy
| | - Harald Prüss
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, 10117, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE) Berlin, 10117 Berlin, Germany
| | - Andrew McKeon
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA
| | - Mark M Davis
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sarosh R Irani
- Department of Neurology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Jérôme Honnorat
- French Reference Center on Paraneoplastic Neurological Syndrome and Autoimmune Encephalitis, Hospices Civils de Lyon, 69677, Lyon, France
- Institut MeLiS INSERM U1314/CNRS UMR 5284, Université Claude Bernard Lyon 1, 69372 Lyon, France
| | - Carles Gaig
- Neurology Service, Hospital Clínic of Barcelona, Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
| | - Carsten Finke
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, 10117, Berlin, Germany
- Berlin Center for Advanced Neuroimaging, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Emmanuel Mignot
- Stanford Center for Sleep Sciences and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
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3
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Manning MC, Holcomb RE, Payne RW, Stillahn JM, Connolly BD, Katayama DS, Liu H, Matsuura JE, Murphy BM, Henry CS, Crommelin DJA. Stability of Protein Pharmaceuticals: Recent Advances. Pharm Res 2024; 41:1301-1367. [PMID: 38937372 DOI: 10.1007/s11095-024-03726-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/03/2024] [Indexed: 06/29/2024]
Abstract
There have been significant advances in the formulation and stabilization of proteins in the liquid state over the past years since our previous review. Our mechanistic understanding of protein-excipient interactions has increased, allowing one to develop formulations in a more rational fashion. The field has moved towards more complex and challenging formulations, such as high concentration formulations to allow for subcutaneous administration and co-formulation. While much of the published work has focused on mAbs, the principles appear to apply to any therapeutic protein, although mAbs clearly have some distinctive features. In this review, we first discuss chemical degradation reactions. This is followed by a section on physical instability issues. Then, more specific topics are addressed: instability induced by interactions with interfaces, predictive methods for physical stability and interplay between chemical and physical instability. The final parts are devoted to discussions how all the above impacts (co-)formulation strategies, in particular for high protein concentration solutions.'
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Affiliation(s)
- Mark Cornell Manning
- Legacy BioDesign LLC, Johnstown, CO, USA.
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA.
| | - Ryan E Holcomb
- Legacy BioDesign LLC, Johnstown, CO, USA
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Robert W Payne
- Legacy BioDesign LLC, Johnstown, CO, USA
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Joshua M Stillahn
- Legacy BioDesign LLC, Johnstown, CO, USA
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | | | | | | | | | | | - Charles S Henry
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
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4
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Wijerathne DV, Karabulut S, Gauld JW. Computational Insights into Protein Aging: Spontaneous Deamidation of Glutamine. J Phys Chem B 2024; 128:5545-5556. [PMID: 38815985 DOI: 10.1021/acs.jpcb.3c07628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Spontaneous deamidation of amino acids is a physiologically important process, particularly for protein aging and diseases. Despite its widespread occurrence, the mechanism of glutamine deamidation particularly within proteins remains poorly understood. We have used a multiscale computational approach to investigate glutamine deamidation in the tripeptide Glycine-Glutamine-Glycine (Gly-Gln-Gly) and γS-Crystallin protein. Specifically, both the 5- and 6-membered water-assisted deamidation pathways in the tripeptide have been elucidated and compared. Both are found to occur in three stages: iminol formation, cyclization, and deamination. The rate-limiting step in each mechanism is nucleophilic attack of the backbone iminol nitrogen, formed in the first stage, at the glutamine's side-chain carbonyl carbon. For the 6- and 5-membered mechanisms, this occurs with a free energy cost of 136.4 and 179.5 kJ mol-1, respectively. Thus, overall, in the Gly-Gln-Gly tripeptide, the 6-membered pathway is preferred. Furthermore, the free energies for forming cyclic intermediates and products at selected Gln residues (based on experimentally reported % deamidation) in γS-Crystallin have been obtained. It is found that the 5-membered product complex is exergonic at -25.3 kJ mol-1, while the 6-membered product complex is calculated to be endergonic at 90.7 kJ mol-1. Thus, the deamidation pathway in folded and constrained proteins may not exclusively follow the 6-membered route. Molecular dynamics (MD) simulations of γS-Crystallin indicate that deamidation is more likely to occur when two or more water molecules are in the proximity of the glutamine residue. Consequently, significant conformational changes are found to accompany Gln120 deamidation in γS-Crystallin. This in turn can influence water availability at the other Gln residues considered and hence potentially their deamidation. Collectively, these results provide comprehensive insights into spontaneous water-assisted deamidation of glutamine residues in peptides and into the role and impact of Gln deamidation in proteins.
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Affiliation(s)
- Dananjana V Wijerathne
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Sedat Karabulut
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - James W Gauld
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
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5
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Gavade A, Nagraj AK, Patel R, Pais R, Dhanure P, Scheele J, Seiz W, Patil J. Understanding the Specific Implications of Amino Acids in the Antibody Development. Protein J 2024; 43:405-424. [PMID: 38724751 DOI: 10.1007/s10930-024-10201-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2024] [Indexed: 06/01/2024]
Abstract
As the demand for immunotherapy to treat and manage cancers, infectious diseases and other disorders grows, a comprehensive understanding of amino acids and their intricate role in antibody engineering has become a prime requirement. Naturally produced antibodies may not have the most suitable amino acids at the complementarity determining regions (CDR) and framework regions, for therapeutic purposes. Therefore, to enhance the binding affinity and therapeutic properties of an antibody, the specific impact of certain amino acids on the antibody's architecture must be thoroughly studied. In antibody engineering, it is crucial to identify the key amino acid residues that significantly contribute to improving antibody properties. Therapeutic antibodies with higher binding affinity and improved functionality can be achieved through modifications or substitutions with highly suitable amino acid residues. Here, we have indicated the frequency of amino acids and their association with the binding free energy in CDRs. The review also analyzes the experimental outcome of two studies that reveal the frequency of amino acids in CDRs and provides their significant correlation between the outcomes. Additionally, it discusses the various bond interactions within the antibody structure and antigen binding. A detailed understanding of these amino acid properties should assist in the analysis of antibody sequences and structures needed for designing and enhancing the overall performance of therapeutic antibodies.
