1
|
Kiang KM, Ahad L, Zhong X, Lu QR. Biomolecular condensates: hubs of Hippo-YAP/TAZ signaling in cancer. Trends Cell Biol 2024:S0962-8924(24)00096-5. [PMID: 38806345 DOI: 10.1016/j.tcb.2024.04.009] [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: 07/27/2023] [Revised: 04/14/2024] [Accepted: 04/30/2024] [Indexed: 05/30/2024]
Abstract
Biomolecular condensates, the membraneless cellular compartments formed by liquid-liquid phase separation (LLPS), represent an important mechanism for physiological and tumorigenic processes. Recent studies have advanced our understanding of how these condensates formed in the cytoplasm or nucleus regulate Hippo signaling, a central player in organogenesis and tumorigenesis. Here, we review recent findings on the dynamic formation and function of biomolecular condensates in regulating the Hippo-yes-associated protein (YAP)/transcription coactivator with PDZ-binding motif (TAZ) signaling pathway under physiological and pathological processes. We further discuss how the nuclear condensates of YAP- or TAZ-fusion oncoproteins compartmentalize crucial transcriptional co-activators and alter chromatin architecture to promote oncogenic programs. Finally, we highlight key questions regarding how these findings may pave the way for novel therapeutics to target cancer.
Collapse
Affiliation(s)
- Karrie M Kiang
- Department of Pediatrics, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Surgery, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong
| | - Leena Ahad
- Department of Pediatrics, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Xiaowen Zhong
- Department of Pediatrics, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Q Richard Lu
- Department of Pediatrics, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
| |
Collapse
|
2
|
Argudo PG. Lipids and proteins: Insights into the dynamics of assembly, recognition, condensate formation. What is still missing? Biointerphases 2024; 19:038501. [PMID: 38922634 DOI: 10.1116/6.0003662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 06/03/2024] [Indexed: 06/27/2024] Open
Abstract
Lipid membranes and proteins, which are part of us throughout our lives, have been studied for decades. However, every year, new discoveries show how little we know about them. In a reader-friendly manner for people not involved in the field, this paper tries to serve as a bridge between physicists and biologists and new young researchers diving into the field to show its relevance, pointing out just some of the plethora of lines of research yet to be unraveled. It illustrates how new ways, from experimental to theoretical approaches, are needed in order to understand the structures and interactions that take place in a single lipid, protein, or multicomponent system, as we are still only scratching the surface.
Collapse
Affiliation(s)
- Pablo G Argudo
- Max Planck Institute for Polymer Research (MPI-P), Mainz 55128, Germany
| |
Collapse
|
3
|
Sarkar S, Kumari A, Tiwari M, Tiwari V. Interaction and simulation studies suggest the possible molecular targets of intrinsically disordered amyloidogenic antimicrobial peptides in Acinetobacter baumannii. J Biomol Struct Dyn 2024; 42:2747-2764. [PMID: 37144752 DOI: 10.1080/07391102.2023.2208219] [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: 01/16/2023] [Accepted: 04/20/2023] [Indexed: 05/06/2023]
Abstract
Acinetobacter baumannii is one of the causing agents of nosocomial infections. A wide range of antibiotics fails to work against these pathogens. Hence, there is an urgent requirement to develop other therapeutics to solve this problem. Antimicrobial peptides (AMPs) are a diverse group of naturally occurring peptides that have the ability to kill diverse groups of microorganisms. The major challenge of using AMPs as therapeutics is their unstable nature and the fact that most of their molecular targets are still unknown. In this study, we have selected intrinsically disordered and amyloidogenic AMPs, showing activity against A. baumannii, that is, Bactenecin, Cath BF, Citropin 1.1, DP7, NA-CATH, Tachyplesin, and WAM-1. To identify the probable target of these AMPs in A. baumannii, calculation of docking score, binding energy, dissociation constant, and molecular dynamics analysis was performed with selected seventeen possible molecular targets. The result showed that the most probable molecular targets of most of the intrinsically disordered amyloidogenic AMPs were UDP-N-acetylenol-pyruvoyl-glucosamine reductase (MurB), followed by 33-36 kDa outer membrane protein (Omp 33-36), UDP-N-acetylmuramoyl-l-alanyl-d-glutamate-2,6-diaminopimelate ligase (MurE), and porin Subfamily Protein (PorinSubF). Further, molecular dynamics analysis concluded that the target of antimicrobial peptide Bactenecin is MurB of A. baumannii, and identified other molecular targets of selected AMPs. Additionally, the oligomerization capacity of the selected AMPs was also investigated, and it was shown that the selected AMPs form oligomeric states, and interact with their molecular targets in that state. Experimental validation using purified AMPs and molecular targets needs to be done to confirm the interaction.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Sayani Sarkar
