1
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Moldovean-Cioroianu NS. Reviewing the Structure-Function Paradigm in Polyglutamine Disorders: A Synergistic Perspective on Theoretical and Experimental Approaches. Int J Mol Sci 2024; 25:6789. [PMID: 38928495 PMCID: PMC11204371 DOI: 10.3390/ijms25126789] [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: 05/16/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Polyglutamine (polyQ) disorders are a group of neurodegenerative diseases characterized by the excessive expansion of CAG (cytosine, adenine, guanine) repeats within host proteins. The quest to unravel the complex diseases mechanism has led researchers to adopt both theoretical and experimental methods, each offering unique insights into the underlying pathogenesis. This review emphasizes the significance of combining multiple approaches in the study of polyQ disorders, focusing on the structure-function correlations and the relevance of polyQ-related protein dynamics in neurodegeneration. By integrating computational/theoretical predictions with experimental observations, one can establish robust structure-function correlations, aiding in the identification of key molecular targets for therapeutic interventions. PolyQ proteins' dynamics, influenced by their length and interactions with other molecular partners, play a pivotal role in the polyQ-related pathogenic cascade. Moreover, conformational dynamics of polyQ proteins can trigger aggregation, leading to toxic assembles that hinder proper cellular homeostasis. Understanding these intricacies offers new avenues for therapeutic strategies by fine-tuning polyQ kinetics, in order to prevent and control disease progression. Last but not least, this review highlights the importance of integrating multidisciplinary efforts to advancing research in this field, bringing us closer to the ultimate goal of finding effective treatments against polyQ disorders.
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Affiliation(s)
- Nastasia Sanda Moldovean-Cioroianu
- Institute of Materials Science, Bioinspired Materials and Biosensor Technologies, Kiel University, Kaiserstraße 2, 24143 Kiel, Germany;
- Faculty of Physics, Babeș-Bolyai University, Kogălniceanu 1, RO-400084 Cluj-Napoca, Romania
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2
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Gupta MN, Uversky VN. Protein structure-function continuum model: Emerging nexuses between specificity, evolution, and structure. Protein Sci 2024; 33:e4968. [PMID: 38532700 DOI: 10.1002/pro.4968] [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: 12/02/2023] [Revised: 02/18/2024] [Accepted: 03/05/2024] [Indexed: 03/28/2024]
Abstract
The rationale for replacing the old binary of structure-function with the trinity of structure, disorder, and function has gained considerable ground in recent years. A continuum model based on the expanded form of the existing paradigm can now subsume importance of both conformational flexibility and intrinsic disorder in protein function. The disorder is actually critical for understanding the protein-protein interactions in many regulatory processes, formation of membrane-less organelles, and our revised notions of specificity as amply illustrated by moonlighting proteins. While its importance in formation of amyloids and function of prions is often discussed, the roles of intrinsic disorder in infectious diseases and protein function under extreme conditions are also becoming clear. This review is an attempt to discuss how our current understanding of protein function, specificity, and evolution fit better with the continuum model. This integration of structure and disorder under a single model may bring greater clarity in our continuing quest for understanding proteins and molecular mechanisms of their functionality.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
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3
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Kandola T, Venkatesan S, Zhang J, Lerbakken BT, Von Schulze A, Blanck JF, Wu J, Unruh JR, Berry P, Lange JJ, Box AC, Cook M, Sagui C, Halfmann R. Pathologic polyglutamine aggregation begins with a self-poisoning polymer crystal. eLife 2023; 12:RP86939. [PMID: 37921648 PMCID: PMC10624427 DOI: 10.7554/elife.86939] [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] [Indexed: 11/04/2023] Open
Abstract
A long-standing goal of amyloid research has been to characterize the structural basis of the rate-determining nucleating event. However, the ephemeral nature of nucleation has made this goal unachievable with existing biochemistry, structural biology, and computational approaches. Here, we addressed that limitation for polyglutamine (polyQ), a polypeptide sequence that causes Huntington's and other amyloid-associated neurodegenerative diseases when its length exceeds a characteristic threshold. To identify essential features of the polyQ amyloid nucleus, we used a direct intracellular reporter of self-association to quantify frequencies of amyloid appearance as a function of concentration, conformational templates, and rational polyQ sequence permutations. We found that nucleation of pathologically expanded polyQ involves segments of three glutamine (Q) residues at every other position. We demonstrate using molecular simulations that this pattern encodes a four-stranded steric zipper with interdigitated Q side chains. Once formed, the zipper poisoned its own growth by engaging naive polypeptides on orthogonal faces, in a fashion characteristic of polymer crystals with intramolecular nuclei. We further show that self-poisoning can be exploited to block amyloid formation, by genetically oligomerizing polyQ prior to nucleation. By uncovering the physical nature of the rate-limiting event for polyQ aggregation in cells, our findings elucidate the molecular etiology of polyQ diseases.