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Affiliation(s)
- Akshata Gavade
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Anil Kumar Nagraj
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Riya Patel
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Roylan Pais
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Pratiksha Dhanure
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | | | | | - Jaspal Patil
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India.
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6
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Dudley JA, Park S, Cho O, Wells NGM, MacDonald ME, Blejec KM, Fetene E, Zanderigo E, Houliston S, Liddle JC, Dashnaw CM, Sabo TM, Shaw BF, Balsbaugh JL, Rocklin GJ, Smith CA. Heat-induced structural and chemical changes to a computationally designed miniprotein. Protein Sci 2024; 33:e4991. [PMID: 38757381 PMCID: PMC11099715 DOI: 10.1002/pro.4991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/22/2024] [Accepted: 03/28/2024] [Indexed: 05/18/2024]
Abstract
The de novo design of miniprotein inhibitors has recently emerged as a new technology to create proteins that bind with high affinity to specific therapeutic targets. Their size, ease of expression, and apparent high stability makes them excellent candidates for a new class of protein drugs. However, beyond circular dichroism melts and hydrogen/deuterium exchange experiments, little is known about their dynamics, especially at the elevated temperatures they seemingly tolerate quite well. To address that and gain insight for future designs, we have focused on identifying unintended and previously overlooked heat-induced structural and chemical changes in a particularly stable model miniprotein, EHEE_rd2_0005. Nuclear magnetic resonance (NMR) studies suggest the presence of dynamics on multiple time and temperature scales. Transiently elevating the temperature results in spontaneous chemical deamidation visible in the NMR spectra, which we validate using both capillary electrophoresis and mass spectrometry (MS) experiments. High temperatures also result in greatly accelerated intrinsic rates of hydrogen exchange and signal loss in NMR heteronuclear single quantum coherence spectra from local unfolding. These losses are in excellent agreement with both room temperature hydrogen exchange experiments and hydrogen bond disruption in replica exchange molecular dynamics simulations. Our analysis reveals important principles for future miniprotein designs and the potential for high stability to result in long-lived alternate conformational states.
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Affiliation(s)
- Joshua A. Dudley
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | - Sojeong Park
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | - Oliver Cho
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | | | | | | | - Emmanuel Fetene
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | - Eric Zanderigo
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | - Scott Houliston
- Structural Genomics ConsortiumUniversity of TorontoTorontoOntarioCanada
| | - Jennifer C. Liddle
- Proteomics and Metabolomics FacilityUniversity of ConnecticutStorrsConnecticutUSA
| | - Chad M. Dashnaw
- Department of Chemistry and BiochemistryBaylor UniversityWacoTexasUSA
| | - T. Michael Sabo
- Department of Medicine and Brown Cancer CenterUniversity of LouisvilleLouisvilleKentuckyUSA
| | - Bryan F. Shaw
- Department of Chemistry and BiochemistryBaylor UniversityWacoTexasUSA
| | - Jeremy L. Balsbaugh
- Proteomics and Metabolomics FacilityUniversity of ConnecticutStorrsConnecticutUSA
| | - Gabriel J. Rocklin
- Department of Pharmacology and Center for Synthetic BiologyNorthwestern UniversityEvanstonIllinoisUSA
| | - Colin A. Smith
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
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7
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Pastrana B, Culyba E, Nieves S, Sazinsky SL, Canto EI, Noda I. Streamlined Multi-Attribute Assessment of an Array of Clinical-Stage Antibodies: Relationship Between Degradation and Stability. APPLIED SPECTROSCOPY 2024:37028241231824. [PMID: 38419510 DOI: 10.1177/00037028241231824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Clinical antibodies are an important class of drugs for the treatment of both chronic and acute diseases. Their manufacturability is subject to evaluation to ensure product quality and efficacy. One critical quality attribute is deamidation, a non-enzymatic process that is observed to occur during thermal stress, at low or high pH, or a combination thereof. Deamidation may induce antibody instability and lead to aggregation, which may pose immunogenicity concerns. The introduction of a negative charge via deamidation may impact the desired therapeutic function (i) within the complementarity-determining region, potentially causing loss of efficacy; or (ii) within the fragment crystallizable region, limiting the effector function involving antibody-dependent cellular cytotoxicity. Here we describe a transformative solution that allows for a comparative assessment of deamidation and its impact on stability and aggregation. The innovative streamlined method evaluates the intact protein in its formulation conditions. This breakthrough platform technology is comprised of a quantum cascade laser microscope, a slide cell array that allows for flexibility in the design of experiments, and dedicated software. The enhanced spectral resolution is achieved using two-dimensional correlation, co-distribution, and two-trace two-dimensional correlation spectroscopies that reveal the molecular impact of deamidation. Eight re-engineered immunoglobulin G4 scaffold clinical antibodies under control and forced degradation conditions were evaluated for deamidation and aggregation. We determined the site of deamidation, the overall extent of deamidation, and where applicable, whether the deamidation event led to self-association or aggregation of the clinical antibody and the molecular events that led to the instability. The results were confirmed using orthogonal techniques for four of the samples.
