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Majumder A, Straub JE. Machine Learning Derived Collective Variables for the Study of Protein Homodimerization in Membrane. J Chem Theory Comput 2024; 20:5774-5783. [PMID: 38918177 DOI: 10.1021/acs.jctc.4c00454] [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: 06/27/2024]
Abstract
The accurate calculation of equilibrium constants for protein-protein association is of fundamental importance to quantitative biology and remains an outstanding challenge for computational biophysics. Traditionally, equilibrium constants have been computed from one-dimensional free energy surfaces derived from sampling along a single collective variable. Importantly, recent advances in enhanced sampling methodology have facilitated the characterization of multidimensional free energy landscapes, often exposing multiple thermodynamically important minima missed by more restrictive sampling methods. A key to the effectiveness of this multidimensional sampling approach is the identification of collective variables that effectively define the configurational space of dissociated and associated states. Here we present the application of two machine learning methods for the unbiased determination of collective variables for enhanced sampling and analysis of protein-protein association. Our results both validate prior work, based on intuition derived collective variables, and demonstrate the effectiveness of the machine learning methods for the identification of collective variables for association reactions in complex biomolecular systems.
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Affiliation(s)
- Ayan Majumder
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - John E Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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2
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Krishnarjuna B, Sharma G, Hiiuk VM, Struppe J, Nagorny P, Ivanova MI, Ramamoorthy A. Nanodisc Reconstitution and Characterization of Amyloid-β Precursor Protein C99. Anal Chem 2024; 96:9362-9369. [PMID: 38826107 DOI: 10.1021/acs.analchem.3c05727] [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: 06/04/2024]
Abstract
Amyloid precursor protein (APP) plays a pivotal role in the pathology of Alzheimer's disease (AD). Since the fragmentation of the membrane-bound APP that results in the production of amyloid-β peptides is the starting point for amyloid toxicity in AD, it is important to investigate the structure and dynamics of APP in a near-native lipid-bilayer environment. However, the reconstitution of APP into a stable and suitable membrane-mimicking lipid environment is a challenging task. In this study, the 99-residue C-terminal domain of APP is successfully reconstituted into polymer nanodiscs and characterized using size-exclusion chromatography, mass spectrometry, solution NMR, and magic-angle spinning solid-state NMR. In addition, the feasibility of using lipid-solubilizing polymers for isolating and characterizing APP in the native Escherichia. coli membrane environment is demonstrated.
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Affiliation(s)
- Bankala Krishnarjuna
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Gaurav Sharma
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Volodymyr M Hiiuk
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, Massachusetts 01821, United States
| | - Pavel Nagorny
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Magdalena I Ivanova
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Neurology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, Florida 32310, United States
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3
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Rahman MM, Wang J, Wang G, Su Z, Li Y, Chen Y, Meng J, Yao Y, Wang L, Wilkens S, Tan J, Luo J, Zhang T, Zhu C, Cho SH, Wang L, Lee LP, Wan Y. Chimeric nanobody-decorated liposomes by self-assembly. NATURE NANOTECHNOLOGY 2024; 19:818-824. [PMID: 38374413 DOI: 10.1038/s41565-024-01620-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 01/23/2024] [Indexed: 02/21/2024]
Abstract
Liposomes as drug vehicles have advantages, such as payload protection, tunable carrying capacity and improved biodistribution. However, due to the dysfunction of targeting moieties and payload loss during preparation, immunoliposomes have yet to be favoured in commercial manufacturing. Here we report a chemical modification-free biophysical approach for producing immunoliposomes in one step through the self-assembly of a chimeric nanobody (cNB) into liposome bilayers. cNB consists of a nanobody against human epidermal growth factor receptor 2 (HER2), a flexible peptide linker and a hydrophobic single transmembrane domain. We determined that 64% of therapeutic compounds can be encapsulated into 100-nm liposomes, and up to 2,500 cNBs can be anchored on liposomal membranes without steric hindrance under facile conditions. Subsequently, we demonstrate that drug-loaded immunoliposomes increase cytotoxicity on HER2-overexpressing cancer cell lines by 10- to 20-fold, inhibit the growth of xenograft tumours by 3.4-fold and improve survival by more than twofold.
