1
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Sanni A, Hakim MA, Goli M, Adeniyi M, Talih F, Lanuzza B, Kobeissy F, Plazzi G, Moresco M, Mondello S, Ferri R, Mechref Y. Serum N-Glycan Profiling of Patients with Narcolepsy Type 1 Using LC-MS/MS. ACS OMEGA 2024; 9:32628-32638. [PMID: 39100283 PMCID: PMC11292663 DOI: 10.1021/acsomega.4c01593] [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: 02/19/2024] [Revised: 05/17/2024] [Accepted: 05/27/2024] [Indexed: 08/06/2024]
Abstract
The neurological condition known as narcolepsy type 1 (NT1) is an uncommon condition marked by extreme daytime sleepiness, cataplexy, sleep paralysis, hallucinations, disrupted nocturnal sleep, and low or undetectable levels of orexin in the CSF fluid. NT1 has been hypothesized to be an immunological disorder; its treatment is currently only symptomatic, and misdiagnosis is not uncommon. This study compares the N-glycome of NT1 patients with healthy controls in search of potential glycan biomarkers using LC-MS/MS. A total of 121 candidate N-glycans were identified, 55 of which were isomeric N-glycan structures and 65 were not. Seventeen N-glycan biomarker candidates showed significant differences between the NT1 and control cohorts. All of the candidate glycan biomarkers were isomeric except HexNAc6Hex7Fuc0NeuAc1 (6701) and HexNAc6Hex7Fuc1NeuAc2 (6712). Therefore, with isomeric and nonisomeric structures, a total of 20 candidate N-glycan biomarkers are reported in this study, and interestingly, all are either sialylated or sialylated-fucosylated and upregulated in NT1 relative to the control. The distribution levels of all the identified N-glycans show that the sialylated glycan type is the most abundant in NT1 and is majorly disialylated, although the trisialylated subtype is three-fold higher in NT1 compared to the healthy control. The first isomers of HexNAc5Hex6Fuc0NeuAc3 (5603), HexNAc6Hex7Fuc0NeuAc2 (6702), and HexNAc6Hex7Fuc1NeuAc4 (6714) expressed a high level of fold changes (FC) of 1.62, 2.19, and 2.98, respectively. These results suggest a different N-glycome profile of NT1 and a relationship between sialylated glycan isomers in NT1 disease development or progression. The revelation of N-glycan expression alterations in this study may improve NT1 diagnostic methods, understanding of NT1 pathology, and the development of new targeted therapeutics.
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Affiliation(s)
- Akeem Sanni
- Chemistry
and Biochemistry Department, Texas Tech
University, Lubbock, Texas 79409, United States
| | - Md Abdul Hakim
- Chemistry
and Biochemistry Department, Texas Tech
University, Lubbock, Texas 79409, United States
| | - Mona Goli
- Chemistry
and Biochemistry Department, Texas Tech
University, Lubbock, Texas 79409, United States
| | - Moyinoluwa Adeniyi
- Chemistry
and Biochemistry Department, Texas Tech
University, Lubbock, Texas 79409, United States
| | - Farid Talih
- Department
of Psychiatry, Faculty of Medicine, American
University of Beirut, Beirut 1107 2020, Lebanon
| | - Bartolo Lanuzza
- Sleep
Research Centre, Department of Neurology IC, Oasi Research Institute-IRCCS, Troina 94018, Italy
| | - Firas Kobeissy
- Department
of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
- Department
of Neurobiology, Center for Neurotrauma, Multiomics and Biomarkers
(CNMB), Neuroscience Institute, Morehouse
School of Medicine (MSM), Atlanta, Georgia 30310-1458, United States
| | - Giuseppe Plazzi
- IRCCS, Istituto
delle Scienze Neurologiche di Bologna, Bologna 40138, Italy
- Department
of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena 41121, Italy
| | - Monica Moresco
- IRCCS, Istituto
delle Scienze Neurologiche di Bologna, Bologna 40138, Italy
| | - Stefania Mondello
- Department
of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina 98122, Italy
| | - Raffaele Ferri
- Sleep
Research Centre, Department of Neurology IC, Oasi Research Institute-IRCCS, Troina 94018, Italy
| | - Yehia Mechref
- Chemistry
and Biochemistry Department, Texas Tech
University, Lubbock, Texas 79409, United States
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2
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Usama, Khan Z, Ali A, Shah M, Imran M. Differential glycosylation in mutant vitamin D-binding protein decimates the binding stability of vitamin D. J Biomol Struct Dyn 2024; 42:5365-5375. [PMID: 37357441 DOI: 10.1080/07391102.2023.2226742] [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: 03/31/2023] [Accepted: 06/10/2023] [Indexed: 06/27/2023]
Abstract
Vitamin D (VD) is produced by the skin upon exposure to sunlight or is obtained from dietary sources. Several risk factors are associated with VD deficiency including mutations and post-translational modifications in its transport protein known as vitamin D binding protein (VDBP) or GC-globulin. The two common single nucleotide polymorphisms rs7041 and rs4588 create three major isoforms of VDBP, including GC-1F also called wild type, GC1S, and GC-2. The 3D models for both GC-1F and GC-2 were constructed in their glycosylated states to decipher the effect of these mutations on the overall conformational changes and VD-binding affinity. The binding affinities were estimated using the Molecular Mechanics Poison-Boltzmann surface area (MM-PBSA) method and conformational changes were investigated after free energy landscapes estimations. Total free energies suggest that GC-1F exhibits stronger affinity (ΔE = -116.09 kJ/mol) than GC-2 (ΔE = -95 kJ/mol) variant with VD. The GC-1F isoforms had more streamlined motion compared to GC-2 isoforms, predicting a trade-off between cross-talk residues that significantly impacts protein structural stability. The data suggest that glycation at Thr418 plays a vital role in the overall VDBP-VD affinity by stabilizing the N-T loop that holds the domain I (VD-pocket) and domain III intact. The loss of glycation in GC-2 has a pivotal role in the inter-domain conformational stability of VDBP, which may ultimately affect VD transportation and maturation. These findings describe a novel mechanism in how mutations distant from the VD-active site change the overall conformational of the VDBP and abrogate the VDBP-VD interaction.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Usama
- Biochemistry Section, Institute of Chemical Sciences, University of Peshawar, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Zahid Khan
- Biochemistry Section, Institute of Chemical Sciences, University of Peshawar, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Aktar Ali
- Biological Screening Core, Warren Family Center for Drug Discovery, University of Notre Dame, Notre Dame, Indiana, USA
| | - Masaud Shah
- Department of Physiology, School of Medicine, Ajou University, Suwon, South Korea
| | - Muhammad Imran
- Biochemistry Section, Institute of Chemical Sciences, University of Peshawar, Peshawar, Khyber Pakhtunkhwa, Pakistan
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3
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Liu HZ, Song XQ, Zhang H. Sugar-coated bullets: Unveiling the enigmatic mystery 'sweet arsenal' in osteoarthritis. Heliyon 2024; 10:e27624. [PMID: 38496870 PMCID: PMC10944269 DOI: 10.1016/j.heliyon.2024.e27624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/19/2024] Open
Abstract
Glycosylation is a crucial post-translational modification process where sugar molecules (glycans) are covalently linked to proteins, lipids, or other biomolecules. In this highly regulated and complex process, a series of enzymes are involved in adding, modifying, or removing sugar residues. This process plays a pivotal role in various biological functions, influencing the structure, stability, and functionality of the modified molecules. Glycosylation is essential in numerous biological processes, including cell adhesion, signal transduction, immune response, and biomolecular recognition. Dysregulation of glycosylation is associated with various diseases. Glycation, a post-translational modification characterized by the non-enzymatic attachment of sugar molecules to proteins, has also emerged as a crucial factor in various diseases. This review comprehensively explores the multifaceted role of glycation in disease pathogenesis, with a specific focus on its implications in osteoarthritis (OA). Glycosylation and glycation alterations wield a profound influence on OA pathogenesis, intertwining with disease onset and progression. Diverse studies underscore the multifaceted role of aberrant glycosylation in OA, particularly emphasizing its intricate relationship with joint tissue degradation and inflammatory cascades. Distinct glycosylation patterns, including N-glycans and O-glycans, showcase correlations with inflammatory cytokines, matrix metalloproteinases, and cellular senescence pathways, amplifying the degenerative processes within cartilage. Furthermore, the impact of advanced glycation end-products (AGEs) formation in OA pathophysiology unveils critical insights into glycosylation-driven chondrocyte behavior and extracellular matrix remodeling. These findings illuminate potential therapeutic targets and diagnostic markers, signaling a promising avenue for targeted interventions in OA management. In this comprehensive review, we aim to thoroughly examine the significant impact of glycosylation or AGEs in OA and explore its varied effects on other related conditions, such as liver-related diseases, immune system disorders, and cancers, among others. By emphasizing glycosylation's role beyond OA and its implications in other diseases, we uncover insights that extend beyond the immediate focus on OA, potentially revealing novel perspectives for diagnosing and treating OA.