- Department of Biochemistry, Central University of Rajasthan, Ajmer, India
| | - Aruna Kumari
- Department of Biochemistry, Central University of Rajasthan, Ajmer, India
| | - Monalisa Tiwari
- Department of Biochemistry, Central University of Rajasthan, Ajmer, India
| | - Vishvanath Tiwari
- Department of Biochemistry, Central University of Rajasthan, Ajmer, India
| |
Collapse
|
4
|
Kravikass M, Koren G, Saleh OA, Beck R. From isolated polyelectrolytes to star-like assemblies: the role of sequence heterogeneity on the statistical structure of the intrinsically disordered neurofilament-low tail domain. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2024; 47:13. [PMID: 38358563 PMCID: PMC10869404 DOI: 10.1140/epje/s10189-024-00409-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 02/02/2024] [Indexed: 02/16/2024]
Abstract
Intrinsically disordered proteins (IDPs) are a subset of proteins that lack stable secondary structure. Given their polymeric nature, previous mean-field approximations have been used to describe the statistical structure of IDPs. However, the amino-acid sequence heterogeneity and complex intermolecular interaction network have significantly impeded the ability to get proper approximations. One such case is the intrinsically disordered tail domain of neurofilament low (NFLt), which comprises a 50 residue-long uncharged domain followed by a 96 residue-long negatively charged domain. Here, we measure two NFLt variants to identify the impact of the NFLt two main subdomains on its complex interactions and statistical structure. Using synchrotron small-angle x-ray scattering, we find that the uncharged domain of the NFLt induces attractive interactions that cause it to self-assemble into star-like polymer brushes. On the other hand, when the uncharged domain is truncated, the remaining charged N-terminal domains remain isolated in solution with typical polyelectrolyte characteristics. We further discuss how competing long- and short-ranged interactions within the polymer brushes dominate their ensemble structure and, in turn, their implications on previously observed phenomena in NFL native and diseased states.
Collapse
Affiliation(s)
- Mathar Kravikass
- School of Physics and Astronomy, The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
- The Center of Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, Israel
| | - Gil Koren
- School of Physics and Astronomy, The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
- The Center of Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, Israel
| | - Omar A Saleh
- Materials Department, Biomolecular Sciences and Engineering Program, University of California, Santa Barbara, USA
- Physics Department, University of California, Santa Barbara, USA
| | - Roy Beck
- School of Physics and Astronomy, The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel.
- The Center of Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, Israel.
| |
Collapse
|
5
|
Tolstova AP, Makarov AA, Adzhubei AA. Structure Comparison of Beta Amyloid Peptide Aβ 1-42 Isoforms. Molecular Dynamics Modeling. J Chem Inf Model 2024; 64:918-932. [PMID: 38241093 DOI: 10.1021/acs.jcim.3c01624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2024]
Abstract
Beta amyloid peptide Aβ 1-42 (Aβ42) has a unique dual role in the human organism, as both the peptide with an important physiological function and one of the most toxic biological compounds provoking Alzheimer's disease (AD). There are several known Aβ42 isoforms that we discuss here that are highly neurotoxic and lead to the early onset of AD. Aβ42 is an intrinsically disordered protein with no experimentally solved structure under physiological conditions. The objective of this research was to establish the appropriate molecular dynamics (MD) methodology and model a uniform set of structures for the Aβ42 isoforms that form the core of this study. For that purpose, force field selection and verification including convergence testing for MD simulations was made. Replica exchange MD and conventional MD modeling of several Aβ42 and Aβ16 isoforms that have neurotoxic and amyloidogenic effects impacting the severity of Alzheimer's disease were carried out with the optimal force field and solvent parameters. A standardized ensemble of structures for the Aβ42 and Aβ16 isoforms covering 30-50% of the conformational ensembles extracted from the free energy minima was calculated from MD trajectories. The resulting data set of modeled structures includes Aβ42 wild type, isoD7, pS8, D7H, and H6R-Aβ42 and Aβ16 wild type, isoD7, pS8, D7H, and H6R-Aβ16. The representative structures are given in the Supporting Information; they are open for public access. In the study, we also evaluated the differences between the structures of Aβ42 isoforms and speculate on their possible relevance to the known functions. Utilizing several representative structures for a single disordered protein for docking, with their subsequent averaging by conformations, would markedly increase the reliability of docking results.