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Affiliation(s)
- Md Mofizur Rahman
- The Pq Laboratory of BiomeDx/Rx, Department of Biomedical Engineering, Binghamton University, Binghamton, NY, USA
- Department of Pharmacy, Daffodil International University, Dhaka, Bangladesh
| | - Jing Wang
- Department of Hematology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
- Department of Oncology and Hematology, Yizheng Hospital of Nanjing Drum Tower Hospital Group, Yizheng, China
| | - Guosheng Wang
- The Pq Laboratory of BiomeDx/Rx, Department of Biomedical Engineering, Binghamton University, Binghamton, NY, USA
- Department of Pulmonary and Critical Care Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhipeng Su
- Nanjing Regenecore Biotech Co. Ltd., Nanjing, China
| | - Yizeng Li
- Biophysics and Mathematical Biology Lab, Department of Biomedical Engineering, Binghamton University, Binghamton, NY, USA
| | - Yundi Chen
- The Pq Laboratory of BiomeDx/Rx, Department of Biomedical Engineering, Binghamton University, Binghamton, NY, USA
| | - Jinguo Meng
- Nanjing Regenecore Biotech Co. Ltd., Nanjing, China
| | - Yao Yao
- Nanjing Regenecore Biotech Co. Ltd., Nanjing, China
| | - Lefei Wang
- Nanjing Regenecore Biotech Co. Ltd., Nanjing, China
| | - Stephan Wilkens
- Department of Biochemistry and Molecular Biology, Upstate Medical University, Syracuse, NY, USA
| | - Jifu Tan
- Department of Mechanical Engineering, Northern Illinois University, Dekalb, IL, USA
| | - Juntao Luo
- Department of Pharmacology, Upstate Medical University, Syracuse, NY, USA
| | - Tao Zhang
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Johnson City, NY, USA
| | - Chuandong Zhu
- The Pq Laboratory of BiomeDx/Rx, Department of Biomedical Engineering, Binghamton University, Binghamton, NY, USA
- Department of Radiotherapy, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Sung Hyun Cho
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Lixue Wang
- The Pq Laboratory of BiomeDx/Rx, Department of Biomedical Engineering, Binghamton University, Binghamton, NY, USA.
- Department of Radiotherapy, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China.
| | - Luke P Lee
- Harvard Medical School, Harvard University; Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Department of Bioengineering, Department of Electrical Engineering and Computer Science, University of California, Berkeley, CA, USA.
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University, Suwon, Korea.
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, Korea.
| | - Yuan Wan
- The Pq Laboratory of BiomeDx/Rx, Department of Biomedical Engineering, Binghamton University, Binghamton, NY, USA.
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4
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Levintov L, Gorai B, Vashisth H. Spontaneous Dimerization and Distinct Packing Modes of Transmembrane Domains in Receptor Tyrosine Kinases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593448. [PMID: 38798363 PMCID: PMC11118388 DOI: 10.1101/2024.05.09.593448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The insulin receptor (IR) and the insulin-like growth factor-1 receptor (IGF1R) are homodimeric transmembrane glycoproteins that transduce signals across the membrane on binding of extracellular peptide ligands. The structures of IR/IGF1R fragments in apo and liganded states have revealed that the extracellular subunits of these receptors adopt Λ-shaped configurations to which are connected the intracellular tyrosine kinase (TK) domains. The binding of peptide ligands induces structural transitions in the extracellular subunits leading to potential dimerization of transmembrane domains (TMDs) and autophosphorylation in TKs. However, the activation mechanisms of IR/IGF1R, especially the role of TMDs in coordinating signal-inducing structural transitions, remain poorly understood, in part due to the lack of structures of full-length receptors in apo or liganded states. While atomistic simulations of IR/IGF1R TMDs showed that these domains can dimerize in single component membranes, spontaneous unbiased dimerization in a plasma membrane having physiologically representative lipid composition has not been observed. We address this limitation by employing coarse-grained (CG) molecular dynamics simulations to probe the dimerization propensity of IR/IGF1R TMDs. We observed that TMDs in both receptors spontaneously dimerized independent of their initial orientations in their dissociated states, signifying their natural propensity for dimerization. In the dimeric state, IR TMDs predominantly adopted X-shaped configurations with asymmetric helical packing and significant tilt relative to the membrane normal, while IGF1R TMDs adopted symmetric V-shaped or parallel configurations with either no tilt or a small tilt relative to the membrane normal. Our results suggest that IR/IGF1R TMDs spontaneously dimerize and adopt distinct dimerized configurations.