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Affiliation(s)
- Hong-zhi Liu
- Department of Orthopaedics, Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xin-qiu Song
- The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Hongmei Zhang
- Department of Orthopaedics, Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing, China
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4
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Seitz C, Deveci İ, McCammon JA. Glycosylation and Crowded Membrane Effects on Influenza Neuraminidase Stability and Dynamics. J Phys Chem Lett 2023; 14:9926-9934. [PMID: 37903229 PMCID: PMC10641874 DOI: 10.1021/acs.jpclett.3c02524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 11/01/2023]
Abstract
All protein simulations are conducted with varying degrees of simplification, oftentimes with unknown ramifications about how these simplifications affect the interpretability of the results. In this work, we investigated how protein glycosylation and lateral crowding effects modulate an array of properties characterizing the stability and dynamics of influenza neuraminidase. We constructed three systems: (1) glycosylated neuraminidase in a whole virion (i.e., crowded membrane) environment, (2) glycosylated neuraminidase in its own lipid bilayer, and (3) unglycosylated neuraminidase in its own lipid bilayer. We saw that glycans tend to stabilize the protein structure and reduce its conformational flexibility while restricting the solvent movement. Conversely, a crowded membrane environment encouraged exploration of the free energy landscape and a large-scale conformational change, while making the protein structure more compact. Understanding these effects informs what factors one must consider in attempting to recapture the desired level of physical accuracy.
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Affiliation(s)
- Christian Seitz
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - İlker Deveci
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - J. Andrew McCammon
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
- Department
of Pharmacology, University of California,
San Diego, La Jolla, California 92093, United States
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5
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Seitz C, Deveci İ, McCammon JA. Glycosylation and Crowded Membrane Effects on Influenza Neuraminidase Stability and Dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.10.556910. [PMID: 37745347 PMCID: PMC10515755 DOI: 10.1101/2023.09.10.556910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
All protein simulations are conducted with varying degrees of simplifications, oftentimes with unknown ramifications on how these simplifications affect the interpretability of the results. In this work we investigated how protein glycosylation and lateral crowding effects modulate an array of properties characterizing the stability and dynamics of influenza neuraminidase. We constructed three systems: 1) Glycosylated neuraminidase in a whole virion (i.e. crowded membrane) environment 2) Glycosylated neuraminidase in its own lipid bilayer 3) Unglycosylated neuraminidase in its own lipid bilayer. We saw that glycans tend to stabilize the protein structure and reduce its conformational flexibility while restricting solvent movement. Conversely, a crowded membrane environment encouraged exploration of the free energy landscape and a large scale conformational change while making the protein structure more compact. Understanding these effects informs what factors one must consider while attempting to recapture the desired level of physical accuracy.
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Affiliation(s)
- Christian Seitz
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - İlker Deveci
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - J. Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
- Department of Pharmacology, University of California, San Diego, La Jolla, California
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6
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Shoup D, Priola SA. Full-length prion protein incorporated into prion aggregates is a marker for prion strain-specific destabilization of aggregate structure following cellular uptake. J Biochem 2023; 174:165-181. [PMID: 37099550 PMCID: PMC10506170 DOI: 10.1093/jb/mvad032] [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: 01/06/2023] [Revised: 03/30/2023] [Accepted: 04/09/2023] [Indexed: 04/27/2023] Open
Abstract
Accumulation of insoluble aggregates of infectious, partially protease-resistant prion protein (PrPD) generated via the misfolding of protease sensitive prion protein (PrPC) into the same infectious conformer, is a hallmark of prion diseases. Aggregated PrPD is taken up and degraded by cells, a process likely involving changes in aggregate structure that can be monitored by accessibility of the N-terminus of full-length PrPD to cellular proteases. We therefore tracked the protease sensitivity of full-length PrPD before and after cellular uptake for two murine prion strains, 22L and 87V. For both strains, PrPD aggregates were less stable following cellular uptake with increased accessibility of the N-terminus to cellular proteases across most aggregate sizes. However, a limited size range of aggregates was able to better protect the N-termini of full-length PrPD, with the N-terminus of 22L-derived PrPD more protected than that of 87V. Interestingly, changes in aggregate structure were associated with minimal changes to the protease-resistant core of PrPD. Our data show that cells destabilize the aggregate quaternary structure protecting PrPD from proteases in a strain-dependent manner, with structural changes exposing protease sensitive PrPD having little effect on the protease-resistant core, and thus conformation, of aggregated PrPD.
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Affiliation(s)
- Daniel Shoup
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy & Infectious Diseases, National Institutes of Health, 903 S. 4th Str, Hamilton, MT 59840 USA
| | - Suzette A Priola
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy & Infectious Diseases, National Institutes of Health, 903 S. 4th Str, Hamilton, MT 59840 USA
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7
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Oliveira RJD. Coordinate-Dependent Drift-Diffusion Reveals the Kinetic Intermediate Traps of Top7-Based Proteins. J Phys Chem B 2022; 126:10854-10869. [PMID: 36519977 DOI: 10.1021/acs.jpcb.2c07031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The computer-designed Top7 served as a scaffold to produce immunoreactive proteins by grafting of the 2F5 HIV-1 antibody epitope (Top7-2F5) followed by biotinylation (Top7-2F5-biotin). The resulting nonimmunoglobulin affinity proteins were effective in inducing and detecting the HIV-1 antibody. However, the grafted Top7-2F5 design led to protein aggregation, as opposed to the soluble biotinylated Top7-2F5-biotin. The structure-based model predicted that the thermodynamic cooperativity of Top7 increases after grafting and biotin-labeling, reducing their intermediate state populations. In this work, the folding kinetic traps that might contribute to the aggregation propensity are investigated by the diffusion theory. Since the engineered proteins have similar sequence and structural homology, they served as protein models to study the kinetic intermediate traps that were uncovered by characterizing the position-dependent drift-velocity (v(Q)) and the diffusion (D(Q)) coefficients. These coordinate-dependent coefficients were taken into account to obtain the folding and transition path times over the free energy transition states containing the intermediate kinetic traps. This analysis may be useful to predict the aggregated kinetic traps of scaffold-epitope proteins that might compose novel diagnostic and therapeutic platforms.