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Affiliation(s)
- Belinda Pastrana
- Research and Development, Protein Dynamic Solutions, Inc., Wakefield, Massachusetts, USA
| | - Elizabeth Culyba
- Research and Development, Protein Dynamic Solutions, Inc., Wakefield, Massachusetts, USA
- Antibody Discovery, Verseau Therapeutics, Inc., Bedford, Massachusetts, USA
| | - Sherly Nieves
- Research and Development, Protein Dynamic Solutions, Inc., Wakefield, Massachusetts, USA
| | - Stephen L Sazinsky
- Antibody Discovery, Verseau Therapeutics, Inc., Bedford, Massachusetts, USA
| | - Eduardo I Canto
- Translational Sciences, Auxilio BioLab, Auxilio Mutuo Hospital, San Juan, Puerto Rico, USA
| | - Isao Noda
- Infectious Disease Research, Department of Materials Sciences and Engineering, University of Delaware, Newark, Delaware, USA
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8
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Barbieri E, Mollica GN, Moore BD, Sripada SA, Shastry S, Kilgore RE, Loudermilk CM, Whitacre ZH, Kilgour KM, Wuestenhagen E, Aldinger A, Graalfs H, Rammo O, Schulte MM, Johnson TF, Daniele MA, Menegatti S. Peptide ligands targeting the vesicular stomatitis virus G (VSV-G) protein for the affinity purification of lentivirus particles. Biotechnol Bioeng 2024; 121:618-639. [PMID: 37947118 DOI: 10.1002/bit.28594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/17/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023]
Abstract
The recent uptick in the approval of ex vivo cell therapies highlights the relevance of lentivirus (LV) as an enabling viral vector of modern medicine. As labile biologics, however, LVs pose critical challenges to industrial biomanufacturing. In particular, LV purification-currently reliant on filtration and anion-exchange or size-exclusion chromatography-suffers from long process times and low yield of transducing particles, which translate into high waiting time and cost to patients. Seeking to improve LV downstream processing, this study introduces peptides targeting the enveloped protein Vesicular stomatitis virus G (VSV-G) to serve as affinity ligands for the chromatographic purification of LV particles. An ensemble of candidate ligands was initially discovered by implementing a dual-fluorescence screening technology and a targeted in silico approach designed to identify sequences with high selectivity and tunable affinity. The selected peptides were conjugated on Poros resin and their LV binding-and-release performance was optimized by adjusting the flow rate, composition, and pH of the chromatographic buffers. Ligands GKEAAFAA and SRAFVGDADRD were selected for their high product yield (50%-60% of viral genomes; 40%-50% of HT1080 cell-transducing particles) upon elution in PIPES buffer with 0.65 M NaCl at pH 7.4. The peptide-based adsorbents also presented remarkable values of binding capacity (up to 3·109 TU per mL of resin, or 5·1011 vp per mL of resin, at the residence time of 1 min) and clearance of host cell proteins (up to a 220-fold reduction of HEK293 HCPs). Additionally, GKEAAFAA demonstrated high resistance to caustic cleaning-in-place (0.5 M NaOH, 30 min) with no observable loss in product yield and quality.
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Affiliation(s)
- Eduardo Barbieri
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Gina N Mollica
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Brandyn D Moore
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Sobhana A Sripada
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Shriarjun Shastry
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, North Carolina, USA
| | - Ryan E Kilgore
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Casee M Loudermilk
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Zachary H Whitacre
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Katie M Kilgour
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | | | | | | | | | | | - Thomas F Johnson
- Department of Biochemical Engineering, University College London, London, UK
| | - Michael A Daniele
- North Carolina Viral Vector Initiative in Research and Learning (NC-VVIRAL), North Carolina State University, Raleigh, North Carolina, USA
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, North Carolina, USA
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, North Carolina, USA
- North Carolina Viral Vector Initiative in Research and Learning (NC-VVIRAL), North Carolina State University, Raleigh, North Carolina, USA
- LigaTrap Technologies LLC, Raleigh, North Carolina, USA
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9
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Adav SS, Ng KW. Recent omics advances in hair aging biology and hair biomarkers analysis. Ageing Res Rev 2023; 91:102041. [PMID: 37634889 DOI: 10.1016/j.arr.2023.102041] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/27/2023] [Accepted: 08/23/2023] [Indexed: 08/29/2023]
Abstract
Aging is a complex natural process that leads to a decline in physiological functions, which is visible in signs such as hair graying, thinning, and loss. Although hair graying is characterized by a loss of pigment in the hair shaft, the underlying mechanism of age-associated hair graying is not fully understood. Hair graying and loss can have a significant impact on an individual's self-esteem and self-confidence, potentially leading to mental health problems such as depression and anxiety. Omics technologies, which have applications beyond clinical medicine, have led to the discovery of candidate hair biomarkers and may provide insight into the complex biology of hair aging and identify targets for effective therapies. This review provides an up-to-date overview of recent omics discoveries, including age-associated alterations of proteins and metabolites in the hair shaft and follicle, and highlights the significance of hair aging and graying biomarker discoveries. The decline in hair follicle stem cell activity with aging decreased the regeneration capacity of hair follicles. Cellular senescence, oxidative damage and altered extracellular matrix of hair follicle constituents characterized hair follicle and hair shaft aging and graying. The review attempts to correlate the impact of endogenous and exogenous factors on hair aging. We close by discussing the main challenges and limitations of the field, defining major open questions and offering an outlook for future research.