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Affiliation(s)
- Lev Levintov
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham 03824, New Hampshire, USA
| | - Biswajit Gorai
- Institute of Chemistry, Technical University of Berlin, Berlin 10623, Germany
| | - Harish Vashisth
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham 03824, New Hampshire, USA
- Department of Chemistry, University of New Hampshire, Durham 03824, New Hampshire, USA
- Integrated Applied Mathematics Program, University of New Hampshire, Durham 03824, New Hampshire, USA
- Molecular and Cellular Biotechnology Program, University of New Hampshire, Durham 03824, New Hampshire, USA
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5
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Krishnarjuna B, Sharma G, Hiiuk VM, Struppe J, Nagorny P, Ivanova MI, Ramamoorthy A. Nanodisc reconstitution and characterization of amyloid-β precursor protein C99. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.21.590446. [PMID: 38659865 PMCID: PMC11042261 DOI: 10.1101/2024.04.21.590446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Amyloid precursor protein (APP) plays a pivotal role in the pathology of Alzheimer's disease. Since the fragmentation of the membrane-bound APP that results in the production of amyloid-beta peptides is the starting point for amyloid toxicity in AD, it is important to investigate the structure and dynamics of APP in a near-native lipid-bilayer environment. However, the reconstitution of APP into a stable/suitable membrane-mimicking lipid environment is a challenging task. In this study, the 99-residue C-terminal domain of APP is successfully reconstituted into polymer nanodiscs and characterized using size-exclusion chromatography, mass spectrometry, solution NMR, and magic-angle spinning solid-state NMR. In addition, the feasibility of using lipid-solubilizing polymers for isolating and characterizing APP in native E. coli membrane environment is demonstrated.
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Affiliation(s)
- Bankala Krishnarjuna
- Biophysics Program, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109, United States
| | - Gaurav Sharma
- Biophysics Program, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109, United States
| | - Volodymyr M Hiiuk
- Biophysics Program, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, Massachusetts 01821, United States
| | - Pavel Nagorny
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Magdalena I Ivanova
- Biophysics Program, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Neurology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, FL 32310, United States
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, United States
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6
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Ito S, Sugita Y. Free-energy landscapes of transmembrane homodimers by bias-exchange adaptively biased molecular dynamics. Biophys Chem 2024; 307:107190. [PMID: 38290241 DOI: 10.1016/j.bpc.2024.107190] [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: 12/03/2023] [Revised: 01/21/2024] [Accepted: 01/21/2024] [Indexed: 02/01/2024]
Abstract
Membrane proteins play essential roles in various biological functions within the cell. One of the most common functional regulations involves the dimerization of two single-pass transmembrane (TM) helices. Glycophorin A (GpA) and amyloid precursor protein (APP) form TM homodimers in the membrane, which have been investigated both experimentally and computationally. The homodimer structures are well characterized using only four collective variables (CVs) when each TM helix is stable. The CVs are the interhelical distance, the crossing angle, and the Crick angles for two TM helices. However, conformational sampling with multi-dimensional replica-exchange umbrella sampling (REUS) requires too many replicas to sample all the CVs for exploring the conformational landscapes. Here, we show that the bias-exchange adaptively biased molecular dynamics (BE-ABMD) with the four CVs effectively explores the free-energy landscapes of the TM helix dimers of GpA, wild-type APP and its mutants in the IMM1 implicit membrane. Compared to the original ABMD, the bias-exchange algorithm in BE-ABMD can provide a more rapidly converged conformational landscape. The BE-ABMD simulations could also reveal TM packing interfaces of the membrane proteins and the dependence of the free-energy landscapes on the membrane thickness. This approach is valuable for numerous other applications, including those involving explicit solvent and a lipid bilayer in all-atom force fields or Martini coarse-grained models, and enhances our understanding of protein-protein interactions in biological membranes.
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Affiliation(s)
- Shingo Ito
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Computational Biophysics Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 1-6-5 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
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7
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Mu J, Lam SM, Shui G. Emerging roles and therapeutic potentials of sphingolipids in pathophysiology: emphasis on fatty acyl heterogeneity. J Genet Genomics 2024; 51:268-278. [PMID: 37364711 DOI: 10.1016/j.jgg.2023.06.006] [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: 04/01/2023] [Revised: 05/29/2023] [Accepted: 06/15/2023] [Indexed: 06/28/2023]
Abstract
Sphingolipids not only exert structural roles in cellular membranes, but also act as signaling molecules in various physiological and pathological processes. A myriad of studies have shown that abnormal levels of sphingolipids and their metabolic enzymes are associated with a variety of human diseases. Moreover, blood sphingolipids can also be used as biomarkers for disease diagnosis. This review summarizes the biosynthesis, metabolism, and pathological roles of sphingolipids, with emphasis on the biosynthesis of ceramide, the precursor for the biosynthesis of complex sphingolipids with different fatty acyl chains. The possibility of using sphingolipids for disease prediction, diagnosis, and treatment is also discussed. Targeting endogenous ceramides and complex sphingolipids along with their specific fatty acyl chain to promote future drug development will also be discussed.