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Affiliation(s)
- Ronaldo Junio de Oliveira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG38064-200, Brazil
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8
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Weigle AT, Feng J, Shukla D. Thirty years of molecular dynamics simulations on posttranslational modifications of proteins. Phys Chem Chem Phys 2022; 24:26371-26397. [PMID: 36285789 PMCID: PMC9704509 DOI: 10.1039/d2cp02883b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Posttranslational modifications (PTMs) are an integral component to how cells respond to perturbation. While experimental advances have enabled improved PTM identification capabilities, the same throughput for characterizing how structural changes caused by PTMs equate to altered physiological function has not been maintained. In this Perspective, we cover the history of computational modeling and molecular dynamics simulations which have characterized the structural implications of PTMs. We distinguish results from different molecular dynamics studies based upon the timescales simulated and analysis approaches used for PTM characterization. Lastly, we offer insights into how opportunities for modern research efforts on in silico PTM characterization may proceed given current state-of-the-art computing capabilities and methodological advancements.
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Affiliation(s)
- Austin T Weigle
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jiangyan Feng
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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9
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Freitas FC, Maldonado M, Oliveira Junior AB, Onuchic JN, Oliveira RJD. Biotin-painted proteins have thermodynamic stability switched by kinetic folding routes. J Chem Phys 2022; 156:195101. [PMID: 35597640 DOI: 10.1063/5.0083875] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Biotin-labeled proteins are widely used as tools to study protein-protein interactions and proximity in living cells. Proteomic methods broadly employ proximity-labeling technologies based on protein biotinylation in order to investigate the transient encounters of biomolecules in subcellular compartments. Biotinylation is a post-translation modification in which the biotin molecule is attached to lysine or tyrosine residues. So far, biotin-based technologies proved to be effective instruments as affinity and proximity tags. However, the influence of biotinylation on aspects such as folding, binding, mobility, thermodynamic stability, and kinetics needs to be investigated. Here, we selected two proteins [biotin carboxyl carrier protein (BCCP) and FKBP3] to test the influence of biotinylation on thermodynamic and kinetic properties. Apo (without biotin) and holo (biotinylated) protein structures were used separately to generate all-atom structure-based model simulations in a wide range of temperatures. Holo BCCP contains one biotinylation site, and FKBP3 was modeled with up to 23 biotinylated lysines. The two proteins had their estimated thermodynamic stability changed by altering their energy landscape. In all cases, after comparison between the apo and holo simulations, differences were observed on the free-energy profiles and folding routes. Energetic barriers were altered with the density of states clearly showing changes in the transition state. This study suggests that analysis of large-scale datasets of biotinylation-based proximity experiments might consider possible alterations in thermostability and folding mechanisms imposed by the attached biotins.
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Affiliation(s)
- Frederico Campos Freitas
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG 38064-200, Brazil
| | - Michelli Maldonado
- Departamento de Matemática, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG 38064-200, Brazil
| | - Antonio Bento Oliveira Junior
- Center for Theoretical Biological Physics, Rice University, BioScience Research Collaborative, 6566 Main St., Houston, Texas 77030, USA
| | - José Nelson Onuchic
- Center for Theoretical Biological Physics, Rice University, BioScience Research Collaborative, 6566 Main St., Houston, Texas 77030, USA
| | - Ronaldo Junio de Oliveira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG 38064-200, Brazil
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10
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Chakraborty S, Wagh K, Gnanakaran S, López CA. Development of Martini 2.2 parameters for N-glycans: a case study of the HIV-1 Env glycoprotein dynamics. Glycobiology 2021; 31:787-799. [PMID: 33755116 PMCID: PMC8351497 DOI: 10.1093/glycob/cwab017] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 02/15/2021] [Accepted: 03/01/2021] [Indexed: 12/18/2022] Open
Abstract
N-linked glycans are ubiquitous in nature and play key roles in biology. For example, glycosylation of pathogenic proteins is a common immune evasive mechanism, hampering the development of successful vaccines. Due to their chemical variability and complex dynamics, an accurate molecular understanding of glycans is still limited by the lack of effective resolution of current experimental approaches. Here, we have developed and implemented a reductive model based on the popular Martini 2.2 coarse-grained force field for the computational study of N-glycosylation. We used the HIV-1 Env as a direct applied example of a highly glycosylated protein. Our results indicate that the model not only reproduces many observables in very good agreement with a fully atomistic force field but also can be extended to study large amount of glycosylation variants, a fundamental property that can aid in the development of drugs and vaccines.
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Affiliation(s)
- Srirupa Chakraborty
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Kshitij Wagh
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Cesar A López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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11
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Füssl F, Barry CS, Pugh KM, Chooi KP, Vijayakrishnan B, Kang GD, von Bulow C, Howard PW, Bones J. Simultaneous monitoring of multiple attributes of pyrrolobenzodiazepine antibody-drug conjugates by size exclusion chromatography - high resolution mass spectrometry. J Pharm Biomed Anal 2021; 205:114287. [PMID: 34385015 DOI: 10.1016/j.jpba.2021.114287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/07/2021] [Accepted: 07/24/2021] [Indexed: 11/24/2022]
Abstract
Antibody-drug conjugates (ADCs) are an emerging class of oncology treatments combining the unique specificity of monoclonal antibodies with the highly cytotoxic properties of small molecule compounds. Pyrrolobenzodiazepines (PBDs) are highly potent agents capable of inhibiting cellular DNA replication which leads to apoptosis. To ensure efficacy and patient safety upon administration of such toxic and heterogeneous molecules, their structure and quality attributes must be closely monitored. Size exclusion chromatography (SEC) is a powerful, fast and robust tool for the separation of compounds varying in molecular weight. When using volatile components in the chromatographic mobile phase, SEC has also been shown to be amenable for interfacing to mass spectrometry, providing potential for reliable identification of protein isoforms across the size variants present. Here, we present a SEC-MS method developed for the characterisation of PBD-based ADCs on the intact molecular level. We demonstrate that information on ADC monomers such as the glycoform distribution and the average drug-antibody ratio (DAR) can be obtained in 15 minutes of analysis time. Qualitative and quantitative information on low and high molecular weight impurities such as aggregates and fragments, fundamental for critical quality attribute analysis of biopharmaceuticals, can be generated simultaneously. SEC-MS enables the characterisation of multiple product quality attributes of complex biotherapeutics at the same time.
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Affiliation(s)
- Florian Füssl
- NIBRT - The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, A94 X099, Ireland
| | - Conor S Barry
- Spirogen, a Member of the AstraZeneca Group, QMB Innovation Centre, 42 New Road, London, E1 2AX, United Kingdom
| | - Kathryn M Pugh
- Spirogen, a Member of the AstraZeneca Group, QMB Innovation Centre, 42 New Road, London, E1 2AX, United Kingdom
| | - K Phin Chooi
- Spirogen, a Member of the AstraZeneca Group, QMB Innovation Centre, 42 New Road, London, E1 2AX, United Kingdom
| | - Balakumar Vijayakrishnan
- Spirogen, a Member of the AstraZeneca Group, QMB Innovation Centre, 42 New Road, London, E1 2AX, United Kingdom
| | - Gyoung-Dong Kang
- Spirogen, a Member of the AstraZeneca Group, QMB Innovation Centre, 42 New Road, London, E1 2AX, United Kingdom
| | - Christina von Bulow
- Spirogen, a Member of the AstraZeneca Group, QMB Innovation Centre, 42 New Road, London, E1 2AX, United Kingdom
| | - Philip W Howard
- Spirogen, a Member of the AstraZeneca Group, QMB Innovation Centre, 42 New Road, London, E1 2AX, United Kingdom
| | - Jonathan Bones
- NIBRT - The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, A94 X099, Ireland; School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland.