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Affiliation(s)
- Tej Kandola
- Stowers Institute for Medical ResearchKansas CityUnited States
- The Open UniversityMilton KeynesUnited Kingdom
| | | | - Jiahui Zhang
- Department of Physics, North Carolina State UniversityRaleighUnited States
| | | | | | | | - Jianzheng Wu
- Stowers Institute for Medical ResearchKansas CityUnited States
- Department of Biochemistry and Molecular Biology, University of Kansas Medical CenterKansas CityUnited States
| | - Jay R Unruh
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Paula Berry
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Jeffrey J Lange
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Andrew C Box
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Malcolm Cook
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Celeste Sagui
- Department of Physics, North Carolina State UniversityRaleighUnited States
| | - Randal Halfmann
- Stowers Institute for Medical ResearchKansas CityUnited States
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4
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Borges-Araújo L, Patmanidis I, Singh AP, Santos LHS, Sieradzan AK, Vanni S, Czaplewski C, Pantano S, Shinoda W, Monticelli L, Liwo A, Marrink SJ, Souza PCT. Pragmatic Coarse-Graining of Proteins: Models and Applications. J Chem Theory Comput 2023; 19:7112-7135. [PMID: 37788237 DOI: 10.1021/acs.jctc.3c00733] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The molecular details involved in the folding, dynamics, organization, and interaction of proteins with other molecules are often difficult to assess by experimental techniques. Consequently, computational models play an ever-increasing role in the field. However, biological processes involving large-scale protein assemblies or long time scale dynamics are still computationally expensive to study in atomistic detail. For these applications, employing coarse-grained (CG) modeling approaches has become a key strategy. In this Review, we provide an overview of what we call pragmatic CG protein models, which are strategies combining, at least in part, a physics-based implementation and a top-down experimental approach to their parametrization. In particular, we focus on CG models in which most protein residues are represented by at least two beads, allowing these models to retain some degree of chemical specificity. A description of the main modern pragmatic protein CG models is provided, including a review of the most recent applications and an outlook on future perspectives in the field.
