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Mondal S, Karmakar T. Insights into the mechanism of peptide fibril growth on gold surface. Biophys Chem 2024; 310:107237. [PMID: 38640598 DOI: 10.1016/j.bpc.2024.107237] [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: 01/23/2024] [Revised: 03/24/2024] [Accepted: 04/10/2024] [Indexed: 04/21/2024]
Abstract
Understanding the formation of β-fibrils over the gold surface is of paramount interest in nano-bio-medicinal Chemistry. The intricate mechanism of self-assembly of neurofibrillogenic peptides and their growth over the gold surface remains elusive, as experiments are limited in unveiling the microscopic dynamic details, in particular, at the early stage of the peptide aggregation. In this work, we carried out equilibrium molecular dynamics and enhanced sampling simulations to elucidate the underlying mechanism of the growth of an amyloid-forming sequence of tau fragments over the gold surface. Our results disclose that the collective intermolecular interactions between the peptide chains and peptides with the gold surface facilitate the peptide adsorption, followed by integration, finally leading to the fibril formation.
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Affiliation(s)
- Soumya Mondal
- Department of Chemistry, Indian Institute of Technology, Delhi, New Delhi 110016, Delhi, India
| | - Tarak Karmakar
- Department of Chemistry, Indian Institute of Technology, Delhi, New Delhi 110016, Delhi, India.
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2
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Iscen A, Kaygisiz K, Synatschke CV, Weil T, Kremer K. Multiscale Simulations of Self-Assembling Peptides: Surface and Core Hydrophobicity Determine Fibril Stability and Amyloid Aggregation. Biomacromolecules 2024; 25:3063-3075. [PMID: 38652055 PMCID: PMC11094720 DOI: 10.1021/acs.biomac.4c00151] [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: 02/02/2024] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 04/25/2024]
Abstract
Assemblies of peptides and proteins through specific intermolecular interactions set the basis for macroscopic materials found in nature. Peptides provide easily tunable hydrogen-bonding interactions, which can lead to the formation of ordered structures such as highly stable β-sheets that can form amyloid-like supramolecular peptide nanofibrils (PNFs). PNFs are of special interest, as they could be considered as mimics of various fibrillar structures found in nature. In their ability to serve as supramolecular scaffolds, they could mimic certain features of the extracellular matrix to provide stability, interact with pathogens such as virions, and transduce signals between the outside and inside of cells. Many PNFs have been reported that reveal rich bioactivities. PNFs supporting neuronal cell growth or lentiviral gene transduction have been studied systematically, and their material properties were correlated to bioactivities. However, the impact of the structure of PNFs, their dynamics, and stabilities on their unique functions is still elusive. Herein, we provide a microscopic view of the self-assembled PNFs to unravel how the amino acid sequence of self-assembling peptides affects their secondary structure and dynamic properties of the peptides within supramolecular fibrils. Based on sequence truncation, amino acid substitution, and sequence reordering, we demonstrate that peptide-peptide aggregation propensity is critical to form bioactive β-sheet-rich structures. In contrast to previous studies, a very high peptide aggregation propensity reduces bioactivity due to intermolecular misalignment and instabilities that emerge when fibrils are in close proximity to other fibrils in solution. Our multiscale simulation approach correlates changes in biological activity back to single amino acid modifications. Understanding these relationships could lead to future material discoveries where the molecular sequence predictably determines the macroscopic properties and biological activity. In addition, our studies may provide new insights into naturally occurring amyloid fibrils in neurodegenerative diseases.
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Affiliation(s)
- Aysenur Iscen
- Department
of Polymer Theory, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Kübra Kaygisiz
- Department
of Synthesis of Macromolecules, Max Planck
Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Christopher V. Synatschke
- Department
of Synthesis of Macromolecules, Max Planck
Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Tanja Weil
- Department
of Synthesis of Macromolecules, Max Planck
Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Kurt Kremer
- Department
of Polymer Theory, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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Zheng X, Ni Z, Pei Q, Wang M, Tan J, Bai S, Shi F, Ye S. Probing the Molecular Structure and Dynamics of Membrane-Bound Proteins during Misfolding Processes by Sum-Frequency Generation Vibrational Spectroscopy. Chempluschem 2024:e202300684. [PMID: 38380553 DOI: 10.1002/cplu.202300684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/17/2024] [Accepted: 02/20/2024] [Indexed: 02/22/2024]
Abstract
Protein misfolding and amyloid formation are implicated in the protein dysfunction, but the underlying mechanism remains to be clarified due to the lack of effective tools for detecting the transient intermediates. Sum frequency generation vibrational spectroscopy (SFG-VS) has emerged as a powerful tool for identifying the structure and dynamics of proteins at the interfaces. In this review, we summarize recent SFG-VS studies on the structure and dynamics of membrane-bound proteins during misfolding processes. This paper first introduces the methods for determining the secondary structure of interfacial proteins: combining chiral and achiral spectra of amide A and amide I bands and combining amide I, amide II, and amide III spectral features. To demonstrate the ability of SFG-VS in investigating the interfacial protein misfolding and amyloid formation, studies on the interactions between different peptides/proteins (islet amyloid polypeptide, amyloid β, prion protein, fused in sarcoma protein, hen egg-white lysozyme, fusing fusion peptide, class I hydrophobin SC3 and class II hydrophobin HFBI) and surfaces such as lipid membranes are discussed. These molecular-level studies revealed that SFG-VS can provide a unique understanding of the mechanism of interfacial protein misfolding and amyloid formation in real time, in situ and without any exogenous labeling.