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12
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Li B, Wang L, Ge H, Zhang X, Ren P, Guo Y, Chen W, Li J, Zhu W, Chen W, Zhu L, Bai F. Identification of Potential Binding Sites of Sialic Acids on the RBD Domain of SARS-CoV-2 Spike Protein. Front Chem 2021; 9:659764. [PMID: 34368076 PMCID: PMC8341434 DOI: 10.3389/fchem.2021.659764] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 02/25/2021] [Indexed: 12/24/2022] Open
Abstract
COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is still an emergent pandemic for humans. The virus infection is achieved by penetrating its spike protein to host cells via binding with ACE2. Moreover, recent studies show that SARS-CoV-2 may have multiple receptors that need to be further revealed. SARS-CoV-2 shares similar sequences of the spike protein with the Middle East Respiratory Syndrome Coronavirus (MERS-CoV), which can invade host cells by binding to either DPP4 or sialic acids. Sialic acids can be linked to the terminal of glycoproteins and gangliosides are used as one of the receptors of many types of viruses. Therefore, it is very interesting to determine whether sialic acid is a potential receptor of SARS-CoV-2. To address this question, we took N-Acetylneuraminic acid (Neu5Ac), a type of predominant sialic acid found in human cells, as the molecular probe to computationally search the surface of the spike protein to locate the potential binding sites of Neu5Ac. SPR analysis and mass spectrum analysis confirmed the interaction between Neu5Ac and spike protein. This study shows that sialic acids can moderately interact with the spike protein of SARS-CoV-2 by binding between the two RBDs of the spike protein, indicating it could be a potential secondary or auxiliary receptor of SARS-CoV-2.
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Affiliation(s)
- Bingqian Li
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,Department of Chemistry, Imperial College London, London, United Kingdom
| | - Lin Wang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Huan Ge
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Xianglei Zhang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Penxuan Ren
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yu Guo
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China
| | - Wuyan Chen
- National Center for Protein Science Shanghai, Shanghai, China
| | - Jie Li
- National Center for Protein Science Shanghai, Shanghai, China
| | - Wei Zhu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Wenzhang Chen
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Lili Zhu
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Fang Bai
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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13
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Ardejani MS, Noodleman L, Powers ET, Kelly JW. Stereoelectronic effects in stabilizing protein-N-glycan interactions revealed by experiment and machine learning. Nat Chem 2021; 13:480-487. [PMID: 33723379 PMCID: PMC8102341 DOI: 10.1038/s41557-021-00646-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 01/27/2021] [Indexed: 01/31/2023]
Abstract
The energetics of protein-carbohydrate interactions, central to many life processes, cannot yet be manipulated predictably. This is mostly due to an incomplete quantitative understanding of the enthalpic and entropic basis of these interactions in aqueous solution. Here, we show that stereoelectronic effects contribute to stabilizing protein-N-glycan interactions in the context of a cooperatively folding protein. Double-mutant cycle analyses of the folding data from 52 electronically varied N-glycoproteins demonstrate an enthalpy-entropy compensation depending on the electronics of the interacting side chains. Linear and nonlinear models obtained using quantum mechanical calculations and machine learning explain up to 79% and 97% of the experimental interaction energy variability, as inferred from the R2 value of the respective models. Notably, the protein-carbohydrate interaction energies strongly correlate with the molecular orbital energy gaps of the interacting substructures. This suggests that stereoelectronic effects must be given a greater weight than previously thought for accurately modelling the short-range dispersive van der Waals interactions between the N-glycan and the protein.
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Affiliation(s)
- Maziar S. Ardejani
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Louis Noodleman
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Evan T. Powers
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jeffery W. Kelly
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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14
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Sepahvandi A, Ghaffari M, Bahmanpour AH, Moztarzadeh F, Zarrintaj P, Uludağ H, Mozafari M. COVID-19: insights into virus-receptor interactions. MOLECULAR BIOMEDICINE 2021; 2:10. [PMID: 34766003 PMCID: PMC8035060 DOI: 10.1186/s43556-021-00033-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 03/03/2021] [Indexed: 01/03/2023] Open
Abstract
The recent outbreak of Coronavirus Disease 2019 (COVID-19) calls for rapid mobilization of scientists to probe and explore solutions to this deadly disease. A limited understanding of the high transmissibility of SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) relative to other coronavirus strains guides a deeper investigation into the virus/receptor interactions. The cutting-edge studies in thermodynamic and kinetic properties of interactions such as protein-protein interplays have been reviewed in many modeling and analysis studies. Highlighting the thermodynamic assessments of biological interactions and emphasizing the boosted transmissibility of SARS-CoV-2 despite its high similarity in structure and sequence with other coronavirus strains is an important and highly valuable investigation that can lead scientists to discover analytical and fundamental approaches in studying virus's interactions. Accordingly, we have attempted to describe the crucial factors such as conformational changes and hydrophobicity particularities that influence on thermodynamic potentials in the SARS-COV-2 S-protein adsorption process. Discussing the thermodynamic potentials and the kinetics of the SARS-CoV-2 S-protein in its interaction with the ACE2 receptors of the host cell is a fundamental approach that would be extremely valuable in designing candidate pharmaceutical agents or exploring alternative treatments.
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Affiliation(s)
- Azadeh Sepahvandi
- Department of Mechanical Engineering College of Engineering and Computing, University of South Carolina, 301 Main St, Columbia, SC 29208 USA
| | - Maryam Ghaffari
- Biomaterial Group, Faculty of Biomedical Engineering (Center of Excellence), Amirkabir University of Technology, Tehran, Iran
| | - Amir Hossein Bahmanpour
- Biomaterial Group, Faculty of Biomedical Engineering (Center of Excellence), Amirkabir University of Technology, Tehran, Iran
| | - Fathollah Moztarzadeh
- Biomaterial Group, Faculty of Biomedical Engineering (Center of Excellence), Amirkabir University of Technology, Tehran, Iran
| | - Payam Zarrintaj
- School of Chemical Engineering, Oklahoma State University, 420 Engineering North, Stillwater, OK 74078 USA
| | - Hasan Uludağ
- Department of Chemical and Material Engineering, Faculty of Engineering, University of Alberta, Edmonton, AB T6G 2V4 Canada
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2E1 Canada
- Department of Biomedical Engineering, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2R3 Canada
| | - Masoud Mozafari
- Department of Tissue Engineering & Regenerative Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran
- Currently at: Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, ON Canada
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15
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Saei AA, Beusch CM, Sabatier P, Wells JA, Gharibi H, Meng Z, Chernobrovkin A, Rodin S, Näreoja K, Thorsell AG, Karlberg T, Cheng Q, Lundström SL, Gaetani M, Végvári Á, Arnér ESJ, Schüler H, Zubarev RA. System-wide identification and prioritization of enzyme substrates by thermal analysis. Nat Commun 2021; 12:1296. [PMID: 33637753 PMCID: PMC7910609 DOI: 10.1038/s41467-021-21540-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 01/26/2021] [Indexed: 02/06/2023] Open
Abstract
Despite the immense importance of enzyme-substrate reactions, there is a lack of general and unbiased tools for identifying and prioritizing substrate proteins that are modified by the enzyme on the structural level. Here we describe a high-throughput unbiased proteomics method called System-wide Identification and prioritization of Enzyme Substrates by Thermal Analysis (SIESTA). The approach assumes that the enzymatic post-translational modification of substrate proteins is likely to change their thermal stability. In our proof-of-concept studies, SIESTA successfully identifies several known and novel substrate candidates for selenoprotein thioredoxin reductase 1, protein kinase B (AKT1) and poly-(ADP-ribose) polymerase-10 systems. Wider application of SIESTA can enhance our understanding of the role of enzymes in homeostasis and disease, opening opportunities to investigate the effect of post-translational modifications on signal transduction and facilitate drug discovery.