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Affiliation(s)
- Luís Borges-Araújo
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
| | - Ilias Patmanidis
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Akhil P Singh
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg CH-1700, Switzerland
| | - Lucianna H S Santos
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Adam K Sieradzan
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg CH-1700, Switzerland
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur, Inserm, CNRS, 06560 Valbonne, France
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Wataru Shinoda
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita, Okayama 700-8530, Japan
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
| | - Adam Liwo
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
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5
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Klein F, Soñora M, Helene Santos L, Nazareno Frigini E, Ballesteros-Casallas A, Rodrigo Machado M, Pantano S. The SIRAH force field: A suite for simulations of complex biological systems at the coarse-grained and multiscale levels. J Struct Biol 2023; 215:107985. [PMID: 37331570 DOI: 10.1016/j.jsb.2023.107985] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/18/2023] [Accepted: 06/13/2023] [Indexed: 06/20/2023]
Abstract
The different combinations of molecular dynamics simulations with coarse-grained representations have acquired considerable popularity among the scientific community. Especially in biocomputing, the significant speedup granted by simplified molecular models opened the possibility of increasing the diversity and complexity of macromolecular systems, providing realistic insights on large assemblies for more extended time windows. However, a holistic view of biological ensembles' structural and dynamic features requires a self-consistent force field, namely, a set of equations and parameters that describe the intra and intermolecular interactions among moieties of diverse chemical nature (i.e., nucleic and amino acids, lipids, solvent, ions, etc.). Nevertheless, examples of such force fields are scarce in the literature at the fully atomistic and coarse-grained levels. Moreover, the number of force fields capable of handling simultaneously different scales is restricted to a handful. Among those, the SIRAH force field, developed in our group, furnishes a set of topologies and tools that facilitate the setting up and running of molecular dynamics simulations at the coarse-grained and multiscale levels. SIRAH uses the same classical pairwise Hamiltonian function implemented in the most popular molecular dynamics software. In particular, it runs natively in AMBER and Gromacs engines, and porting it to other simulation packages is straightforward. This review describes the underlying philosophy behind the development of SIRAH over the years and across families of biological molecules, discussing current limitations and future implementations.
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Affiliation(s)
- Florencia Klein
- Laboratoire de Biochimie Théorique, UPR9080, CNRS, Paris, France
| | - Martín Soñora
- Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay
| | | | - Ezequiel Nazareno Frigini
- Instituto Multidisciplinario de Investigaciones Biológicas de San Luis (IMIBIO-SL), Universidad Nacional de San Luis - CONICET, San Luis, Argentina
| | - Andrés Ballesteros-Casallas
- Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay; Area Bioinformática, DETEMA, Facultad de Química, Universidad de la República, General Flores 2124, Montevideo, 11600, Uruguay
| | | | - Sergio Pantano
- Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay; Area Bioinformática, DETEMA, Facultad de Química, Universidad de la República, General Flores 2124, Montevideo, 11600, Uruguay.
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6
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Barrera EE, Pantano S. Early stages in Aβ1-42 spontaneous aggregation: An unbiased dataset from coarse-grained molecular dynamics simulations. Data Brief 2023; 49:109359. [PMID: 37456111 PMCID: PMC10344647 DOI: 10.1016/j.dib.2023.109359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 06/07/2023] [Accepted: 06/26/2023] [Indexed: 07/18/2023] Open
Abstract
The small soluble aggregates of Aβ1-42 are broadly documented as potential targets for the development of new compounds with the capacity to inhibit the early stages of Alzheimer´s disease. Nevertheless, Aβ1-42 peptides show an intrinsically disordered character with a high propensity for aggregation, which complicates the identification of conserved structural patterns. Because of this, experimental techniques find substantial difficulties in the characterization of such soluble oligomers. Theoretical techniques, such as molecular dynamics (MD) simulations, provide a possible workaround for this problem. However, the computational cost associated with comprehensively sampling the vast conformational space accessible to these peptides might become prohibitive. In this sense, coarse-grained (CG) simulations can effectively overcome that hurdle at a fraction of the computational cost. In this dataset, we furnish an extensive collection of Aβ1-42 peptides in dimeric conformation generated with the SIRAH force field for CG MD simulation. It comprises 25 independent trajectories in .xtc (gromacs) format of Aβ1-42 couples of peptides that evolve towards dimeric states along eleven µs-long unbiased simulations. Thanks to the backmapping capabilities of our force field, pseudo atomistic coordinates can be straightforwardly recovered from MD trajectories reported here and analyzed with popular molecular editing programs. This set of simulations performed at room conditions and physiological salt concentrations may furnish a complete collection of inter-peptide interfaces that can be used in high-throughput docking or as new starting states for peptide oligomerization seeding of Aβ1-42 dimerization.
