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Min D. Folding speeds of helical membrane proteins. Biochem Soc Trans 2024; 52:491-501. [PMID: 38385525 PMCID: PMC10903471 DOI: 10.1042/bst20231315] [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: 01/09/2024] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/23/2024]
Abstract
Membrane proteins play key roles in human health, contributing to cellular signaling, ATP synthesis, immunity, and metabolite transport. Protein folding is the pivotal early step for their proper functioning. Understanding how this class of proteins adopts their native folds could potentially aid in drug design and therapeutic interventions for misfolding diseases. It is an essential piece in the whole puzzle to untangle their kinetic complexities, such as how rapid membrane proteins fold, how their folding speeds are influenced by changing conditions, and what mechanisms are at play. This review explores the folding speed aspect of multipass α-helical membrane proteins, encompassing plausible folding scenarios based on the timing and stability of helix packing interactions, methods for characterizing the folding time scales, relevant folding steps and caveats for interpretation, and potential implications. The review also highlights the recent estimation of the so-called folding speed limit of helical membrane proteins and discusses its consequent impact on the current picture of folding energy landscapes.
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Affiliation(s)
- Duyoung Min
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
- Center for Wave Energy Materials, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
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Ersoy U, Kanakis I, Alameddine M, Pedraza-Vazquez G, Ozanne SE, Peffers MJ, Jackson MJ, Goljanek-Whysall K, Vasilaki A. Lifelong dietary protein restriction accelerates skeletal muscle loss and reduces muscle fibre size by impairing proteostasis and mitochondrial homeostasis. Redox Biol 2024; 69:102980. [PMID: 38064763 PMCID: PMC10755587 DOI: 10.1016/j.redox.2023.102980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 01/01/2024] Open
Abstract
The early life environment significantly affects the development of age-related skeletal muscle disorders. However, the long-term effects of lactational protein restriction on skeletal muscle are still poorly defined. Our study revealed that male mice nursed by dams fed a low-protein diet during lactation exhibited skeletal muscle growth restriction. This was associated with a dysregulation in the expression levels of genes related to the ribosome, mitochondria and skeletal muscle development. We reported that lifelong protein restriction accelerated loss of type-IIa muscle fibres and reduced muscle fibre size by impairing mitochondrial homeostasis and proteostasis at 18 months of age. However, feeding a normal-protein diet following lactational protein restriction prevented accelerated fibre loss and fibre size reduction in later life. These findings provide novel insight into the mechanisms by which lactational protein restriction hinders skeletal muscle growth and includes evidence that lifelong dietary protein restriction accelerated skeletal muscle loss in later life.
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Affiliation(s)
- Ufuk Ersoy
- Department of Musculoskeletal & Ageing Science, Institute of Life Course & Medical Sciences (ILCaMS), The MRC - Versus Arthritis Centre for Integrated Research Into Musculoskeletal Ageing (CIMA), University of Liverpool, Liverpool, UK
| | - Ioannis Kanakis
- Department of Musculoskeletal & Ageing Science, Institute of Life Course & Medical Sciences (ILCaMS), The MRC - Versus Arthritis Centre for Integrated Research Into Musculoskeletal Ageing (CIMA), University of Liverpool, Liverpool, UK; Chester Medical School, Faculty of Medicine and Life Sciences, University of Chester, Chester, UK
| | - Moussira Alameddine
- Department of Musculoskeletal & Ageing Science, Institute of Life Course & Medical Sciences (ILCaMS), The MRC - Versus Arthritis Centre for Integrated Research Into Musculoskeletal Ageing (CIMA), University of Liverpool, Liverpool, UK
| | - Gibran Pedraza-Vazquez
- Department of Physiology, School of Medicine and REMEDI, CMNHS, University of Galway, Galway, Ireland
| | - Susan E Ozanne
- MRC Metabolic Diseases Unit, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, University of Cambridge Metabolic Research Laboratories, Cambridge, UK
| | - Mandy Jayne Peffers
- Department of Musculoskeletal & Ageing Science, Institute of Life Course & Medical Sciences (ILCaMS), The MRC - Versus Arthritis Centre for Integrated Research Into Musculoskeletal Ageing (CIMA), University of Liverpool, Liverpool, UK
| | - Malcolm J Jackson
- Department of Musculoskeletal & Ageing Science, Institute of Life Course & Medical Sciences (ILCaMS), The MRC - Versus Arthritis Centre for Integrated Research Into Musculoskeletal Ageing (CIMA), University of Liverpool, Liverpool, UK
| | - Katarzyna Goljanek-Whysall
- Department of Musculoskeletal & Ageing Science, Institute of Life Course & Medical Sciences (ILCaMS), The MRC - Versus Arthritis Centre for Integrated Research Into Musculoskeletal Ageing (CIMA), University of Liverpool, Liverpool, UK; Department of Physiology, School of Medicine and REMEDI, CMNHS, University of Galway, Galway, Ireland
| | - Aphrodite Vasilaki
- Department of Musculoskeletal & Ageing Science, Institute of Life Course & Medical Sciences (ILCaMS), The MRC - Versus Arthritis Centre for Integrated Research Into Musculoskeletal Ageing (CIMA), University of Liverpool, Liverpool, UK.