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Affiliation(s)
- Amir Ata Saei
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
| | - Christian M Beusch
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Pierre Sabatier
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Juan Astorga Wells
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Hassan Gharibi
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Zhaowei Meng
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Alexey Chernobrovkin
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Pelago Bioscience AB, Solna, Sweden
| | - Sergey Rodin
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Katja Näreoja
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Ann-Gerd Thorsell
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Tobias Karlberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Qing Cheng
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Susanna L Lundström
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Massimiliano Gaetani
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- SciLifeLab, Stockholm, Sweden
- Chemical Proteomics Core Facility, Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ákos Végvári
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Proteomics Biomedicum, Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Elias S J Arnér
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Herwig Schüler
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Roman A Zubarev
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
- Department of Pharmacological & Technological Chemistry, I.M. Sechenov First Moscow State Medical University, Moscow, Russia.
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16
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Cui X, Mi W, Hu Z, Li X, Meng B, Zhao X, Qian X, Zhu T, Ying W. Global characterization of modifications to the charge isomers of IgG antibody. J Pharm Anal 2020; 12:156-163. [PMID: 35573890 PMCID: PMC9073142 DOI: 10.1016/j.jpha.2020.11.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 11/08/2020] [Accepted: 11/17/2020] [Indexed: 11/02/2022] Open
Abstract
Posttranslational modifications of antibody products affect their stability, charge distribution, and drug activity and are thus a critical quality attribute. The comprehensive mapping of antibody modifications and different charge isomers (CIs) is of utmost importance, but is challenging. We intended to quantitatively characterize the posttranslational modification status of CIs of antibody drugs and explore the impact of posttranslational modifications on charge heterogeneity. The CIs of antibodies were fractionated by strong cation exchange chromatography and verified by capillary isoelectric focusing-whole column imaging detection, followed by stepwise structural characterization at three levels. First, the differences between CIs were explored at the intact protein level using a top-down mass spectrometry approach; this showed differences in glycoforms and deamidation status. Second, at the peptide level, common modifications of oxidation, deamidation, and glycosylation were identified. Peptide mapping showed nonuniform deamidation and glycoform distribution among CIs. In total, 10 N-glycoforms were detected by peptide mapping. Finally, an in-depth analysis of glycan variants of CIs was performed through the detection of enriched glycopeptides. Qualitative and quantitative analyses demonstrated the dynamics of 24 N-glycoforms. The results revealed that sialic acid modification is a critical factor accounting for charge heterogeneity, which is otherwise missed in peptide mapping and intact molecular weight analyses. This study demonstrated the importance of the comprehensive analyses of antibody CIs and provides a reference method for the quality control of biopharmaceutical analysis. A stepwise investigation on the diversity and dynamics of modifications of antibody charge isomers (CIs) was performed. The results from SCX-HPLC and cIEF-WCID supported each other. In-depth analysis on glycan variants of CIs was achieved by analyzing the enriched glycopeptides. Sialic acid and deamidation modifications were critical factors for the charge heterogeneity.
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17
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Liu X, Liu J, Zhang W, Pearce R, Chen M, Zhang T, Liu B. Effect of the degree of glycation on the stability and aggregation of bovine serum albumin. Food Hydrocoll 2020. [DOI: 10.1016/j.foodhyd.2020.105892] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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18
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Mikolajczyk K, Kaczmarek R, Czerwinski M. How glycosylation affects glycosylation: the role of N-glycans in glycosyltransferase activity. Glycobiology 2020; 30:941-969. [PMID: 32363402 DOI: 10.1093/glycob/cwaa041] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 04/22/2020] [Accepted: 04/24/2020] [Indexed: 12/15/2022] Open
Abstract
N-glycosylation is one of the most important posttranslational modifications of proteins. It plays important roles in the biogenesis and functions of proteins by influencing their folding, intracellular localization, stability and solubility. N-glycans are synthesized by glycosyltransferases, a complex group of ubiquitous enzymes that occur in most kingdoms of life. A growing body of evidence shows that N-glycans may influence processing and functions of glycosyltransferases, including their secretion, stability and substrate/acceptor affinity. Changes in these properties may have a profound impact on glycosyltransferase activity. Indeed, some glycosyltransferases have to be glycosylated themselves for full activity. N-glycans and glycosyltransferases play roles in the pathogenesis of many diseases (including cancers), so studies on glycosyltransferases may contribute to the development of new therapy methods and novel glycoengineered enzymes with improved properties. In this review, we focus on the role of N-glycosylation in the activity of glycosyltransferases and attempt to summarize all available data about this phenomenon.
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Affiliation(s)
- Krzysztof Mikolajczyk
- Laboratory of Glycobiology, Hirszfeld Institute of Immunology and Experimental Therapy, Weigla 12, 53-114 Wroclaw, Poland
| | - Radoslaw Kaczmarek
- Laboratory of Glycobiology, Hirszfeld Institute of Immunology and Experimental Therapy, Weigla 12, 53-114 Wroclaw, Poland
| | - Marcin Czerwinski
- Laboratory of Glycobiology, Hirszfeld Institute of Immunology and Experimental Therapy, Weigla 12, 53-114 Wroclaw, Poland
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19
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Goutham S, Kumari I, Pally D, Singh A, Ghosh S, Akhter Y, Bhat R. Mutually exclusive locales for N-linked glycans and disorder in human glycoproteins. Sci Rep 2020; 10:6040. [PMID: 32269229 PMCID: PMC7142085 DOI: 10.1038/s41598-020-61427-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 01/30/2020] [Indexed: 11/08/2022] Open
Abstract
Several post-translational protein modifications lie predominantly within regions of disorder: the biased localization has been proposed to expand the binding versatility of disordered regions. However, investigating a representative dataset of 500 human N-glycoproteins, we observed the sites of N-linked glycosylations or N-glycosites, to be predominantly present in the regions of predicted order. When compared with disordered stretches, ordered regions were not found to be enriched for asparagines, serines and threonines, residues that constitute the sequon signature for conjugation of N-glycans. We then investigated the basis of mutual exclusivity between disorder and N-glycosites on the basis of amino acid distribution: when compared with control ordered residue stretches without any N-glycosites, residue neighborhoods surrounding N-glycosites showed a depletion of bulky, hydrophobic and disorder-promoting amino acids and an enrichment for flexible and accessible residues that are frequently found in coiled structures. When compared with control disordered residue stretches without any N-glycosites, N-glycosite neighborhoods were depleted of charged, polar, hydrophobic and flexible residues and enriched for aromatic, accessible and order-promoting residues with a tendency to be part of coiled and β structures. N-glycosite neighborhoods also showed greater phylogenetic conservation among amniotes, compared with control ordered regions, which in turn were more conserved than disordered control regions. Our results lead us to propose that unique primary structural compositions and differential propensities for evolvability allowed for the mutual spatial exclusion of N-glycosite neighborhoods and disordered stretches.