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Affiliation(s)
- Sunil S Adav
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Kee Woei Ng
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore; Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, CleanTech One, 637141, Singapore.
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10
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Motone K, Kontogiorgos-Heintz D, Wee J, Kurihara K, Yang S, Roote G, Fang Y, Cardozo N, Nivala J. Multi-pass, single-molecule nanopore reading of long protein strands with single-amino acid sensitivity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.19.563182. [PMID: 37905023 PMCID: PMC10614977 DOI: 10.1101/2023.10.19.563182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
The ability to sequence single protein molecules in their native, full-length form would enable a more comprehensive understanding of proteomic diversity. Current technologies, however, are limited in achieving this goal. Here, we establish a method for long-range, single-molecule reading of intact protein strands on a commercial nanopore sensor array. By using the ClpX unfoldase to ratchet proteins through a CsgG nanopore, we achieve single-amino acid level sensitivity, enabling sequencing of combinations of amino acid substitutions across long protein strands. For greater sequencing accuracy, we demonstrate the ability to reread individual protein molecules, spanning hundreds of amino acids in length, multiple times, and explore the potential for high accuracy protein barcode sequencing. Further, we develop a biophysical model that can simulate raw nanopore signals a priori, based on amino acid volume and charge, enhancing the interpretation of raw signal data. Finally, we apply these methods to examine intact, folded protein domains for complete end-to-end analysis. These results provide proof-of-concept for a platform that has the potential to identify and characterize full-length proteoforms at single-molecule resolution.
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Affiliation(s)
- Keisuke Motone
- Paul. G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
- These authors contributed equally: Keisuke Motone, Daphne Kontogiorgos-Heintz
| | - Daphne Kontogiorgos-Heintz
- Paul. G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
- These authors contributed equally: Keisuke Motone, Daphne Kontogiorgos-Heintz
| | - Jasmine Wee
- Paul. G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Kyoko Kurihara
- Paul. G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Sangbeom Yang
- Paul. G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Gwendolin Roote
- Paul. G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Yishu Fang
- Paul. G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Nicolas Cardozo
- Molecular Engineering and Science Institute, University of Washington, Seattle, WA, USA
| | - Jeff Nivala
- Paul. G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
- Molecular Engineering and Science Institute, University of Washington, Seattle, WA, USA
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11
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Reinert T, Houzé P, Mignet N, Francois YN, Gahoual R. Post-translational modifications comparative identification and kinetic study of infliximab innovator and biosimilars in serum using capillary electrophoresis-tandem mass spectrometry. J Pharm Biomed Anal 2023; 234:115541. [PMID: 37399702 DOI: 10.1016/j.jpba.2023.115541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 06/18/2023] [Accepted: 06/20/2023] [Indexed: 07/05/2023]
Abstract
Despite reports indicating the potential impact of post-translational modifications on the activity of a monoclonal antibody, their prediction or monitoring post-administration remains a challenge. In addition, with the expiration of patents concerning the early generation of mAbs, the production of biosimilars is constantly increasing. Structural differences of biosimilars compared to the innovator product are commonly evaluated for the formulated product in the context of biosimilarity assessment. However, estimating their structural outcome after administration is particularly difficult. Due to the complexity of in vivo studies, there is a need to develop analytical strategies to predict PTMs consequently to their administration and their impact on mAbs potency. Here, we identified and evaluated the modification kinetics of 4 asparagine deamidations and 2 aspartate isomerizations of infliximab innovator product (Remicade®) and two biosimilars (Inflectra® and Remsima®) in vitro using serum incubation at 37 °C. The methodology was based on a bottom-up approach with capillary electrophoresis hyphenated with mass spectrometry analysis for an unequivocal assignment of modified and unmodified forms. 2 asparagines demonstrated a gradual deamidation correlated with incubation time. The specific extraction efficiency was evaluated to determine possible changes in the antigen binding affinity of infliximab with the incubation. Results showed the possibility to achieve an additional aspect concerning biosimilarity assessment, oriented on the study of the structural stability after administration.
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Affiliation(s)
- Tessa Reinert
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS) UMR 7140 (Unistra-CNRS), Université de Strasbourg, France; Université Paris Cité, Unité de Technologies Chimiques et Biologiques pour la Santé (UTCBS), CNRS UMR8258, Inserm, Faculté de sciences pharmaceutiques et biologiques, Paris, France
| | - Pascal Houzé
- Université Paris Cité, Unité de Technologies Chimiques et Biologiques pour la Santé (UTCBS), CNRS UMR8258, Inserm, Faculté de sciences pharmaceutiques et biologiques, Paris, France; Laboratoire de Toxicologie Biologique, Hôpital Lariboisière, Assistance Publique - Hôpitaux de Paris (AP-HP), Paris, France
| | - Nathalie Mignet
- Université Paris Cité, Unité de Technologies Chimiques et Biologiques pour la Santé (UTCBS), CNRS UMR8258, Inserm, Faculté de sciences pharmaceutiques et biologiques, Paris, France
| | - Yannis-Nicolas Francois
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS) UMR 7140 (Unistra-CNRS), Université de Strasbourg, France
| | - Rabah Gahoual
- Université Paris Cité, Unité de Technologies Chimiques et Biologiques pour la Santé (UTCBS), CNRS UMR8258, Inserm, Faculté de sciences pharmaceutiques et biologiques, Paris, France.