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Affiliation(s)
- Exequiel E. Barrera
- Instituto de Histología y Embriología (IHEM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CC56, Universidad Nacional de Cuyo (UNCuyo), Mendoza, Argentina
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, CP 11400 Montevideo, Uruguay
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, CP 11400 Montevideo, Uruguay
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7
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Kandola T, Venkatesan S, Zhang J, Lerbakken B, Schulze AV, Blanck JF, Wu J, Unruh J, Berry P, Lange JJ, Box A, Cook M, Sagui C, Halfmann R. Pathologic polyglutamine aggregation begins with a self-poisoning polymer crystal. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.20.533418. [PMID: 36993401 PMCID: PMC10055281 DOI: 10.1101/2023.03.20.533418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
A long-standing goal of amyloid research has been to characterize the structural basis of the rate-determining nucleating event. However, the ephemeral nature of nucleation has made this goal unachievable with existing biochemistry, structural biology, and computational approaches. Here, we addressed that limitation for polyglutamine (polyQ), a polypeptide sequence that causes Huntington's and other amyloid-associated neurodegenerative diseases when its length exceeds a characteristic threshold. To identify essential features of the polyQ amyloid nucleus, we used a direct intracellular reporter of self-association to quantify frequencies of amyloid appearance as a function of concentration, conformational templates, and rational polyQ sequence permutations. We found that nucleation of pathologically expanded polyQ involves segments of three glutamine (Q) residues at every other position. We demonstrate using molecular simulations that this pattern encodes a four-stranded steric zipper with interdigitated Q side chains. Once formed, the zipper poisoned its own growth by engaging naive polypeptides on orthogonal faces, in a fashion characteristic of polymer crystals with intramolecular nuclei. We further show that self-poisoning can be exploited to block amyloid formation, by genetically oligomerizing polyQ prior to nucleation. By uncovering the physical nature of the rate-limiting event for polyQ aggregation in cells, our findings elucidate the molecular etiology of polyQ diseases.
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Affiliation(s)
- Tej Kandola
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- The Open University, Milton Keyes, MK7 6AA, UK
| | | | - Jiahui Zhang
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | | | - Alex Von Schulze
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jillian F Blanck
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jianzheng Wu
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Jay Unruh
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Paula Berry
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jeffrey J Lange
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Andrew Box
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Malcolm Cook
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Celeste Sagui
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Randal Halfmann
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
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8
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Amundarain MJ, Vietri A, Dodero VI, Costabel MD. IDP Force Fields Applied to Model PPII-Rich 33-mer Gliadin Peptides. J Phys Chem B 2023; 127:2407-2417. [PMID: 36884001 DOI: 10.1021/acs.jpcb.3c00200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
The 33-mer gliadin peptide and its deamidated metabolite, 33-mer DGP, are the immunodominant peptides responsible for the adaptive immune response in celiac disease (CD). CD is a complex autoimmune chronic disorder triggered by gluten ingestion that affects the small intestine and affects ∼1% of the global population. The 33-mers are polyproline II-rich (PPII) and intrinsically disordered peptides (IDPs), whose structures remain elusive. We sampled the conformational ensembles of both 33-mer peptides via molecular dynamics simulations employing two force fields (FFs) (Amber ff03ws and Amber ff99SB-disp) specifically validated for other IDPs. Our results show that both FFs allow the extensive exploration of the conformational landscape, which was not possible with the standard FF GROMOS53A6 reported before. Clustering analysis of the trajectories showed that the five largest clusters (78-88% of the total structures) present elongated, semielongated, and curved conformations in both FFs. Large average radius of gyration and solvent-exposed surfaces characterized these structures. While the structures sampled are similar, the Amber ff99SB-disp trajectories explored folded conformations with a higher probability. In addition, PPII secondary structure was preserved throughout the trajectories (58-73%) together with a non-negligible content of β structures (11-23%), in agreement with previous experimental results. This work represents the initial step in studying further the interaction of these peptides with other biologically relevant molecules, which could lead to finally disclose the molecular events that lead to CD.