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Affiliation(s)
- Shyamili Goutham
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Sciences, Bangalore, 560012, India
| | - Indu Kumari
- School of Earth and Environmental Sciences, Central University of Himachal Pradesh, District-Kangra, Shahpur, Himachal Pradesh, 176206, India
| | - Dharma Pally
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Sciences, Bangalore, 560012, India
| | - Alvina Singh
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Sciences, Bangalore, 560012, India
| | - Sujasha Ghosh
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Sciences, Bangalore, 560012, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh, 226025, India
| | - Ramray Bhat
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Sciences, Bangalore, 560012, India.
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20
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Bigman LS, Levy Y. Proteins: molecules defined by their trade-offs. Curr Opin Struct Biol 2020; 60:50-56. [DOI: 10.1016/j.sbi.2019.11.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/07/2019] [Accepted: 11/11/2019] [Indexed: 12/30/2022]
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21
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Shi Z, Yin B, Li Y, Zhou G, Li C, Xu X, Luo X, Zhang X, Qi J, Voglmeir J, Liu L. N-Glycan Profile as a Tool in Qualitative and Quantitative Analysis of Meat Adulteration. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:10543-10551. [PMID: 31464438 DOI: 10.1021/acs.jafc.9b03756] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Adulteration of meat and meat products causes concerns to consumers. It is necessary to develop novel robust and sensitive methods that can authenticate the origin of meat by qualitative and quantitative means to minimize the drawbacks of the existing methods. This study has shown that the protein N-glycosylation profiles of different meats are species specific and thus can be used for meat authentication. Based on the N-glycan pattern, the investigated five meat species (beef, chicken, pork, duck, and mutton) can be distinguished by principal component analysis, and partial least square regression was performed to build a calibration and validation model for the prediction of adulteration ratio. Using this method, beef samples adulterated with a lower-value duck meat could be detected down to the addition ratio as low as 2.2%. The most distinguishing N-glycans from beef and duck were elucidated for the detailed structures.
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Affiliation(s)
| | | | | | | | | | | | - Xin Luo
- Lab of Beef Processing and Quality Control, College of Food Science and Engineering , Shandong Agricultural University , Taian , Shandong 271018 , China
| | - Xibin Zhang
- Lab of Beef Processing and Quality Control, College of Food Science and Engineering , Shandong Agricultural University , Taian , Shandong 271018 , China
- New Hope Liuhe Co. Ltd. , Beijing 100102 , China
| | - Jun Qi
- Anhui Engineering Laboratory for Agro-products Processing , Anhui Agricultural University , Hefei , Anhui 230036 , China
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22
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Neuraminidase 1 regulates proliferation, apoptosis and the expression of Cadherins in mammary carcinoma cells. Mol Cell Biochem 2019; 462:207-215. [DOI: 10.1007/s11010-019-03623-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 09/04/2019] [Indexed: 12/19/2022]
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23
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Modulation of protein activity and assembled structure by polymer conjugation: PEGylation vs glycosylation. Eur Polym J 2019. [DOI: 10.1016/j.eurpolymj.2019.01.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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24
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Franco A, Cano M, Giner-Casares JJ, Rodríguez-Castellón E, Luque R, Puente-Santiago AR. Boosting the electrochemical oxygen reduction activity of hemoglobin on fructose@graphene-oxide nanoplatforms. Chem Commun (Camb) 2019; 55:4671-4674. [DOI: 10.1039/c9cc01625b] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A metal-free oxygen reduction reaction (ORR) electrocatalyst with outstanding performance was obtained through an easy and one-pot synthesis of hemoglobin functionalized fructose@graphene-oxide (GO) nanocomposites.
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Affiliation(s)
- Ana Franco
- Departamento de Química Orgánica
- Facultad de Ciencias
- Universidad de Córdoba
- E-14071 Córdoba
- Spain
| | - Manuel Cano
- Dpto. de Química Física y Termodinámica Aplicada
- Instituto Universitario de Nanoquímica IUNAN
- Facultad de Ciencias
- Universidad de Córdoba
- E-14071 Córdoba
| | - Juan J. Giner-Casares
- Dpto. de Química Física y Termodinámica Aplicada
- Instituto Universitario de Nanoquímica IUNAN
- Facultad de Ciencias
- Universidad de Córdoba
- E-14071 Córdoba
| | - E. Rodríguez-Castellón
- Dpto. de Química Inorgánica
- Cristalografía y Mineralogía
- Facultad de Ciencias
- Universidad de Málaga
- Málaga
| | - Rafael Luque
- Departamento de Química Orgánica
- Facultad de Ciencias
- Universidad de Córdoba
- E-14071 Córdoba
- Spain
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25
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Smith J, Mittermayr S, Váradi C, Bones J. Quantitative glycomics using liquid phase separations coupled to mass spectrometry. Analyst 2018; 142:700-720. [PMID: 28170017 DOI: 10.1039/c6an02715f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Post-translational modification of proteins by the attachment of glycans is governed by a variety of highly specific enzymes and is associated with fundamental impacts on the parent protein's physical, chemical and biological properties. The inherent connection between cellular physiology and specific glycosylation patterns has been shown to offer potential for diagnostic and prognostic monitoring of altered glycosylation in the disease state. Conversely, glycoprotein based biopharmaceuticals have emerged as dominant therapeutic strategies in the treatment of intricate diseases. Glycosylation present on these biopharmaceuticals represents a major critical quality attribute with impacts on both pharmacokinetics and pharmacodynamics. The structural variety of glycans, based upon their non-template driven assembly, poses a significant analytical challenge for both qualitative and quantitative analysis. Labile monosaccharide constituents, isomeric species and often low sample availability from biological sources necessitates meticulous sample handling, ultra-high-resolution analytical separation and sensitive detection techniques, respectively. In this article a critical review of analytical quantitation approaches using liquid phase separations coupled to mass spectrometry for released glycans of biopharmaceutical and biomedical significance is presented. Considerations associated with sample derivatisation strategies, ionisation, relative quantitation through isotopic as well as isobaric labelling, metabolic/enzymatic incorporation and targeted analysis are all thoroughly discussed.
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Affiliation(s)
- Josh Smith
- National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin, A94 X099, Ireland. and School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, D02 R590, Ireland
| | - Stefan Mittermayr
- National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin, A94 X099, Ireland.
| | - Csaba Váradi
- National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin, A94 X099, Ireland.
| | - Jonathan Bones
- National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin, A94 X099, Ireland. and School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, D04 V1 W8, Ireland
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Uslupehlivan M, Deveci R, Ün C. In silico investigation of the prion protein glycosylation profiles in relation to scrapie disease resistance in domestic sheep (Ovis aries). Mol Cell Probes 2018; 42:1-9. [PMID: 30261281 DOI: 10.1016/j.mcp.2018.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 09/07/2018] [Accepted: 09/23/2018] [Indexed: 01/04/2023]
Abstract
The prion protein is a membrane-bound glycoprotein which consists mainly α-helix structure. In contrast, the infectious prion protein shows the beta-sheet structure. The prion-associated diseases are all lethal neurodegenerative abnormalities, called transmissible spongiform encephalopathies. Scrapie is the most common type of these illnesses affecting sheep, goats, and moufflon. The VRQ, AHQ, ARR and N146S polymorphisms in the sheep prion gene have been found to be associated with resistance to scrapie disease. So far, the relationship of polymorphisms to three-dimensional protein structures, post-translational modifications, and scrapie resistance has not been studied. In this study, the potential N- and O-glycosylation positions of sheep prion protein polymorphisms were analyzed, the secondary and three-dimensional protein structure models were predicted, three-dimensional glycoprotein models were constructed and the role of glycosylation positions in protein interactions was investigated. Here, we found that protein secondary and three-dimensional structures vary among polymorphisms. Moreover, we found wild-type prion and all polymorphic variants show N-glycosylation at Asn184 and Asn200 positions, while O-glycosylation profiles are variant-specific. We also found that structural changes among prion polymorphisms leads to the formation of variant spesific O-glycosylation profiles and these positions are associated with protein interactions. Based on these findings, we suggest that O-glycosylation may be effective on resistance/susceptibility of sheep prion polymorphisms to scrapie disease.