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Affiliation(s)
- Jinming Mu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Sin Man Lam
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Lipidall Technologies Company Limited, Changzhou, Jiangsu 213000, China.
| | - Guanghou Shui
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China.
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8
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Wu Y, Thomas GM, Thomsen M, Bahri S, Lieberman RL. Lipid environment modulates processivity and kinetics of a presenilin homolog acting on multiple substrates in vitro. J Biol Chem 2023; 299:105401. [PMID: 38270390 PMCID: PMC10679502 DOI: 10.1016/j.jbc.2023.105401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/12/2023] [Accepted: 10/11/2023] [Indexed: 01/26/2024] Open
Abstract
Intramembrane proteases (IPs) hydrolyze peptides in the lipid membrane. IPs participate in a number of cellular pathways including immune response and surveillance, and cholesterol biosynthesis, and they are exploited by viruses for replication. Despite their broad importance across biology, how activity is regulated in the cell to control protein maturation and release of specific bioactive peptides at the right place and right time remains largely unanswered, particularly for the intramembrane aspartyl protease (IAP) subtype. At a molecular biochemical level, different IAP homologs can cleave non-biological substrates, and there is no sequence recognition motif among the nearly 150 substrates identified for just one IAP, presenilin-1, the catalytic component of γ-secretase known for its involvement in the production of amyloid-β plaques associated with Alzheimer disease. Here we used gel-based assays combined with quantitative mass spectrometry and FRET-based kinetics assays to probe the cleavage profile of the presenilin homolog from the methanogen Methanoculleus marisnigri JR1 as a function of the surrounding lipid-mimicking environment, either detergent micelles or bicelles. We selected four biological IAP substrates that have not undergone extensive cleavage profiling previously, namely, the viral core protein of Hepatitis C virus, the viral core protein of Classical Swine Fever virus, the transmembrane segment of Notch-1, and the tyrosine receptor kinase ErbB4. Our study demonstrates a proclivity toward cleavage of substrates at positions of low average hydrophobicity and a consistent role for the lipid environment in modulating kinetic properties.
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Affiliation(s)
- Yuqi Wu
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Gwendell M Thomas
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Max Thomsen
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Sara Bahri
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Raquel L Lieberman
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA.
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9
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Putri RA, Rohman MS, Swasono RT, Raharjo TJ. A novel synthetic peptide analog enhanced antibacterial activity of the frog-derived skin peptide wuchuanin-A1. J Biomol Struct Dyn 2023:1-11. [PMID: 37968993 DOI: 10.1080/07391102.2023.2281633] [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: 09/05/2023] [Accepted: 11/04/2023] [Indexed: 11/17/2023]
Abstract
In recent years, there has been a growing focus on the development of novel antibacterial compounds for clinical applications, such as antimicrobial peptide (AMP). Among the developed AMP, wuchuanin-A1, a coil-shaped bioactive peptide derived from Odorrana wuchuanensis frog skin, has been reported to exhibit antibacterial, antifungal, and antioxidant activity, but there are limited studies on its potential as an antibacterial agent. Therefore, this study aims to molecularly modify the sequence of wuchuanin-A1 to enhance its antibacterial properties. The interaction of both the native and analog peptide with bacterial inner membranes was initially assessed using computational methods. Specific amino acid substitutions were then used to enhance the modified peptide's antibacterial efficacy, followed by several preliminary tests to evaluate its activity. This study bridges the gap in exploring the potential of wuchuanin-A1 for antibacterial purposes, providing insights into the design of effective antimicrobial agents.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | | | - Tri Joko Raharjo
- Department of Chemistry, Universitas Gadjah Mada, Bulaksumur, Indonesia
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10
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Willet AH, Wos M, Igarashi MG, Ren L, Turner LA, Gould KL. Elevated levels of sphingolipid MIPC in the plasma membrane disrupt the coordination of cell growth with cell wall formation in fission yeast. PLoS Genet 2023; 19:e1010987. [PMID: 37792890 PMCID: PMC10578601 DOI: 10.1371/journal.pgen.1010987] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/16/2023] [Accepted: 09/19/2023] [Indexed: 10/06/2023] Open
Abstract