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Affiliation(s)
- María J Amundarain
- Departamento de Física, Instituto de Física del Sur (IFISUR), Universidad Nacional del Sur (UNS), CONICET, Avenida Leandro N. Alem 1253, B8000CPB Bahía Blanca, Argentina
- Department of Chemistry, Organic Chemistry III, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Agustín Vietri
- Departamento de Física, Instituto de Física del Sur (IFISUR), Universidad Nacional del Sur (UNS), CONICET, Avenida Leandro N. Alem 1253, B8000CPB Bahía Blanca, Argentina
| | - Verónica I Dodero
- Department of Chemistry, Organic Chemistry III, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Marcelo D Costabel
- Departamento de Física, Instituto de Física del Sur (IFISUR), Universidad Nacional del Sur (UNS), CONICET, Avenida Leandro N. Alem 1253, B8000CPB Bahía Blanca, Argentina
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9
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A Diphenylalanine Based Pentapeptide with Fibrillating Self-Assembling Properties. Pharmaceutics 2023; 15:pharmaceutics15020371. [PMID: 36839694 PMCID: PMC9966497 DOI: 10.3390/pharmaceutics15020371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 01/24/2023] Open
Abstract
Peptides and their related compounds can self-assemble into diverse nanostructures of different shapes and sizes in response to various stimuli such as pH, temperature or ionic strength. Here we report the synthesis and characterization of a lysozyme derived pentapeptide and its ability to build well-defined fibrillar structures. Lysozyme FESNF peptide fragment was synthesized by solid phase peptide synthesis using the Fmoc/t-Bu strategy, purified by analytical high-performance liquid chromatography (HPLC) and its molecular weight was confirmed by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Spectroscopic features of this pentapeptide were investigated by UV-visible spectroscopy and fluorimetry showing the pattern of marginal phenylalanine residues within the peptide sequence. Self-assembling properties were determined using atomic force microscopy (AFM), aggregation index and thioflavin T assay (ThT). FESNF generating fibrillar structures observed by AFM and aggregation propensity were primarily influenced by pH conditions. Moreover, the experimental data were confirmed by molecular dynamics simulation studies. The obtained fibrils will be used next to explore their potential to act as support material for medical and cosmetic application.
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10
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Monti A, Ronca R, Campiani G, Ruvo M, Doti N. Expression, Purification, Structural and Functional Characterization of Recombinant Human Parvulin 17. Mol Biotechnol 2023; 65:337-349. [PMID: 35467256 PMCID: PMC9935730 DOI: 10.1007/s12033-022-00493-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/08/2022] [Indexed: 11/29/2022]
Abstract
Parvulins, peptidyl-prolyl isomerase enzymes (PPIase), catalyze the cis-trans isomerization of prolyl bonds in polypeptides, contributing to folding and function regulation of many proteins. Among Parvulins, Par17, exclusively expressed in hominids, is the least examined in terms of structure, catalytic function and cellular activity. Setting the conditions for the preparation of recombinant active Par17 may therefore significantly foster future studies. Here, we comparatively evaluated the impact of several parameters, including host strains, culture media, isopropyl ß-D-1-thiogalactopyranoside concentration, post-induction incubation time and temperature, on the overexpression of Par17 in E. coli cells. A similar approach was also comparatively adopted for the preparation of the recombinant full-length Pin1 protein, the most representative Parvulin, and the catalytic domains of both enzymes. Proteins were efficiently expressed and purified to homogeneity and were subjected to a structural characterization by Size Exclusion Chromatography and Circular Dichroism. Moreover, a single-step homogeneous protease-based fluorimetric assay, potentially scalable in HTS format, has been developed for determining the peptidyl-prolyl cis-trans isomerase activity of recombinant Parvulins. Results obtained show that proteins are folded and active. These new data mark an important milestone for progressing the investigation of Parvulins.