Collapse
Affiliation(s)
- Anna P Tolstova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexander A Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexei A Adzhubei
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Washington University School of Medicine and Health Sciences, Washington 20052, D.C., United States
| |
Collapse
|
6
|
Hofmaier M, Heger JE, Lentz S, Schwarz S, Müller-Buschbaum P, Scheibel T, Fery A, Müller M. Influence of the Sequence Motive Repeating Number on Protein Folding in Spider Silk Protein Films. Biomacromolecules 2023; 24:5707-5721. [PMID: 37934893 DOI: 10.1021/acs.biomac.3c00688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
Like multiblock copolymers, spider silk proteins are built of repetitive sequence motives. One prominent repetitive motif is based on the consensus sequence of spidroin 4 of the spider Araneus diadematus ADF4. The number x of the repeating sequence motives (C) determines the molecular weight of the recombinant ADF4-based, engineered spider silk protein denoted as eADF4(Cx). eADF4(Cx) can be used as a model for intrinsically disordered proteins (IDP) and to elucidate their folding. Herein, the influence of the variation of the sequence motive repeating number x (x = 1, 2, 4, 8, 16) on the protein folding within eADF4(Cx) films was investigated. eADF4(Cx) films were cast from 1,1,1,3,3,3-hexafluoropropan-2-ol (HFIP) solutions onto planar silicon model substrates, revealing mainly helical or random coil structure. Upon treatment with methanol vapor (ptm), the formation of crystalline β-sheets was triggered. Dichroic Fourier-transform infrared (FTIR) spectroscopy, circular dichroism, spectroscopic ellipsometry, atomic force microscopy, grazing-incidence small-angle X-ray scattering (GISAXS), grazing-incidence wide-angle X-ray scattering (GIWAXS), and electrokinetic and contact angle measurements were used to get information concerning the secondary structure and folding kinetics, orientation of β-sheets, the ratio of parallel/antiparallel β-sheets, domain sizes and distributions, surface topography, surface potential, hydrophobicity and the film integrity under water. Significant differences in the final β-sheet content, the share of antiparallel β-sheet structures, film integrity, surface potential, and isoelectric points between eADF4(Cx) with x = 1, 2 and eADF4(Cx) with x = 4, 8, 16 gave new insights in the molecular weight-dependent structure formation and film properties of IDP systems. GISAXS and kinetic measurements confirmed a relation between β-sheet crystal growth rate and final β-sheet crystal size. Further, competing effects of reduced diffusibility hindering accelerated crystal growth and enhanced backfolding promoting accelerated crystal growth with increasing molecular weight were discussed.