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12
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Long CC, Antevska A, Mast DH, Okyem S, Sweedler JV, Do TD. Nonenzymatic Posttranslational Modifications and Peptide Cleavages Observed in Peptide Epimers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1898-1907. [PMID: 37102735 PMCID: PMC10524105 DOI: 10.1021/jasms.3c00092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Posttranslational modifications (PTMs) play vital roles in cellular homeostasis and are implicated in various pathological conditions. This work uses two ion mobility spectrometry-mass spectrometry (IMS-MS) modalities, drift-tube IMS (DT-IMS) and trapped IMS (TIMS), to characterize three important nonenzymatic PTMs that induce no mass loss: l/d isomerization, aspartate/isoaspartate isomerization, and cis/trans proline isomerization. These PTMs are assessed in a single peptide system, the recently discovered pleurin peptides, Plrn2, from Aplysia californica. We determine that the DT-IMS-MS/MS can capture and locate asparagine deamidation into aspartate and its subsequent isomerization to isoaspartate, a key biomarker for age-related diseases. Additionally, nonenzymatic peptide cleavage via in-source fragmentation is evaluated for differences in the intensities and patterns of fragment peaks between these PTMs. Peptide fragments resulting from in-source fragmentation, preceded by peptide denaturation by liquid chromatography (LC) mobile phase, exhibited cis/trans proline isomerization. Finally, the effects of differing the fragmentation voltage at the source and solution-based denaturation conditions on in-source fragmentation profiles are evaluated, confirming that LC denaturation and in-source fragmentation profoundly impact N-terminal peptide bond cleavages of Plrn2 and the structures of their fragment ions. With that, LC-IMS-MS/MS coupled with in-source fragmentation could be a robust method to identify three important posttranslational modifications: l/d isomerization, Asn-deamidation leading to Asp/IsoAsp isomerization, and cis/trans proline isomerization.
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Affiliation(s)
- Connor C. Long
- Department of Biochemistry, Cellular, and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | | | - David H. Mast
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801
| | - Samuel Okyem
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801
| | - Jonathan V. Sweedler
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801
| | - Thanh D. Do
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, USA
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13
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Kato K, Nakayoshi T, Kitamura Y, Kurimoto E, Oda A, Ishikawa Y. Identification of the Most Impactful Asparagine Residues for γS-Crystallin Aggregation by Deamidation. Biochemistry 2023. [PMID: 37155656 DOI: 10.1021/acs.biochem.3c00097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Crystallin aggregation in the eye lens is involved in the pathogenesis of cataracts. The aggregation is considered to be promoted by non-enzymatic post-translational modifications, such as the deamidation and stereoinversion of amino acid residues. Although in a previous study, the deamidated asparagine residues were detected in γS-crystallin in vivo, it is unclear which deamidated residues have the most impact on the aggregation under physiological conditions. In this study, we investigated the deamidation impacts of all Asn residues in γS-crystallin for the structural and aggregation properties utilizing deamidation mimetic mutants (N14D, N37D, N53D, N76D, and N143D). The structural impacts were investigated using circular dichroism analysis and molecular dynamics simulations, and the aggregation properties were analyzed by gel filtration chromatography and spectrophotometric methods. No significant structural impacts of all mutations were detected. However, the N37D mutation decreased thermal stability and changed some intermolecular hydrogen-bond formations. Aggregation analysis indicated that the superiority of the aggregation rate in each mutant varied with temperature. Deamidation at any Asn residues promoted γS-crystallin aggregation, and the deamidation at Asn37, Asn53, and Asn76 were suggested to be the most impactful in the formation of insoluble aggregations.
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Affiliation(s)
- Koichi Kato
- Faculty of Pharmaceutical Sciences, Shonan University of Medical Sciences, 16-48 Kamishinano, Totsuka-ku, Yokohama, Kanagawa 244-0806, Japan
- College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan
- Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan
| | - Tomoki Nakayoshi
- Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigasi, Asaminami-ku, Hiroshima, Hiroshima 731-3194, Japan
| | - Yuki Kitamura
- College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan
- School of Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi 329-0498, Japan
| | - Eiji Kurimoto
- Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan
| | - Akifumi Oda
- Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoshinobu Ishikawa
- Faculty of Pharmaceutical Sciences, Shonan University of Medical Sciences, 16-48 Kamishinano, Totsuka-ku, Yokohama, Kanagawa 244-0806, Japan
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14
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Beaudoin CA, Petsolari E, Hamaia SW, Hala S, Alofi FS, Pandurangan AP, Blundell TL, Chaitanya Vedithi S, Huang CLH, Jackson AP. SARS-CoV-2 Omicron subvariant spike N405 unlikely to rapidly deamidate. Biochem Biophys Res Commun 2023; 666:61-67. [PMID: 37178506 PMCID: PMC10152834 DOI: 10.1016/j.bbrc.2023.04.088] [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: 04/04/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
The RGD motif on the SARS-CoV-2 spike protein has been suggested to interact with RGD-binding integrins αVβ3 and α5β1 to enhance viral cell entry and alter downstream signaling cascades. The D405N mutation on the Omicron subvariant spike proteins, resulting in an RGN motif, has recently been shown to inhibit binding to integrin αVβ3. Deamidation of asparagines in protein ligand RGN motifs has been demonstrated to generate RGD and RGisoD motifs that permit binding to RGD-binding integrins. Two asparagines, N481 and N501, on the Wild-type spike receptor-binding domain have been previously shown to have deamidation half-lives of 16.5 and 123 days, respectively, which may occur during the viral life cycle. Deamidation of Omicron subvariant N405 may recover the ability to interact with RGD-binding integrins. Thus, herein, all-atom molecular dynamics simulations of the Wild-type and Omicron subvariant spike protein receptor-binding domains were conducted to investigate the potential for asparagines, the Omicron subvariant N405 in particular, to assume the optimized geometry for deamidation to occur. In summary, the Omicron subvariant N405 was primarily found to be stabilized in a state unfavourable for deamidation after hydrogen bonding with downstream E406. Nevertheless, a small number of RGD or RGisoD motifs on the Omicron subvariant spike proteins may restore the ability to interact with RGD-binding integrins. The simulations also provided structural clarification regarding the deamidation rates of Wild-type N481 and N501 and highlighted the utility of tertiary structure dynamics information in predicting asparagine deamidation. Further work is needed to characterize the effects of deamidation on spike-integrin interactions.