Coupling cell wall expansion with cell growth is a universal challenge faced by walled organisms. Mutations in Schizosaccharomyces pombe css1, which encodes a PM inositol phosphosphingolipid phospholipase C, prevent cell wall expansion but not synthesis of cell wall material. To probe how Css1 modulates cell wall formation we used classical and chemical genetics coupled with quantitative mass spectrometry. We found that elevated levels of the sphingolipid biosynthetic pathway's final product, mannosylinositol phosphorylceramide (MIPC), specifically correlated with the css1-3 phenotype. We also found that an apparent indicator of sphingolipids and a sterol biosensor accumulated at the cytosolic face of the PM at cell tips and the division site of css1-3 cells and, in accord, the PM in css1-3 was less dynamic than in wildtype cells. Interestingly, disrupting the protein glycosylation machinery recapitulated the css1-3 phenotype and led us to investigate Ghs2, a glycosylated PM protein predicted to modify cell wall material. Disrupting Ghs2 function led to aberrant cell wall material accumulation suggesting Ghs2 is dysfunctional in css1-3. We conclude that preventing an excess of MIPC in the S. pombe PM is critical to the function of key PM-localized proteins necessary for coupling growth with cell wall formation.
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Affiliation(s)
- Alaina H. Willet
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Marcin Wos
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Maya G. Igarashi
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Liping Ren
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Lesley A. Turner
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Kathleen L. Gould
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, United States of America
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11
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Rudajev V, Novotny J. Cholesterol-dependent amyloid β production: space for multifarious interactions between amyloid precursor protein, secretases, and cholesterol. Cell Biosci 2023; 13:171. [PMID: 37705117 PMCID: PMC10500844 DOI: 10.1186/s13578-023-01127-y] [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: 05/17/2023] [Accepted: 09/05/2023] [Indexed: 09/15/2023] Open
Abstract
Amyloid β is considered a key player in the development and progression of Alzheimer's disease (AD). Many studies investigating the effect of statins on lowering cholesterol suggest that there may be a link between cholesterol levels and AD pathology. Since cholesterol is one of the most abundant lipid molecules, especially in brain tissue, it affects most membrane-related processes, including the formation of the most dangerous form of amyloid β, Aβ42. The entire Aβ production system, which includes the amyloid precursor protein (APP), β-secretase, and the complex of γ-secretase, is highly dependent on membrane cholesterol content. Moreover, cholesterol can affect amyloidogenesis in many ways. Cholesterol influences the stability and activity of secretases, but also dictates their partitioning into specific cellular compartments and cholesterol-enriched lipid rafts, where the amyloidogenic machinery is predominantly localized. The most complicated relationships have been found in the interaction between cholesterol and APP, where cholesterol affects not only APP localization but also the precise character of APP dimerization and APP processing by γ-secretase, which is important for the production of Aβ of different lengths. In this review, we describe the intricate web of interdependence between cellular cholesterol levels, cholesterol membrane distribution, and cholesterol-dependent production of Aβ, the major player in AD.
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Affiliation(s)
- Vladimir Rudajev
- Department of Physiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jiri Novotny
- Department of Physiology, Faculty of Science, Charles University, Prague, Czech Republic
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12
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Müller W, Beales PA, Muniz AR, Jeuken LJC. Unraveling the Phase Behavior, Mechanical Stability, and Protein Reconstitution Properties of Polymer-Lipid Hybrid Vesicles. Biomacromolecules 2023; 24:4156-4169. [PMID: 37539954 PMCID: PMC10498451 DOI: 10.1021/acs.biomac.3c00498] [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: 05/17/2023] [Revised: 07/20/2023] [Indexed: 08/05/2023]
Abstract
Hybrid vesicles consisting of natural phospholipids and synthetic amphiphilic copolymers have shown remarkable material properties and potential for biotechnology, combining the robustness of polymers with the biocompatibility of phospholipid membranes. To predict and optimize the mixing behavior of lipids and copolymers, as well as understand the interaction between the hybrid membrane and macromolecules like membrane proteins, a comprehensive understanding at the molecular level is essential. This can be achieved by a combination of molecular dynamics simulations and experiments. Here, simulations of POPC and PBD22-b-PEO14 hybrid membranes are shown, uncovering different copolymer configurations depending on the polymer-to-lipid ratio. High polymer concentrations created thicker membranes with an extended polymer conformation, while high lipid content led to the collapse of the polymer chain. High concentrations of polymer were further correlated with a decreased area compression modulus and altered lateral pressure profiles, hypothesized to result in the experimentally observed improvement in membrane protein reconstitution and resistance toward destabilization by detergents. Finally, simulations of a WALP peptide embedded in the bilayer showed that only membranes with up to 50% polymer content favored a transmembrane configuration. These simulations correlate with previous and new experimental results and provide a deeper understanding of the properties of lipid-copolymer hybrid membranes.