Collapse
Affiliation(s)
- Mirjam Hofmaier
- Institute of Physical Chemistry and Polymer Physics, Leibniz Institute of Polymer Research Dresden (IPF), Dresden 01069, Germany
- Chair of Physical Chemistry of Polymeric Materials, Technical University Dresden (TUD), Dresden 01069, Germany
| | - Julian E Heger
- TUM School of Natural Sciences, Department of Physics, Chair for Functional Materials, Technical University of Munich, Garching 85748, Germany
| | - Sarah Lentz
- Functional Polymer Interfaces Group, University of Bayreuth, Bayreuth 95447, Germany
| | - Simona Schwarz
- Institute of Physical Chemistry and Polymer Physics, Leibniz Institute of Polymer Research Dresden (IPF), Dresden 01069, Germany
| | - Peter Müller-Buschbaum
- TUM School of Natural Sciences, Department of Physics, Chair for Functional Materials, Technical University of Munich, Garching 85748, Germany
- Heinz Maier-Leibnitz Zentrum (MLZ), Technical University of Munich, Garching 85748, Germany
| | - Thomas Scheibel
- Chair of Biomaterials, University of Bayreuth, Bayreuth 95447, Germany
- Bayreuth Center of Colloids and Interfaces (BZKG), University of Bayreuth, Bayreuth 95440, Germany
- Bayreuth Center for Molecular Bioscience (BZMB), University of Bayreuth, Bayreuth 95440, Germany
- Bayreuth Center for Material Science and Engineering (BayMAT), Universität Bayreuth, Bayreuth 95440, Germany
- Bavarian Polymer Institute (BPI), University of Bayreuth, Bayreuth 95440, Germany
| | - Andreas Fery
- Institute of Physical Chemistry and Polymer Physics, Leibniz Institute of Polymer Research Dresden (IPF), Dresden 01069, Germany
- Chair of Physical Chemistry of Polymeric Materials, Technical University Dresden (TUD), Dresden 01069, Germany
| | - Martin Müller
- Institute of Physical Chemistry and Polymer Physics, Leibniz Institute of Polymer Research Dresden (IPF), Dresden 01069, Germany
- Chair of Macromolecular Chemistry, Technical University of Dresden (TUD), Dresden 01062, Germany
| |
Collapse
|
7
|
Fenton M, Gregory E, Daughdrill G. Protein disorder and autoinhibition: The role of multivalency and effective concentration. Curr Opin Struct Biol 2023; 83:102705. [PMID: 37778184 PMCID: PMC10841074 DOI: 10.1016/j.sbi.2023.102705] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 10/03/2023]
Abstract
Regulation of protein binding through autoinhibition commonly occurs via interactions involving intrinsically disordered regions (IDRs). These intramolecular interactions can directly or allosterically inhibit intermolecular protein or DNA binding, regulate enzymatic activity, and control the assembly of large macromolecular complexes. Autoinhibitory interactions mediated by protein disorder are inherently transient, making their identification and characterization challenging. In this review, we explore the structural and functional diversity of disorder-mediated autoinhibition for a variety of biological mechanisms, with a focus on the role of multivalency and effective concentration. We also discuss the evolution of disordered motifs that participate in autoinhibition using examples where sequence conservation varies from high to low. In some cases, identifiable motifs that are essential for autoinhibition remain intact within a rapidly evolving sequence, over long evolutionary distances. Finally, we examine the potential of AlphaFold2 to predict autoinhibitory intramolecular interactions involving IDRs.
Collapse
Affiliation(s)
- Malissa Fenton
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Emily Gregory
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Gary Daughdrill
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
| |
Collapse
|
8
|
Chepsergon J, Moleleki LN. "Order from disordered": Potential role of intrinsically disordered regions in phytopathogenic oomycete intracellular effector proteins. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102402. [PMID: 37329857 DOI: 10.1016/j.pbi.2023.102402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 05/13/2023] [Accepted: 05/17/2023] [Indexed: 06/19/2023]
Abstract
There is a continuous arms race between pathogens and their host plants. However, successful pathogens, such as phytopathogenic oomycetes, secrete effector proteins to manipulate host defense responses for disease development. Structural analyses of these effector proteins reveal the existence of regions that fail to fold into three-dimensional structures, intrinsically disordered regions (IDRs). Because of their flexibility, these regions are involved in important biological functions of effector proteins, such as effector-host protein interactions that perturb host immune responses. Despite their significance, the role of IDRs in phytopathogenic oomycete effector-host protein interactions is not clear. This review, therefore, searched the literature for functionally characterized oomycete intracellular effectors with known host interactors. We further classify regions that mediate effector-host protein interactions into globular or disordered binding sites in these proteins. To fully appreciate the potential role of IDRs, five effector proteins encoding potential disordered binding sites were used as case studies. We also propose a pipeline that can be used to identify, classify as well as characterize potential binding regions in effector proteins. Understanding the role of IDRs in these effector proteins can aid in the development of new disease-control strategies.