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Affiliation(s)
- Muhammet Uslupehlivan
- Ege University, Faculty of Science, Department of Biology, Molecular Biology Section, Izmir, Turkey.
| | - Remziye Deveci
- Ege University, Faculty of Science, Department of Biology, Molecular Biology Section, Izmir, Turkey.
| | - Cemal Ün
- Ege University, Faculty of Science, Department of Biology, Molecular Biology Section, Izmir, Turkey.
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28
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Bigman LS, Levy Y. Stability Effects of Protein Mutations: The Role of Long-Range Contacts. J Phys Chem B 2018; 122:11450-11459. [DOI: 10.1021/acs.jpcb.8b07379] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lavi S. Bigman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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29
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Glycosylation Significantly Inhibits the Aggregation of Human Prion Protein and Decreases Its Cytotoxicity. Sci Rep 2018; 8:12603. [PMID: 30135544 PMCID: PMC6105643 DOI: 10.1038/s41598-018-30770-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 08/06/2018] [Indexed: 12/22/2022] Open
Abstract
Prion diseases are primarily caused by the misfolding of prion proteins in humans, cattle, sheep, and cervid species. The effects of glycosylation on prion protein (PrP) structure and function have not been thoroughly elucidated to date. In this study, we attempt to elucidate the effects of glycosylation on the aggregation and toxicity of human PrP. As revealed by immunocytochemical staining, wild-type PrP and its monoglycosylated mutants N181D, N197D, and T199N/N181D/N197D are primarily attached to the plasma membrane. In contrast, PrP F198S, a pathological mutant with an altered residue within the glycosylation site, and an unglycosylated PrP mutant, N181D/N197D, primarily exist in the cytoplasm. In the pathological mutant V180I, there is an equal mix of membranous and cytoplasmic PrP, indicating that N-linked glycosylation deficiency impairs the correct localization of human PrP at the plasma membrane. As shown by immunoblotting and flow cytometry, human PrP located in the cytoplasm displays considerably greater PK resistance and aggregation ability and is associated with considerably higher cellular ROS levels than PrP located on the plasma membrane. Furthermore, glycosylation deficiency enhances human PrP cytotoxicity induced by MG132 or the toxic prion peptide PrP 106-126. Therefore, we propose that glycosylation acts as a necessary cofactor in determining PrP localization on the plasma membrane and that it significantly inhibits the aggregation of human PrP and decreases its cytotoxicity.
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30
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Feng X, Wang X, Han B, Zou C, Hou Y, Zhao L, Li C. Design of Glyco-Linkers at Multiple Structural Levels to Modulate Protein Stability. J Phys Chem Lett 2018; 9:4638-4645. [PMID: 30060662 DOI: 10.1021/acs.jpclett.8b01570] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
N-glycosylation has critical roles in regulating protein stability, but the molecular basis is poorly understood. In this study, we integrated experimental and computational techniques to investigate the mechanism by which full-length N-glycans modulate protein stability from quaternary structure perspective. We found the two inherent N-glycans of β-glucuronidase expressed in Pichia pastoris function as "glyco-linkers" that hold spatially proximal motifs together to compact the local protein structure. We further designed and placed glyco-linkers in the unusual form of glyco-bridge and glyco-hairpin at the interfaces between domains and monomers with higher structural level, respectively, which conferred dramatically higher kinetic stability and thermodynamic stability than the inherent N-glycans. Our study not only provides unique insight into the interactions between glycans and proteins from a quaternary structure perspective but also facilitates the rational design of N-glycans as general tools that can enhance protein stability.
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Affiliation(s)
- Xudong Feng
- Department of Biochemical Engineering/Institute for Synthetic Biosystem, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , China
| | - Xiaoyan Wang
- Department of Biochemical Engineering/Institute for Synthetic Biosystem, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , China
- Center of Biotechnology , COFCO Nutrition & Health Research Institute , Beijing 102209 , China
| | - Beijia Han
- Department of Biochemical Engineering/Institute for Synthetic Biosystem, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , China
| | - Changling Zou
- Department of Biochemical Engineering/Institute for Synthetic Biosystem, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , China
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics , Chinese Academy of Sciences , Beijing 100049 , China
| | - Yuhui Hou
- Department of Biochemical Engineering/Institute for Synthetic Biosystem, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , China
| | - Lina Zhao
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics , Chinese Academy of Sciences , Beijing 100049 , China
| | - Chun Li
- Department of Biochemical Engineering/Institute for Synthetic Biosystem, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , China
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31
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Gligorijević N, Minić S, Križáková M, Katrlík J, Nedić O. Structural changes of fibrinogen as a consequence of cirrhosis. Thromb Res 2018; 166:43-49. [PMID: 29655002 DOI: 10.1016/j.thromres.2018.04.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/14/2018] [Accepted: 04/06/2018] [Indexed: 12/19/2022]
Abstract
Cirrhosis is a disease which may develop as a consequence of various conditions. In advanced liver disease, blood coagulation can be seriously affected. Portal hypertension, vascular abnormalities and/or a dysbalance in coagulation factors may result in bleeding disorders or in the development of thrombosis. Fibrinogen is the main protein involved in clot formation and wound healing. The aim of this work was to analyse the glycosylation pattern of the isolated fibrinogen molecules by lectin-based protein microarray, together with the carbonylation pattern of the individual fibrinogen chains, possible changes in the molecular secondary and tertiary structure and reactivity with the insulin-like growth factor-binding protein 1 (IGFBP-1) in patients with cirrhosis. The results pointed to an increase in several carbohydrate moieties: tri/tetra-antennary structures, Gal β-1,4 GlcNAc, terminal α-2,3 Sia and α-1,3 Man, and a decrease in core α-1,6 Fuc and bi-antennary galactosylated N-glycans with bisecting GlcNAc. Fibrinogen Aα chain was the most susceptible to carbonylation, followed by the Bβ chain. Cirrhosis induced additional protein carbonylation, mostly on the α chain. Spectrofluorimetry and CD spectrometry detected reduction in the α-helix content, protein unfolding and/or appearance of modified amino acid residues in cirrhosis. The amount of complexes which fibrinogen forms with IGFBP-1, another factor involved in wound healing was significantly greater in patients with cirrhosis than in healthy individuals. A more detailed knowledge of individual molecules in coagulation process may contribute to deeper understanding of coagulopathies and the results of this study offer additional information on the possible mechanisms involved in impaired coagulation due to cirrhosis.
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Affiliation(s)
- Nikola Gligorijević
- Institute for the Application of Nuclear Energy (INEP), Department of Metabolism, University of Belgrade, Banatska 31b, 11000 Belgrade, Serbia.
| | - Simeon Minić
- Center of Excellence for Molecular Food Sciences, Faculty of Chemistry, University of Belgrade, 11000 Belgrade, Serbia.
| | - Martina Križáková
- Institute of Chemistry, Slovak Academy of Sciences, Department of Glycobiotechnology, Dúbravskácesta 9, 84538 Bratislava, Slovak Republic.
| | - Jaroslav Katrlík
- Institute of Chemistry, Slovak Academy of Sciences, Department of Glycobiotechnology, Dúbravskácesta 9, 84538 Bratislava, Slovak Republic.
| | - Olgica Nedić
- Institute for the Application of Nuclear Energy (INEP), Department of Metabolism, University of Belgrade, Banatska 31b, 11000 Belgrade, Serbia.