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Affiliation(s)
- Alessandra Monti
- Instituto di Biostrutture e Bioimmagini-CNR, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Raffaele Ronca
- Instituto di Biostrutture e Bioimmagini-CNR, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Giuseppe Campiani
- Dipartimento di Biotecnologie, Chimica e Farmacia, Via Aldo Moro, 2, 53100 Siena, Italy
| | - Menotti Ruvo
- Instituto di Biostrutture e Bioimmagini-CNR, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Nunzianna Doti
- Instituto di Biostrutture e Bioimmagini-CNR, Via Pietro Castellino 111, 80131, Napoli, Italy.
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11
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Voroshilin R, Kurbanova M, Ostapova E, Makhambetov E, Petrov A, Khelef MEA. Effect of gelatin drying methods on its amphiphilicity. FOODS AND RAW MATERIALS 2022. [DOI: 10.21603/2308-4057-2022-2-534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Gelatin is a natural amphiphilic biopolymer that is widely used in food products, pharmaceuticals, and cosmetics. We studied the effect of spray and freeze drying on the solubility and amphiphilicity of gelatin samples.
The control sample was a commercially produced edible gelatin. The experimental samples were spray- and freeze-dried gelatins obtained by enzymatic-acid hydrolysis of cattle bone. Amino acid sequences were determined by matrix-activated laser desorption/ionization. Solubility was assessed visually. Bloom strength of the gelatin gels was measured by a texture analyzer. The ProtScale online service was used to predict the amphiphilic topology of gelatin proteins. Molecular weight distribution of proteins was carried out by electrophoresis in polyacrylamide gel in the presence of sodium dodecyl sulfate.
Spray drying reduced protein degradation and retained more α-chains, while freeze drying increased gelatin’s hydrophobicity and decreased its solubility. The predicted topology of protein hydrophobicity based on the amino acid sequences was in line with our results on solubility. The freeze-dried gelatin had a 18% larger amount of low-molecular weight peptides, compared to the control and the spray-dried samples. This was probably caused by the cleavage of peptides during the drying process. Thus, freeze drying can lead to maximum degradation of gelatin components, which may be associated with a longer heat treatment, compared to spray drying.
Thus, spray drying is more suitable for gelatin, since this method improves the stability of its outer and inner structure, ensuring high hydrophilic properties.
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12
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Kyu Ko S, Berner C, Kulakova A, Schneider M, Antes I, Winter G, Harris P, Peters GH. Investigation of the pH-dependent aggregation mechanisms of GCSF using low resolution protein characterization techniques and advanced molecular dynamics simulations. Comput Struct Biotechnol J 2022; 20:1439-1455. [PMID: 35386098 PMCID: PMC8956964 DOI: 10.1016/j.csbj.2022.03.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/13/2022] [Accepted: 03/14/2022] [Indexed: 01/19/2023] Open
Abstract
Granulocyte-colony stimulating factor (GCSF) is a widely used therapeutic protein to treat neutropenia. GCSF has an increased propensity to aggregate if the pH is increased above 5.0. Although GCSF is very well experimentally characterized, the exact pH-dependent aggregation mechanism of GCSF is still under debate. This study aimed to model the complex pH-dependent aggregation behavior of GCSF using state-of-the-art simulation techniques. The conformational stability of GCSF was investigated by performing metadynamics simulations, while the protein-protein interactions were investigated using coarse-grained (CG) simulations of multiple GCSF monomers. The CG simulations were directly compared with small-angle X-ray (SAXS) data. The metadynamics simulations demonstrated that the orientations of Trp residues in GCSF are dependent on pH. The conformational change of Trp residues is due to the loss of Trp-His interactions at the physiological pH, which in turn may increase protein flexibility. The helical structure of GCSF was not affected by the pH conditions of the simulations. Our CG simulations indicate that at pH 4.0, the colloidal stability may be more important than the conformational stability of GCSF. The electrostatic potential surface and CG simulations suggested that the basic residues are mainly responsible for colloidal stability as deprotonation of these residues causes a reduction of the highly positively charged electrostatic barrier close to the aggregation-prone long loop regions.