Collapse
Affiliation(s)
- Jane Chepsergon
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Lucy Novungayo Moleleki
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa.
| |
Collapse
|
9
|
A Molecular Mechanism to Explain the Nickel-Induced Changes in Protamine-like Proteins and Their DNA Binding Affecting Sperm Chromatin in Mytilus galloprovincialis: An In Vitro Study. Biomolecules 2023; 13:biom13030520. [PMID: 36979455 PMCID: PMC10046793 DOI: 10.3390/biom13030520] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 02/03/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023] Open
Abstract
Nickel is associated with reproductive toxicity, but little is known about the molecular mechanisms of nickel-induced effects on sperm chromatin and protamine-like proteins (PLs). In the present work, we analyzed PLs from Mytilus galloprovincialis by urea-acetic acid polyacrylamide gel electrophoresis (AU-PAGE) and SDS-PAGE and assessed their binding to DNA by Electrophoretic Mobility Shift Assay (EMSA) after exposing mussels to 5, 15, and 35 µM NiCl2 for 24 h. In addition, a time course of digestion with MNase and release of PLs from sperm nuclei by the NaCl gradient was performed. For all exposure doses, in AU-PAGE, there was an additional migrating band between PL-III and PL-IV, corresponding to a fraction of PLs in the form of peptides detected by SDS-PAGE. Alterations in DNA binding of PLs were observed by EMSA after exposure to 5 and 15 µM NiCl2, while, at all NiCl2 doses, increased accessibility of MNase to sperm chromatin was found. The latter was particularly relevant at 15 µM NiCl2, a dose at which increased release of PLII and PLIII from sperm nuclei and the highest value of nickel accumulated in the gonads were also found. Finally, at all exposure doses, there was also an increase in PARP expression, but especially at 5 µM NiCl2. A possible molecular mechanism for the toxic reproductive effects of nickel in Mytilus galloprovincialis is discussed.
Collapse
|
10
|
Hofmaier M, Malanin M, Bittrich E, Lentz S, Urban B, Scheibel T, Fery A, Müller M. β-Sheet Structure Formation within Binary Blends of Two Spider Silk Related Peptides. Biomacromolecules 2023; 24:825-840. [PMID: 36632028 DOI: 10.1021/acs.biomac.2c01266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Intrinsically disordered proteins (IDPs) play an important role in molecular biology and medicine because their induced folding can lead to so-called conformational diseases, where β-amyloids play an important role. Still, the molecular folding process into the different substructures, such as parallel/antiparallel or extended β-sheet/crossed β-sheet is not fully understood. The recombinant spider silk protein eADF4(Cx) consisting of repeating modules C, which are composed of a crystalline (pep-c) and an amorphous peptide sequence (pep-a), can be used as a model system for IDP since it can assemble into similar structures. In this work, blend films of the pep-c and pep-a sequences were investigated to modulate the β-sheet formation by varying the molar fraction of pep-c and pep-a. Dichroic Fourier-transform infrared spectroscopy (FTIR), circular dichroism, spectroscopic ellipsometry, atomic force microscopy, and IR nanospectroscopy were used to examine the secondary structure, the formation of parallel and antiparallel β-sheets, their orientation, and the microscopic roughness and phase formation within peptide blend films upon methanol post-treatment. New insights into the formation of filament-like structures in these silk blend films were obtained. Filament-like structures could be locally assigned to β-sheet-rich structures. Further, the antiparallel or parallel character and the orientation of the formed β-sheets could be clearly determined. Finally, the ideal ratio of pep-a and pep-c sequences found in the fibroin 4 of the major ampullate silk of spiders could also be rationalized by comparing the blend and spider silk protein systems.