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Affiliation(s)
- Wagner
A. Müller
- Department
of Chemical Engineering, Universidade Federal
do Rio Grande do Sul, Porto
Alegre 90035-003, Brazil
| | - Paul A. Beales
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - André R. Muniz
- Department
of Chemical Engineering, Universidade Federal
do Rio Grande do Sul, Porto
Alegre 90035-003, Brazil
| | - Lars J. C. Jeuken
- Leiden
Institute of Chemistry, University Leiden, PO Box 9502, 2300RA Leiden, The
Netherlands
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13
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Formation of extramembrane β-strands controls dimerization of transmembrane helices in amyloid precursor protein C99. Proc Natl Acad Sci U S A 2022; 119:e2212207119. [PMID: 36538482 PMCID: PMC9907117 DOI: 10.1073/pnas.2212207119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The 99-residue C-terminal domain of amyloid precursor protein (APP-C99), precursor to amyloid beta (Aβ), is a transmembrane (TM) protein containing intrinsically disordered N- and C-terminal extramembrane domains. Using molecular dynamics (MD) simulations, we show that the structural ensemble of the C99 monomer is best described in terms of thousands of states. The C99 monomer has a propensity to form β-strand in the C-terminal extramembrane domain, which explains the slow spin relaxation times observed in paramagnetic probe NMR experiments. Surprisingly, homodimerization of C99 not only narrows the conformational ensemble from thousands to a few states through the formation of metastable β-strands in extramembrane domains but also stabilizes extramembrane α-helices. The extramembrane domain structure is observed to dramatically impact the homodimerization motif, resulting in the modification of TM domain conformations. Our study provides an atomic-level structural basis for communication between the extramembrane domains of the C99 protein and TM homodimer formation. This finding could serve as a general model for understanding the influence of disordered extramembrane domains on TM protein structure.
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14
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Vergilio J, Lockhart C, Klimov DK. De Novo Transmembrane Aggregation of Aβ10-40 Peptides in an Anionic Lipid Bilayer. J Chem Inf Model 2022; 62:6228-6241. [PMID: 36455155 DOI: 10.1021/acs.jcim.2c01192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Using the all-atom model and 10 μs serial replica-exchange molecular dynamics (SREMD), we investigated the binding of Alzheimer's Aβ10-40 peptides to the anionic dimyristoylphosphatidylcholine/dimyristoylphosphatidylglycerol (DMPC/DMPG) lipid bilayer. Our objective was to probe de novo transmembrane Aβ10-40 aggregation and to test the utility of SREMD. Our results are threefold. First, upon binding, Aβ10-40 adopts a helical structure in the C-terminus and deeply inserts into the bilayer. Binding is primarily controlled by electrostatic interactions of the peptides with water, ions, and lipids, particularly, anionic DMPG. Second, Aβ-bilayer interactions reorganize lipids in the proximity of the bound peptides, causing an influx of DMPG lipids into the Aβ binding footprint. Third and most important, computed free energy landscapes reveal that Aβ10-40 peptides partition into monomeric and dimeric species. The dimers result from transmembrane aggregation of the peptides and induce a striking lipid density void throughout both leaflets in the bilayer. There are multiple factors stabilizing transmembrane dimers, including van der Waals and steric interactions, electrostatic interactions, and hydrogen bonding, hydration, and entropic gains originating from dimer conformations and lipid disorder. We argue that helix dipole-dipole interactions underestimated in the all-atom force field must be a contributing factor to stabilizing antiparallel transmembrane dimers. We propose that transmembrane aggregates serve as mechanistic links between the populations of extra- and intracellular Aβ peptides. From the computational perspective, SREMD is found to be a viable alternative to traditional replica-exchange simulations.