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Gliadin proteolytical resistant peptides: the interplay between structure and self-assembly in gluten-related disorders. Biophys Rev 2022; 13:1147-1154. [PMID: 35047092 PMCID: PMC8724473 DOI: 10.1007/s12551-021-00856-z] [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: 08/14/2021] [Accepted: 10/14/2021] [Indexed: 11/29/2022] Open
Abstract
In recent years, the evaluation of the structural properties of food has become of crucial importance in the understanding of food-related disorders. One of the most exciting systems is gliadin, a protein in wheat gluten, that plays a protagonist role in gluten-related disorders with a worldwide prevalence of 5%, including autoimmune celiac disease (CeD) (1%) and non-celiac wheat sensitivity (0.5–13%). It is accepted that gliadin is not fully digested by humans, producing large peptides that reach the gut mucosa. The gliadin peptides cross the lamina propria eliciting different immune responses in susceptible patients. Many clinical and biomedical efforts aim to diagnose and understand gluten-related disorders; meanwhile, the early stages of the inflammatory events remain elusive. Interestingly, although the primary sequence of many gliadin peptides is well known, it was only recently revealed the self-assembly capability of two pathogenic gliadin fragments and their connection to the early stage of diseases. This review is dedicated to the most relevant biophysical characterization of the complex gliadin digest and the two most studied gliadin fragments, the immunodominant 33-mer peptide and the toxic p31-43 in connection with inflammation and innate immune response. Here, we want to emphasize that combining different biophysical methods with cellular and in vivo models is of key importance to get an integrative understanding of a complex biological problem, as discussed here.
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Barrera EE, Pantano S, Zonta F. A homogeneous dataset of polyglutamine and glutamine rich aggregating peptides simulations. Data Brief 2021; 36:107109. [PMID: 34036130 PMCID: PMC8138716 DOI: 10.1016/j.dib.2021.107109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/13/2021] [Accepted: 04/20/2021] [Indexed: 11/30/2022] Open
Abstract
This dataset contains a collection of molecular dynamics (MD) simulations of polyglutamine (polyQ) and glutamine-rich (Q-rich) peptides in the multi-microsecond timescale. Primary data from coarse-grained simulations performed using the SIRAH force field has been processed to provide fully atomistic coordinates. The dataset encloses MD trajectories of polyQs of 4 (Q4), 11 (Q11), and 36 (Q36) amino acids long. In the case of Q11, simulations in presence of Q5 and QEQQQ peptides, which modulate aggregation, are also included. The dataset also comprises MD trajectories of the gliadin related p31-43 peptide, and Insulin's C-peptide at pH=7 and pH=3.2, which constitute examples of Q-rich and Q-poor aggregating peptides. The dataset grants molecular insights on the role of glutamines in spontaneous and unbiased ab-initio aggregation of a series of peptides using a homogeneous set of simulations [1]. The trajectory files are provided in Protein Data Bank (PDB) format containing the Cartesian coordinates of all heavy atoms in the aggregating peptides. Further analyses of the trajectories can be performed directly using any molecular visualization/analysis software suites.
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Affiliation(s)
- Exequiel E Barrera
- Instituto de Histología y Embriología (IHEM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CC56, Universidad Nacional de Cuyo (UNCuyo), Mendoza, Argentina.,Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, CP 11400 Montevideo, Uruguay
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, CP 11400 Montevideo, Uruguay.,Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Francesco Zonta
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
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