Collapse
Affiliation(s)
- Mirjam Hofmaier
- Institute of Physical Chemistry and Polymer Physics, Leibniz Institute of Polymer Research Dresden (IPF), Hohe Strasse 6, D-01069Dresden, Germany.,Chair of Physical Chemistry of Polymeric Materials, Technical University Dresden (TUD), D-01069Dresden, Germany
| | - Mikhail Malanin
- Leibniz Institute of Polymer Research Dresden (IPF), Institute of Macromolecular Chemistry, Hohe Strasse 6, D-01069Dresden, Germany
| | - Eva Bittrich
- Leibniz Institute of Polymer Research Dresden (IPF), Institute of Macromolecular Chemistry, Hohe Strasse 6, D-01069Dresden, Germany
| | - Sarah Lentz
- Chair of Biomaterials, University of Bayreuth, Prof.-Rüdiger-Bormann-Str. 1, D-95447Bayreuth, Germany
| | - Birgit Urban
- Institute of Physical Chemistry and Polymer Physics, Leibniz Institute of Polymer Research Dresden (IPF), Hohe Strasse 6, D-01069Dresden, Germany
| | - Thomas Scheibel
- Chair of Biomaterials, University of Bayreuth, Prof.-Rüdiger-Bormann-Str. 1, D-95447Bayreuth, Germany.,Bayreuther Zentrum für Kolloide und Grenzflächen (BZKG), Universität Bayreuth, Universitätsstraße 30, D-95440Bayreuth, Germany.,Bayreuther Zentrum für Molekulare Biowissenschaften (BZMB), Universität Bayreuth, Universitätsstraße 30, D-95440Bayreuth, Germany.,Bayreuther Materialzentrum (BayMAT), Universität Bayreuth, Universitätsstraße 30, D-95440Bayreuth, Germany.,Bayerisches Polymerinstitut (BPI), Universität Bayreuth, Universitätsstraße 30, D-95440Bayreuth, Germany
| | - Andreas Fery
- Institute of Physical Chemistry and Polymer Physics, Leibniz Institute of Polymer Research Dresden (IPF), Hohe Strasse 6, D-01069Dresden, Germany.,Chair of Physical Chemistry of Polymeric Materials, Technical University Dresden (TUD), D-01069Dresden, Germany
| | - Martin Müller
- Institute of Physical Chemistry and Polymer Physics, Leibniz Institute of Polymer Research Dresden (IPF), Hohe Strasse 6, D-01069Dresden, Germany.,Chair of Macromolecular Chemistry, Technical University of Dresden (TUD), Mommsenstraße 4, D-01062Dresden, Germany
| |
Collapse
|
11
|
Reid LM, Guzzetti I, Svensson T, Carlsson AC, Su W, Leek T, von Sydow L, Czechtizky W, Miljak M, Verma C, De Maria L, Essex JW. How well does molecular simulation reproduce environment-specific conformations of the intrinsically disordered peptides PLP, TP2 and ONEG? Chem Sci 2022; 13:1957-1971. [PMID: 35308859 PMCID: PMC8848758 DOI: 10.1039/d1sc03496k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 01/03/2022] [Indexed: 12/31/2022] Open
Abstract
Understanding the conformational ensembles of intrinsically disordered proteins and peptides (IDPs) in their various biological environments is essential for understanding their mechanisms and functional roles in the proteome, leading to a greater knowledge of, and potential treatments for, a broad range of diseases. To determine whether molecular simulation is able to generate accurate conformational ensembles of IDPs, we explore the structural landscape of the PLP peptide (an intrinsically disordered region of the proteolipid membrane protein) in aqueous and membrane-mimicking solvents, using replica exchange with solute scaling (REST2), and examine the ability of four force fields (ff14SB, ff14IDPSFF, CHARMM36 and CHARMM36m) to reproduce literature circular dichroism (CD) data. Results from variable temperature (VT) 1H and Rotating frame Overhauser Effect SpectroscopY (ROESY) nuclear magnetic resonance (NMR) experiments are also presented and are consistent with the structural observations obtained from the simulations and CD. We also apply the optimum simulation protocol to TP2 and ONEG (a cell-penetrating peptide (CPP) and a negative control peptide, respectively) to gain insight into the structural differences that may account for the observed difference in their membrane-penetrating abilities. Of the tested force fields, we find that CHARMM36 and CHARMM36m are best suited to the study of IDPs, and accurately predict a disordered to helical conformational transition of the PLP peptide accompanying the change from aqueous to membrane-mimicking solvents. We also identify an α-helical structure of TP2 in the membrane-mimicking solvents and provide a discussion of the mechanistic implications of this observation with reference to the previous literature on the peptide. From these results, we recommend the use of CHARMM36m with the REST2 protocol for the study of environment-specific IDP conformations. We believe that the simulation protocol will allow the study of a broad range of IDPs that undergo conformational transitions in different biological environments.