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Almeida PF. In Search of a Molecular View of Peptide-Lipid Interactions in Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023. [PMID: 37478368 DOI: 10.1021/acs.langmuir.3c00538] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Lipid bilayer membranes are often represented as a continuous nonpolar slab with a certain thickness bounded by two more polar interfaces. Phenomena such as peptide binding to the membrane surface, folding, insertion, translocation, and diffusion are typically interpreted on the basis of this view. In this Perspective, I argue that this membrane representation as a hydrophobic continuum solvent is not adequate to understand peptide-lipid interactions. Lipids are not small compared to membrane-active peptides: their sizes are similar. Therefore, peptide diffusion needs to be understood in terms of free volume, not classical continuum mechanics; peptide solubility or partitioning in membranes cannot be interpreted in terms of hydrophobic mismatch between membrane thickness and peptide length; peptide folding and translocation, often involving cationic peptides, can only be understood if realizing that lipids adapt to the presence of peptides and the membrane may undergo considerable lipid redistribution in the process. In all of those instances, the detailed molecular interactions between the peptide residues and the lipid components are essential to understand the mechanisms involved.
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Affiliation(s)
- Paulo F Almeida
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina 28403, United States
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Wijesinghe WCB, Min D. Single-Molecule Force Spectroscopy of Membrane Protein Folding. J Mol Biol 2023; 435:167975. [PMID: 37330286 DOI: 10.1016/j.jmb.2023.167975] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 06/19/2023]
Abstract
Single-molecule force spectroscopy is a unique method that can probe the structural changes of single proteins at a high spatiotemporal resolution while mechanically manipulating them over a wide force range. Here, we review the current understanding of membrane protein folding learned by using the force spectroscopy approach. Membrane protein folding in lipid bilayers is one of the most complex biological processes in which diverse lipid molecules and chaperone proteins are intricately involved. The approach of single protein forced unfolding in lipid bilayers has produced important findings and insights into membrane protein folding. This review provides an overview of the forced unfolding approach, including recent achievements and technical advances. Progress in the methods can reveal more interesting cases of membrane protein folding and clarify general mechanisms and principles.
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Affiliation(s)
- W C Bhashini Wijesinghe
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Duyoung Min
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea; Center for Wave Energy Materials, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.
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Bailoni E, Partipilo M, Coenradij J, Grundel DAJ, Slotboom DJ, Poolman B. Minimal Out-of-Equilibrium Metabolism for Synthetic Cells: A Membrane Perspective. ACS Synth Biol 2023; 12:922-946. [PMID: 37027340 PMCID: PMC10127287 DOI: 10.1021/acssynbio.3c00062] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Indexed: 04/08/2023]
Abstract
Life-like systems need to maintain a basal metabolism, which includes importing a variety of building blocks required for macromolecule synthesis, exporting dead-end products, and recycling cofactors and metabolic intermediates, while maintaining steady internal physical and chemical conditions (physicochemical homeostasis). A compartment, such as a unilamellar vesicle, functionalized with membrane-embedded transport proteins and metabolic enzymes encapsulated in the lumen meets these requirements. Here, we identify four modules designed for a minimal metabolism in a synthetic cell with a lipid bilayer boundary: energy provision and conversion, physicochemical homeostasis, metabolite transport, and membrane expansion. We review design strategies that can be used to fulfill these functions with a focus on the lipid and membrane protein composition of a cell. We compare our bottom-up design with the equivalent essential modules of JCVI-syn3a, a top-down genome-minimized living cell with a size comparable to that of large unilamellar vesicles. Finally, we discuss the bottlenecks related to the insertion of a complex mixture of membrane proteins into lipid bilayers and provide a semiquantitative estimate of the relative surface area and lipid-to-protein mass ratios (i.e., the minimal number of membrane proteins) that are required for the construction of a synthetic cell.
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Affiliation(s)
- Eleonora Bailoni
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Michele Partipilo
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Jelmer Coenradij
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Douwe A. J. Grundel
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Dirk J. Slotboom
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Bert Poolman
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
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