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32
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Füssl F, Cook K, Scheffler K, Farrell A, Mittermayr S, Bones J. Charge Variant Analysis of Monoclonal Antibodies Using Direct Coupled pH Gradient Cation Exchange Chromatography to High-Resolution Native Mass Spectrometry. Anal Chem 2018; 90:4669-4676. [DOI: 10.1021/acs.analchem.7b05241] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Florian Füssl
- NIBRT−The National Institute for Bioprocessing Research and Training, Foster Avenue,
Mount Merrion, Blackrock, Co. Dublin, A94 X099, Ireland
| | - Ken Cook
- Thermo Fisher Scientific, Stafford House, 1 Boundary Park, Hemel Hempstead, HP2 7GE, United Kingdom
| | - Kai Scheffler
- Thermo Fisher Scientific, Dornierstrasse 4, 82110 Germering, Germany
| | - Amy Farrell
- NIBRT−The National Institute for Bioprocessing Research and Training, Foster Avenue,
Mount Merrion, Blackrock, Co. Dublin, A94 X099, Ireland
| | - Stefan Mittermayr
- NIBRT−The National Institute for Bioprocessing Research and Training, Foster Avenue,
Mount Merrion, Blackrock, Co. Dublin, A94 X099, Ireland
| | - Jonathan Bones
- NIBRT−The National Institute for Bioprocessing Research and Training, Foster Avenue,
Mount Merrion, Blackrock, Co. Dublin, A94 X099, Ireland
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, D04 V1W8, Ireland
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33
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Rogers JR, McHugh SM, Lin YS. Predictions for α-Helical Glycopeptide Design from Structural Bioinformatics Analysis. J Chem Inf Model 2017; 57:2598-2611. [DOI: 10.1021/acs.jcim.7b00123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Julia R. Rogers
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Sean M. McHugh
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
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34
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Levy Y. Protein Assembly and Building Blocks: Beyond the Limits of the LEGO Brick Metaphor. Biochemistry 2017; 56:5040-5048. [PMID: 28809494 DOI: 10.1021/acs.biochem.7b00666] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Proteins, like other biomolecules, have a modular and hierarchical structure. Various building blocks are used to construct proteins of high structural complexity and diverse functionality. In multidomain proteins, for example, domains are fused to each other in different combinations to achieve different functions. Although the LEGO brick metaphor is justified as a means of simplifying the complexity of three-dimensional protein structures, several fundamental properties (such as allostery or the induced-fit mechanism) make deviation from it necessary to respect the plasticity, softness, and cross-talk that are essential to protein function. In this work, we illustrate recently reported protein behavior in multidomain proteins that deviates from the LEGO brick analogy. While earlier studies showed that a protein domain is often unaffected by being fused to another domain or becomes more stable following the formation of a new interface between the tethered domains, destabilization due to tethering has been reported for several systems. We illustrate that tethering may sometimes result in a multidomain protein behaving as "less than the sum of its parts". We survey these cases for which structure additivity does not guarantee thermodynamic additivity. Protein destabilization due to fusion to other domains may be linked in some cases to biological function and should be taken into account when designing large assemblies.
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Affiliation(s)
- Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science , Rehovot 76100, Israel
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35
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Role of glycosylation in nucleating protein folding and stability. Biochem J 2017; 474:2333-2347. [PMID: 28673927 DOI: 10.1042/bcj20170111] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 04/14/2017] [Accepted: 04/19/2017] [Indexed: 12/17/2022]
Abstract
Glycosylation constitutes one of the most common, ubiquitous and complex forms of post-translational modification. It commences with the synthesis of the protein and plays a significant role in deciding its folded state, oligomerization and thus its function. Recent studies have demonstrated that N-linked glycans help proteins to fold as the stability and folding kinetics are altered with the removal of the glycans from them. Several studies have shown that it alters not only the thermodynamic stability but also the structural features of the folded proteins modulating their interactions and functions. Their inhibition and perturbations have been implicated in diseases from diabetes to degenerative disorders. The intent of this review is to provide insight into the recent advancements in the general understanding on the aspect of glycosylation driven stability of proteins that is imperative to their function and finally their role in health and disease states.
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36
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Sergeant K, Printz B, Gutsch A, Behr M, Renaut J, Hausman JF. Didehydrophenylalanine, an abundant modification in the beta subunit of plant polygalacturonases. PLoS One 2017; 12:e0171990. [PMID: 28207764 PMCID: PMC5313189 DOI: 10.1371/journal.pone.0171990] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 01/30/2017] [Indexed: 01/07/2023] Open
Abstract
The structure and the activity of proteins are often regulated by transient or stable post- translational modifications (PTM). Different from well-known, abundant modifications such as phosphorylation and glycosylation some modifications are limited to one or a few proteins across a broad range of related species. Although few examples of the latter type are known, the evolutionary conservation of these modifications and the enzymes responsible for their synthesis suggest an important physiological role. Here, the first observation of a new, fold-directing PTM is described. During the analysis of alfalfa cell wall proteins a -2Da mass shift was observed on phenylalanine residues in the repeated tetrapeptide FxxY of the beta-subunit of polygalacturonase. This modular protein is known to be involved in developmental and stress-responsive processes. The presence of this modification was confirmed using in-house and external datasets acquired by different commonly used techniques in proteome studies. Based on these analyses it was found that all identified phenylalanine residues in the sequence FxxY of this protein were modified to α,β-didehydro-Phe (ΔPhe). Besides showing the reproducible identification of ΔPhe in different species arguments that substantiate the fold-determining role of ΔPhe are given.
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Affiliation(s)
- Kjell Sergeant
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) department, Esch-sur-Alzette, Luxembourg
- * E-mail:
| | - Bruno Printz
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) department, Esch-sur-Alzette, Luxembourg
- Université catholique de Louvain, Earth and Life Institute Agronomy, Groupe de Recherche en Physiologie Végétale Louvain-la-Neuve, Belgium
| | - Annelie Gutsch
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) department, Esch-sur-Alzette, Luxembourg
- University of Hasselt, Centre for Environmental Sciences, Environmental Biology, Diepenbeek, Belgium
| | - Marc Behr
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) department, Esch-sur-Alzette, Luxembourg
- Université catholique de Louvain, Earth and Life Institute Agronomy, Groupe de Recherche en Physiologie Végétale Louvain-la-Neuve, Belgium
| | - Jenny Renaut
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) department, Esch-sur-Alzette, Luxembourg
| | - Jean-Francois Hausman
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) department, Esch-sur-Alzette, Luxembourg
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37
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Li Z, Guan W, Lu C, Zhou XR, Luo SZ, You Y, Ouyang J. Hydrophobicity-induced prestaining for protein detection in polyacrylamide gel electrophoresis. Chem Commun (Camb) 2016; 52:2807-10. [DOI: 10.1039/c5cc09377e] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An aggregation-induced emission fluorescent surfactant has been used to prestain protein by means of strong hydrophobic interaction between fluorescent surfactants and proteins.
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Affiliation(s)
- Zhe Li
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Weijiang Guan
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Chao Lu
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Xi-Rui Zhou
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Shi-Zhong Luo
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Ying You
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- China
| | - Jin Ouyang
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- China
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