Collapse
Affiliation(s)
- Lauren M Reid
- School of Chemistry, University of Southampton Highfield Southampton SO17 1BJ UK
- Bioinformatics Institute (ASTAR) 30 Biolpolis Street Matrix 138671 Singapore
- MedChemica Ltd Alderley Park Macclesfield Cheshire SK10 4TG UK
| | - Ileana Guzzetti
- Medical Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D AstraZeneca Gothenburg Sweden
| | - Tor Svensson
- Medical Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D AstraZeneca Gothenburg Sweden
| | - Anna-Carin Carlsson
- Early Chemical Development, Pharmaceutical Sciences, BioPharmaceuticals R&D AstraZeneca Gothenburg Sweden
| | - Wu Su
- Medical Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D AstraZeneca Gothenburg Sweden
| | - Tomas Leek
- Medical Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D AstraZeneca Gothenburg Sweden
| | - Lena von Sydow
- Medical Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D AstraZeneca Gothenburg Sweden
| | - Werngard Czechtizky
- Medical Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D AstraZeneca Gothenburg Sweden
| | - Marija Miljak
- School of Chemistry, University of Southampton Highfield Southampton SO17 1BJ UK
| | - Chandra Verma
- Bioinformatics Institute (ASTAR) 30 Biolpolis Street Matrix 138671 Singapore
- Department of Biological Sciences, National University of Singapore 16 Science Drive 4 117558 Singapore
- School of Biological Sciences, Nanyang Technological University 60 Nanyang Dr 637551 Singapore
| | - Leonardo De Maria
- Medical Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D AstraZeneca Gothenburg Sweden
| | - Jonathan W Essex
- School of Chemistry, University of Southampton Highfield Southampton SO17 1BJ UK
| |
Collapse
|
12
|
La Manna S, Di Natale C, Onesto V, Marasco D. Self-Assembling Peptides: From Design to Biomedical Applications. Int J Mol Sci 2021; 22:12662. [PMID: 34884467 PMCID: PMC8657556 DOI: 10.3390/ijms222312662] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/15/2021] [Accepted: 11/19/2021] [Indexed: 12/20/2022] Open
Abstract
Self-assembling peptides could be considered a novel class of agents able to harvest an array of micro/nanostructures that are highly attractive in the biomedical field. By modifying their amino acid composition, it is possible to mime several biological functions; when assembled in micro/nanostructures, they can be used for a variety of purposes such as tissue regeneration and engineering or drug delivery to improve drug release and/or stability and to reduce side effects. Other significant advantages of self-assembled peptides involve their biocompatibility and their ability to efficiently target molecular recognition sites. Due to their intrinsic characteristics, self-assembled peptide micro/nanostructures are capable to load both hydrophobic and hydrophilic drugs, and they are suitable to achieve a triggered drug delivery at disease sites by inserting in their structure's stimuli-responsive moieties. The focus of this review was to summarize the most recent and significant studies on self-assembled peptides with an emphasis on their application in the biomedical field.