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Affiliation(s)
- Xiaoxuan Zheng
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Zijian Ni
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Quanbing Pei
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Mengmeng Wang
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Junjun Tan
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Shiyu Bai
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Fangwen Shi
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Shuji Ye
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
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4
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Gahtori P, Gunwant V, Pandey R. How Does pH Affect the Adsorption of Human Serum Protein in the Presence of Hydrophobic and Hydrophilic Nanoparticles at Air-Water and Lipid-Water Interfaces? LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:15487-15498. [PMID: 37878019 DOI: 10.1021/acs.langmuir.3c01755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
This study investigates interaction between hydrophilic (11-mercaptoundecanoic acid (MUA)) and hydrophobic (1-undecanethiol (UDT)) gold nanoparticles (GNPs) with human serum albumin (HSA) protein on air-water and lipid-water interfaces at pH 3 and 7. Vibrational sum frequency generation (VSFG) spectroscopy is used to analyze changes in the intensity of interfacial water molecules and the C-H group of the protein. At the air-water interface, the hydrophobic interaction between the HSA protein and hydrophobic GNPs at pH 3 leads to their accumulation at the interface, resulting in an increased C-H intensity of the protein with a slight decrease in water intensity. Whereas, at pH 7, where the negative charge of the protein results in the reduced surface activity of the HSA compared to pH 3, the interaction between alkyl chain of the hydrophobic GNPs and alkyl group of the protein results in the adsorption of the protein-capped GNPs at the interface. This leads to an increased intensity of the C-H group of protein and water molecules. However, negatively charged hydrophilic GNPs do not induce significant changes in the interfacial water structure or the C-H group of the protein due to the electrostatic force of repulsion with the negatively charged HSA at pH 7. In contrast, at the lipid-water interface, both hydrophobic and hydrophilic GNPs interact with HSA protein, causing disordering of interfacial water molecules at pH 3 and ordering at pH 7. Interestingly, similar behavior of the protein with both types of GNPs results in comparable ordering/disordering at the interface depending on the pH of solution. Furthermore, the VSFG results obtained with the deuterated lipid suggest that changes in ordering and disorder occur due to increased protein adsorption in the presence of GNPs, causing alterations in the membrane structure. These findings give a better understanding of the mechanisms that govern protein-nanoparticle interaction and their consequential effects on the structure, function, and behavior of molecules at the biological membrane interface, which is crucial for developing safe and effective nanoparticle-based therapeutics.
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Affiliation(s)
- Preeti Gahtori
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Vineet Gunwant
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Ravindra Pandey
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
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Maltseva D, Chatterjee S, Yu CC, Brzezinski M, Nagata Y, Gonella G, Murthy AC, Stachowiak JC, Fawzi NL, Parekh SH, Bonn M. Fibril formation and ordering of disordered FUS LC driven by hydrophobic interactions. Nat Chem 2023:10.1038/s41557-023-01221-1. [PMID: 37231298 PMCID: PMC10396963 DOI: 10.1038/s41557-023-01221-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 04/25/2023] [Indexed: 05/27/2023]
Abstract
Biomolecular condensates, protein-rich and dynamic membrane-less organelles, play critical roles in a range of subcellular processes, including membrane trafficking and transcriptional regulation. However, aberrant phase transitions of intrinsically disordered proteins in biomolecular condensates can lead to the formation of irreversible fibrils and aggregates that are linked to neurodegenerative diseases. Despite the implications, the interactions underlying such transitions remain obscure. Here we investigate the role of hydrophobic interactions by studying the low-complexity domain of the disordered 'fused in sarcoma' (FUS) protein at the air/water interface. Using surface-specific microscopic and spectroscopic techniques, we find that a hydrophobic interface drives fibril formation and molecular ordering of FUS, resulting in solid-like film formation. This phase transition occurs at 600-fold lower FUS concentration than required for the canonical FUS low-complexity liquid droplet formation in bulk. These observations highlight the importance of hydrophobic effects for protein phase separation and suggest that interfacial properties drive distinct protein phase-separated structures.
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Affiliation(s)
- Daria Maltseva
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Sayantan Chatterjee
- Max Planck Institute for Polymer Research, Mainz, Germany
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Chun-Chieh Yu
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Mateusz Brzezinski
- Max Planck Institute for Polymer Research, Mainz, Germany
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Yuki Nagata
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Grazia Gonella
- Max Planck Institute for Polymer Research, Mainz, Germany
- Institute of Biochemistry and Bringing Materials to Life Initiative, ETH Zurich, Zürich, Switzerland
| | - Anastasia C Murthy
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - Jeanne C Stachowiak
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Nicolas L Fawzi
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - Sapun H Parekh
- Max Planck Institute for Polymer Research, Mainz, Germany.
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA.
| | - Mischa Bonn
- Max Planck Institute for Polymer Research, Mainz, Germany.
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