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Affiliation(s)
- Christopher A Beaudoin
- Department of Biochemistry, Hopkins Building, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, United Kingdom.
| | - Emmanouela Petsolari
- Department of Biochemistry, Sanger Building, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Samir W Hamaia
- Department of Biochemistry, Hopkins Building, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, United Kingdom
| | - Sharif Hala
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Ministry of National Guard Health Affairs, Jeddah, Saudi Arabia; King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Jeddah, Saudi Arabia
| | - Fadwa S Alofi
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Ministry of National Guard Health Affairs, Jeddah, Saudi Arabia
| | - Arun P Pandurangan
- Heart and Lung Research Institute, University of Cambridge, Papworth Road, Cambridge, CB2 0BB, United Kingdom
| | - Tom L Blundell
- Heart and Lung Research Institute, University of Cambridge, Papworth Road, Cambridge, CB2 0BB, United Kingdom
| | - Sundeep Chaitanya Vedithi
- Heart and Lung Research Institute, University of Cambridge, Papworth Road, Cambridge, CB2 0BB, United Kingdom
| | - Christopher L-H Huang
- Department of Biochemistry, Hopkins Building, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, United Kingdom; Physiological Laboratory, University of Cambridge, Downing Street, Cambridge, CB2 3EG, United Kingdom
| | - Antony P Jackson
- Department of Biochemistry, Hopkins Building, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, United Kingdom.
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15
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Zhou Y, Wang Y. Direct deamidation analysis of intact adeno-associated virus serotype 9 capsid proteins using reversed-phase liquid chromatography. Anal Biochem 2023; 668:115099. [PMID: 36871622 DOI: 10.1016/j.ab.2023.115099] [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: 01/10/2023] [Revised: 02/24/2023] [Accepted: 03/01/2023] [Indexed: 03/07/2023]
Abstract
Recombinant adeno-associated viral (AAV) vectors have taken center stage as gene delivery vehicles for gene therapy. Asparagine deamidation of AAV capsid proteins has been reported to reduce vector stability and potency of AAV gene therapy products. Deamidation of asparagine residue is a common post-translational modification of proteins that is detected and quantified by liquid chromatography-tandem mass spectrometry (LC-MS)-based peptide mapping. However, artificial deamidation can be spontaneously induced during sample preparation for peptide mapping prior to LC-MS analysis. We have developed an optimized sample preparation method to reduce and minimize deamidation artifacts induced during sample preparation for peptide mapping, which typically takes several hours to complete. To shorten turnaround time of deamidation results and to avoid artificial deamidation, we developed orthogonal RPLC-MS and RPLC-fluorescence detection methods for direct deamidation analysis at the intact AAV9 capsid protein level to routinely support downstream purification, formulation development, and stability testing. Similar trends of increasing deamidation of AAV9 capsid proteins in stability samples were observed at the intact protein level and peptide level, indicating that the developed direct deamidation analysis of intact AAV9 capsid proteins is comparable to the peptide mapping-based deamidation analysis and both methods are suitable for deamidation monitoring of AAV9 capsid proteins.
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Affiliation(s)
- Yu Zhou
- Analytical Development & Operation, Novartis Pharmaceuticals, 10210 Campus Point Drive, SanDiego, CA92121, USA.
| | - Yueju Wang
- Analytical Development & Operation, Novartis Pharmaceuticals, 10210 Campus Point Drive, SanDiego, CA92121, USA
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16
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Designing Formulation Strategies for Enhanced Stability of Therapeutic Peptides in Aqueous Solutions: A Review. Pharmaceutics 2023; 15:pharmaceutics15030935. [PMID: 36986796 PMCID: PMC10056213 DOI: 10.3390/pharmaceutics15030935] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/04/2023] [Accepted: 03/09/2023] [Indexed: 03/15/2023] Open
Abstract
Over the past few decades, there has been a tremendous increase in the utilization of therapeutic peptides. Therapeutic peptides are usually administered via the parenteral route, requiring an aqueous formulation. Unfortunately, peptides are often unstable in aqueous solutions, affecting stability and bioactivity. Although a stable and dry formulation for reconstitution might be designed, from a pharmaco-economic and practical convenience point of view, a peptide formulation in an aqueous liquid form is preferred. Designing formulation strategies that optimize peptide stability may improve bioavailability and increase therapeutic efficacy. This literature review provides an overview of various degradation pathways and formulation strategies to stabilize therapeutic peptides in aqueous solutions. First, we introduce the major peptide stability issues in liquid formulations and the degradation mechanisms. Then, we present a variety of known strategies to inhibit or slow down peptide degradation. Overall, the most practical approaches to peptide stabilization are pH optimization and selecting the appropriate type of buffer. Other practical strategies to reduce peptide degradation rates in solution are the application of co-solvency, air exclusion, viscosity enhancement, PEGylation, and using polyol excipients.