Collapse
Affiliation(s)
- Sara La Manna
- Department of Pharmacy, University of Naples “Federico II”, 80131 Naples, Italy;
| | - Concetta Di Natale
- Istituto Italiano di Tecnologia, IIT@CRIB, Largo Barsanti e Matteucci, 53, 80125 Napoli, Italy
- Centro di Ricerca Interdipartimentale sui Biomateriali CRIB, Università di Napoli Federico II, Piazzale Tecchio, 80, 80125 Napoli, Italy
| | - Valentina Onesto
- Institute of Nanotechnology, Consiglio Nazionale delle Ricerche, CNR NANOTEC, via Monteroni, c/o Campus Ecotekne, 73100 Lecce, Italy;
| | - Daniela Marasco
- Department of Pharmacy, University of Naples “Federico II”, 80131 Naples, Italy;
| |
Collapse
|
13
|
Xing Z, Chen Y, Qiu F. Alternative Causal Link between Peptide Fibrillization and β-Strand Conformation. ACS OMEGA 2021; 6:12904-12912. [PMID: 34056442 PMCID: PMC8154227 DOI: 10.1021/acsomega.1c01423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/23/2021] [Indexed: 02/08/2023]
Abstract
In the prevailing phenomenon of peptide fibrillization, β-strand conformation has long been believed to be an important structural basis for peptide assembly. According to a widely accepted theory, in most peptide fibrillization processes, peptide monomers need to intrinsically take or transform to β-strand conformation before they can undergo ordered packing to form nanofibers. In this study, we reported our findings on an alternative peptide fibrillization pathway starting from a disordered secondary structure, which could then transform to β-strand after fibrillization. By using circular dichroism, thioflavin-T binding test, and transmission electron microscopy, we studied the secondary structure and assembly behavior of Ac-RADARADARADARADA-NH2 (RADA16-I) in a low concentration range. The effects of peptide concentration, solvent polarity, pH, and temperature were investigated in detail. Our results showed that at very low concentrations, even though the peptide was in a disordered secondary structure, it could still form nanofibers through intermolecular assembly, and under higher peptide concentrations, the transformation from the disordered structure to β-strand could happen with the growth of nanofibers. Our results indicated that even without ordered β-strand conformation, driving forces such as hydrophobic interaction and electrostatic interaction could still play a determinative role in the self-assembly of peptides. At least in some cases, the formation of β-strand might be the consequence rather than the cause of peptide fibrillization.
Collapse
Affiliation(s)
- Zhihua Xing
- Laboratory
of Anesthesia and Critical Care Medicine, Translational Neuroscience
Center and National Clinical Research Center for Geriatrics, West
China Hospital, Sichuan University, Chengdu 610041, China
- Laboratory
of Ethnopharmacology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yongzhu Chen
- Laboratory
of Anesthesia and Critical Care Medicine, Translational Neuroscience
Center and National Clinical Research Center for Geriatrics, West
China Hospital, Sichuan University, Chengdu 610041, China
- Periodical
Press of West China Hospital, Sichuan University, Chengdu 610041, China
| | - Feng Qiu
- Laboratory
of Anesthesia and Critical Care Medicine, Translational Neuroscience
Center and National Clinical Research Center for Geriatrics, West
China Hospital, Sichuan University, Chengdu 610041, China
- National-Local
Joint Engineering Research Center of Translational Medicine of Anesthesiology,
West China Hospital, Sichuan University, Chengdu 610041, China
| |
Collapse
|
14
|
Russell MJ. The "Water Problem"( sic), the Illusory Pond and Life's Submarine Emergence-A Review. Life (Basel) 2021; 11:429. [PMID: 34068713 PMCID: PMC8151828 DOI: 10.3390/life11050429] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 04/30/2021] [Accepted: 05/01/2021] [Indexed: 01/10/2023] Open
Abstract
The assumption that there was a "water problem" at the emergence of life-that the Hadean Ocean was simply too wet and salty for life to have emerged in it-is here subjected to geological and experimental reality checks. The "warm little pond" that would take the place of the submarine alkaline vent theory (AVT), as recently extolled in the journal Nature, flies in the face of decades of geological, microbiological and evolutionary research and reasoning. To the present author, the evidence refuting the warm little pond scheme is overwhelming given the facts that (i) the early Earth was a water world, (ii) its all-enveloping ocean was never less than 4 km deep, (iii) there were no figurative "Icelands" or "Hawaiis", nor even an "Ontong Java" then because (iv) the solidifying magma ocean beneath was still too mushy to support such salient loadings on the oceanic crust. In place of the supposed warm little pond, we offer a well-protected mineral mound precipitated at a submarine alkaline vent as life's womb: in place of lipid membranes, we suggest peptides; we replace poisonous cyanide with ammonium and hydrazine; instead of deleterious radiation we have the appropriate life-giving redox and pH disequilibria; and in place of messy chemistry we offer the potential for life's emergence from the simplest of geochemically available molecules and ions focused at a submarine alkaline vent in the Hadean-specifically within the nano-confined flexible and redox active interlayer walls of the mixed-valent double layer oxyhydroxide mineral, fougerite/green rust comprising much of that mound.
Collapse
Affiliation(s)
- Michael J Russell
- Dipartimento di Chimica, Università degli Studi di Torino, via P. Giuria 7, 10125 Turin, Italy
| |
Collapse
|