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Affiliation(s)
- James Vergilio
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| | - Christopher Lockhart
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| | - Dmitri K Klimov
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
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15
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Boopathi S, Garduño‐Juárez R. Calcium inhibits penetration of Alzheimer's Aβ 1 - 42 monomers into the membrane. Proteins 2022; 90:2124-2143. [PMID: 36321654 PMCID: PMC9804374 DOI: 10.1002/prot.26403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/08/2022] [Accepted: 07/25/2022] [Indexed: 01/05/2023]
Abstract
Calcium ion regulation plays a crucial role in maintaining neuronal functions such as neurotransmitter release and synaptic plasticity. Copper (Cu2+ ) coordination to amyloid-β (Aβ) has accelerated Aβ1-42 aggregation that can trigger calcium dysregulation by enhancing the influx of calcium ions by extensive perturbing integrity of the membranes. Aβ1-42 aggregation, calcium dysregulation, and membrane damage are Alzheimer disease (AD) implications. To gain a detail of calcium ions' role in the full-length Aβ1-42 and Aβ1-42 -Cu2+ monomers contact, the cellular membrane before their aggregation to elucidate the neurotoxicity mechanism, we carried out 2.5 μs extensive molecular dynamics simulation (MD) to rigorous explorations of the intriguing feature of the Aβ1-42 and Aβ1-42 -Cu2+ interaction with the dimyristoylphosphatidylcholine (DMPC) bilayer in the presence of calcium ions. The outcome of the results compared to the same simulations without calcium ions. We surprisingly noted robust binding energies between the Aβ1-42 and membrane observed in simulations containing without calcium ions and is two and a half fold lesser in the simulation with calcium ions. Therefore, in the case of the absence of calcium ions, N-terminal residues of Aβ1-42 deeply penetrate from the surface to the center of the bilayer; in contrast to calcium ions presence, the N- and C-terminal residues are involved only in surface contacts through binding phosphate moieties. On the other hand, Aβ1-42 -Cu2+ actively participated in surface bilayer contacts in the absence of calcium ions. These contacts are prevented by forming a calcium bridge between Aβ1-42 -Cu2+ and the DMPC bilayer in the case of calcium ions presence. In a nutshell, Calcium ions do not allow Aβ1-42 penetration into the membranes nor contact of Aβ1-42 -Cu2+ with the membranes. These pieces of information imply that the calcium ions mediate the membrane perturbation via the monomer interactions but do not damage the membrane; they agree with the western blot experimental results of a higher concentration of calcium ions inhibit the membrane pore formation by Aβ peptides.
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Affiliation(s)
- Subramanian Boopathi
- Instituto de Ciencias FísicasUniversidad Nacional Autónoma de MéxicoCuernavacaMexico
| | - Ramón Garduño‐Juárez
- Instituto de Ciencias FísicasUniversidad Nacional Autónoma de MéxicoCuernavacaMexico
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16
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Papadopoulos N, Suelves N, Perrin F, Vadukul DM, Vrancx C, Constantinescu SN, Kienlen-Campard P. Structural Determinant of β-Amyloid Formation: From Transmembrane Protein Dimerization to β-Amyloid Aggregates. Biomedicines 2022; 10:2753. [PMID: 36359274 PMCID: PMC9687742 DOI: 10.3390/biomedicines10112753] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/18/2022] [Accepted: 10/21/2022] [Indexed: 10/03/2023] Open
Abstract
Most neurodegenerative diseases have the characteristics of protein folding disorders, i.e., they cause lesions to appear in vulnerable regions of the nervous system, corresponding to protein aggregates that progressively spread through the neuronal network as the symptoms progress. Alzheimer's disease is one of these diseases. It is characterized by two types of lesions: neurofibrillary tangles (NFTs) composed of tau proteins and senile plaques, formed essentially of amyloid peptides (Aβ). A combination of factors ranging from genetic mutations to age-related changes in the cellular context converge in this disease to accelerate Aβ deposition. Over the last two decades, numerous studies have attempted to elucidate how structural determinants of its precursor (APP) modify Aβ production, and to understand the processes leading to the formation of different Aβ aggregates, e.g., fibrils and oligomers. The synthesis proposed in this review indicates that the same motifs can control APP function and Aβ production essentially by regulating membrane protein dimerization, and subsequently Aβ aggregation processes. The distinct properties of these motifs and the cellular context regulate the APP conformation to trigger the transition to the amyloid pathology. This concept is critical to better decipher the patterns switching APP protein conformation from physiological to pathological and improve our understanding of the mechanisms underpinning the formation of amyloid fibrils that devastate neuronal functions.