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17
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Pérez-Robles R, Salmerón-García A, Hermosilla J, Torrente-López A, Clemente-Bautista S, Jiménez-Lozano I, Cabañas-Poy MJ, Cabeza J, Navas N. Comprehensive physicochemical characterization of a peptide-based medicine: Teduglutide (Revestive®) structural description and stress testing. Eur J Pharm Biopharm 2023; 184:103-115. [PMID: 36669672 DOI: 10.1016/j.ejpb.2023.01.001] [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: 10/18/2022] [Revised: 12/29/2022] [Accepted: 01/02/2023] [Indexed: 01/19/2023]
Abstract
Teduglutide (Revestive®) is a glucagon-like peptide-2 analogue used for the treatment of short bowel syndrome, a rare life-threatening condition in which the amount of functional gut is too short to enable proper absorption of nutrients and fluids. During handling prior to administration to the patient in hospital, it is possible that peptide-based medicines may be exposed to environmental stress conditions that could affect their quality. It is therefore essential to carry out stress testing studies to evaluate how such medicines respond to these stresses. For this reason, in this paper we present a strategy for a comprehensive analytical characterization of a peptide and a stress testing study in which it was subjected to various stress conditions: heating at 40 °C and 60 °C, light exposure and shaking. Several complementary analytical techniques were used throughout this study: Far UV circular dichroism, intrinsic protein fluorescence spectroscopy, dynamic light scattering, size-exclusion chromatography and intact and peptide mapping reverse-phase chromatography coupled to mass spectrometry. To the best of our knowledge, this is the first study to offer an in-depth description of the chemical structure of teduglutide peptide and its physicochemical characteristics after stress stimuli were applied to the reconstituted medicine Revestive®.
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Affiliation(s)
- Raquel Pérez-Robles
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain; Department of Analytical Chemistry, Science Faculty, University of Granada, Granada, Spain; Fundación para la Investigación Biosanitaria de Andalucía Oriental-Alejandro Otero, Granada, Spain
| | - Antonio Salmerón-García
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain; Department of Clinical Pharmacy, San Cecilio University Hospital, Granada, Spain
| | - Jesus Hermosilla
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain; Department of Analytical Chemistry, Science Faculty, University of Granada, Granada, Spain
| | - Anabel Torrente-López
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain; Department of Analytical Chemistry, Science Faculty, University of Granada, Granada, Spain
| | | | - Inés Jiménez-Lozano
- Maternal and Child Pharmacy Service, Vall d'Hebron Hospital, Pharmacy, Barcelona, Spain
| | | | - Jose Cabeza
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain; Department of Clinical Pharmacy, San Cecilio University Hospital, Granada, Spain
| | - Natalia Navas
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain; Department of Analytical Chemistry, Science Faculty, University of Granada, Granada, Spain.
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Rotondo M, Honisch C, Tartaggia S, Ruzza P. Circular Dichroism Study of Orexin B under Oxidative Stress Conditions. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020484. [PMID: 36677542 PMCID: PMC9863598 DOI: 10.3390/molecules28020484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/23/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023]
Abstract
The neuropeptides orexin A and B regulate various vital functions of the body, such as sleep/wake states, metabolism, and energy homeostasis. A loss of their physiological activity, with reduced ability to recognize their receptors, is suspected to be associated with oxidative stress conditions. These are related to excessive presence of reactive oxygen and nitrogen species, as well as of reactive lipoxidation byproducts. With the aim of evaluating the effects of oxidative stress on the secondary structure of orexin peptides, orexin B was synthesized and characterized by circular dichroism spectroscopy under different conditions. In aqueous solution it presents an unordered conformation, while in a membrane mimetic environment it assumes a helical structure. The effects of oxidative stress were evaluated exposing it to both oxygen and nitrogen radicals as well as to lipoxidation byproducts. The results showed that ROS, but not NRS, induced appreciable conformational changes, and only in the membrane mimetic environment. Lipoxidation byproducts, instead, led to secondary structure modifications much more evident than those induced by the direct action of ROS and RNS, and in both analyzed media. Additionally, MALDI-TOF analyses detected mass variations in the peptide attributable to oxidation of the C-terminal Met residue and deamination of asparagine in the Asn-His sequence. Taken together, all these data seem to confirm the involvement of oxidative processes in dysfunctions of the orexinergic system.
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Nakayoshi T, Kato K, Kurimoto E, Takano Y, Oda A. Predicting Reaction Mechanisms for the Threonine-Residue Stereoinversion Catalyzed by a Dihydrogen Phosphate Ion. ACS OMEGA 2022; 7:18306-18314. [PMID: 35694452 PMCID: PMC9178615 DOI: 10.1021/acsomega.2c00372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
The stereoinversion of amino acid residues in proteins is considered to trigger various age-related diseases. Serine (Ser) residues are relatively prone to stereoinversion. It is assumed that threonine (Thr) residues also undergo stereoinversion, which results in the formation of the d-allo-Thr residue, by the same mechanisms as those for Ser-residue stereoinversion; however, d-allo-Thr residues have not been detected in vivo. To date, although Ser-residue stereoinversion has been suggested to progress via enolization, plausible reaction mechanisms for Thr-residue stereoinversion have not been proposed. In this study, we investigated the pathway of Thr-residue enolization and successfully identified the three types of plausible reaction pathways of Thr-residue stereoinversion catalyzed by a dihydrogen phosphate ion. The geometries of reactant complexes, transition states, and enolized product complexes were optimized using B3LYP density functional methods, and single-point calculations were performed for all optimized geometries using Møller-Plesset perturbation theory to obtain reliable energies. As a result, the calculated activation energies of Thr-residue stereoinversion were 105-106 kJ mol-1, which were comparable with those of Ser-residue stereoinversion reported previously. The infrequency of Thr-residue stereoinversion may be due to other factors, such as the hydrophobicity and/or the steric hindrance of the γ-methyl group, rather than the high activation energies.
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Affiliation(s)
- Tomoki Nakayoshi
- Graduate
School of Information Sciences, Hiroshima
City University, 3-4-1 Ozukahigashi, Asaminami-ku, Hiroshima, Hiroshima 731-3194, Japan
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan
- Institute
of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Koichi Kato
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan
- Faculty
of Pharmaceutical Sciences, Shonan University
of Medical Sciences, 16-48 Kamishinano, Totsuka-ku, Yokohama, Kanagawa 244-0806, Japan
- College
of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan
| | - Eiji Kurimoto
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan
| | - Yu Takano
- Graduate
School of Information Sciences, Hiroshima
City University, 3-4-1 Ozukahigashi, Asaminami-ku, Hiroshima, Hiroshima 731-3194, Japan
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Akifumi Oda
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan
- Institute
of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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Zhou Y, Wang Y. Sample Preparation Matters for Peptide Mapping to Evaluate Deamidation of Adeno-Associated Virus (AAV) Capsid Proteins using LC-MS/MS. Hum Gene Ther 2022; 33:821-828. [PMID: 35570652 DOI: 10.1089/hum.2021.207] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Adeno-associated viral capsid proteins (AAV VP) are the major components that determine the tissue specificity and immunogenicity, and in vivo transduction performance of the vector. It was reported that asparagine deamidation of AAV capsid proteins leads to charge variants/heterogeneity and altered vector function, reduction of stability and potency of AAV gene therapy products. Deamidation of asparagine residue is a common post-translational modification of proteins and is mostly detected and quantified by liquid chromatography-tandem mass spectrometry (LC-MS/MS) based peptide mapping. However, deamidation can be spontaneously introduced during sample preparation prior to LC-MS/MS analysis. So far, no optimal sample preparations, instead, traditional sample preparation has been used for AAV VP peptide mapping, resulting in exaggerating the original deamidation levels. It is important to accurately monitor and provide true value of asparagine deamidation for development of AAV gene therapy products. In this study, we evaluated denaturation temperatures, digestion durations, and digestion temperatures using three different sample preparation formats for LC-MS/MS based assessment of deamidation of AAV9 capsid proteins. The results demonstrated that the optimal sample preparation method for AAV9 VP peptide mapping minimized asparagine deamidation artifacts. Although AAV9 was used for method optimization, this study may also provide a guidance on how to control deamidation artifacts for other AAV serotypes.
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Affiliation(s)
- Yu Zhou
- Novartis Gene Therapies, Analytical Development, 10210 Campus Point Drive, 250 Suite, San Diego, California, United States, 92121;
| | - Yueju Wang
- Novartis Gene Therapies, Analytical Development, San Diego, California, United States;
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Kato K, Nakayoshi T, Ishikawa Y, Kurimoto E, Oda A. Computational Analysis of the Mechanism of Nonenzymatic Peptide Bond Cleavage at the C-Terminal Side of an Asparagine Residue. ACS OMEGA 2021; 6:30078-30084. [PMID: 34778679 PMCID: PMC8582265 DOI: 10.1021/acsomega.1c04821] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
The nonenzymatic peptide bond cleavage at the C-terminal side of Asn residues is a protein post-translational modification that occurs under physiological conditions. This reaction proceeds much slower than the deamidation of the Asn side chain and causes denaturation and hypofunction of proteins. The peptide bond cleavage of Asn is detected primarily in crystallins and aquaporin 0 in the eye lens. Therefore, cleavage is thought to be involved in age-related cataracts. In this study, to clarify the mechanism underlying succinimide formation for the peptide bond cleavage of the Asn residue, we performed quantum chemical calculations on the model compound Ace-Asn-Gly-Nme (Ace = acetyl and Nme = methylamino). The density functional theory with the B3LYP/6-31+G(d,p) level of theory was used to obtain optimized geometries. The results suggested that the reaction proceeds through two steps, cyclization and C-terminal fragment release, and the required proton transfers can be mediated by H2PO4 - and HCO3 - ions. The conformational change of the main chain on the N-terminal side of Asn was needed for the C-terminal fragmentation step, and a separate conformational change at the C-terminal side was required for the cyclization step. Furthermore, the calculated activation barriers of the reactions catalyzed by the H2PO4 - ion (130 kJ mol-1) and the HCO3 - ion (123 kJ mol-1) were sufficiently low for the reactions to occur under normal physiological conditions.
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Affiliation(s)
- Koichi Kato
- Faculty
of Pharmaceutical Sciences, Shonan University
of Medical Sciences, 16-48 Kamishinano, Totsuka-ku, Yokohama, Kanagawa 244-0806, Japan
- College
of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
| | - Tomoki Nakayoshi
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
- Graduate
School of Information Sciences, Hiroshima
City University, 3-4-1 Ozukahigasi, Asaminami-ku, Hiroshima, Hiroshima 731-3194, Japan
| | - Yoshinobu Ishikawa
- Faculty
of Pharmaceutical Sciences, Shonan University
of Medical Sciences, 16-48 Kamishinano, Totsuka-ku, Yokohama, Kanagawa 244-0806, Japan
| | - Eiji Kurimoto
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
| | - Akifumi Oda
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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