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Affiliation(s)
- Nicolas Papadopoulos
- SIGN Unit, de Duve Institute, UCLouvain, 1200 Brussels, Belgium
- Ludwig Institute for Cancer Research Brussels, 1348 Brussels, Belgium
| | - Nuria Suelves
- Aging and Dementia Research Group, Cellular and Molecular (CEMO) Division, Institute of Neuroscience, UCLouvain, 1200 Brussels, Belgium
| | - Florian Perrin
- Memory Disorders Unit, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Devkee M. Vadukul
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London SW7 2BX, UK
| | - Céline Vrancx
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, KU Leuven, 3000 Leuven, Belgium
- Department of Neurosciences, KU Leuven, 3000 Leuven, Belgium
| | - Stefan N. Constantinescu
- SIGN Unit, de Duve Institute, UCLouvain, 1200 Brussels, Belgium
- Ludwig Institute for Cancer Research Brussels, 1348 Brussels, Belgium
- Walloon Excellence in Life Sciences and Biotechnology (WELBIO), 1300 Wavre, Belgium
- Nuffield Department of Medicine, Ludwig Institute for Cancer Research, Oxford University, Oxford OX1 2JD, UK
| | - Pascal Kienlen-Campard
- Aging and Dementia Research Group, Cellular and Molecular (CEMO) Division, Institute of Neuroscience, UCLouvain, 1200 Brussels, Belgium
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17
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Jackson V, Hermann J, Tynan CJ, Rolfe DJ, Corey RA, Duncan AL, Noriega M, Chu A, Kalli AC, Jones EY, Sansom MSP, Martin-Fernandez ML, Seiradake E, Chavent M. The guidance and adhesion protein FLRT2 dimerizes in cis via dual small-X 3-small transmembrane motifs. Structure 2022; 30:1354-1365.e5. [PMID: 35700726 DOI: 10.1016/j.str.2022.05.014] [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: 08/02/2021] [Revised: 03/03/2022] [Accepted: 05/18/2022] [Indexed: 10/18/2022]
Abstract
Fibronectin Leucine-rich Repeat Transmembrane (FLRT 1-3) proteins are a family of broadly expressed single-spanning transmembrane receptors that play key roles in development. Their extracellular domains mediate homotypic cell-cell adhesion and heterotypic protein interactions with other receptors to regulate cell adhesion and guidance. These in trans FLRT interactions determine the formation of signaling complexes of varying complexity and function. Whether FLRTs also interact at the surface of the same cell, in cis, remains unknown. Here, molecular dynamics simulations reveal two dimerization motifs in the FLRT2 transmembrane helix. Single particle tracking experiments show that these Small-X3-Small motifs synergize with a third dimerization motif encoded in the extracellular domain to permit the cis association and co-diffusion patterns of FLRT2 receptors on cells. These results may point to a competitive switching mechanism between in cis and in trans interactions, which suggests that homotypic FLRT interaction mirrors the functionalities of classic adhesion molecules.
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Affiliation(s)
- Verity Jackson
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK
| | - Julia Hermann
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK
| | - Christopher J Tynan
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Harwell Campus, Didcot, OX11 0FA, UK
| | - Daniel J Rolfe
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Harwell Campus, Didcot, OX11 0FA, UK
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK
| | - Anna L Duncan
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK
| | - Maxime Noriega
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 205 route de Narbonne, 31400 Toulouse, France
| | - Amy Chu
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK
| | - Antreas C Kalli
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine and Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, LS2 9NL, UK
| | - E Yvonne Jones
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK
| | - Marisa L Martin-Fernandez
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Harwell Campus, Didcot, OX11 0FA, UK.
| | - Elena Seiradake
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK.
| | - Matthieu Chavent
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 205 route de Narbonne, 31400 Toulouse, France.
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18
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Lu Y, Salsbury F, Derreumaux P. Impact of A2T and D23N mutations on C99 homodimer conformations. J Chem Phys 2022; 157:085102. [DOI: 10.1063/5.0101622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The proteolytic cleavage of C99 by γ-secretase is the last step in the production of amyloid-β (Aβ) peptides. Previous studies have shown that membrane lipid composition, cholesterol concentration, and mutation in the transmembrane helix modified the structures and fluctuations of C99. In this study, we performed atomistic molecular dynamics simulations of the homodimer of the 55-residue congener of the C-terminal domain of the amyloid protein precursor, C99(1-55), in a POPC-cholesterol lipid bilayer, and we compared the conformational ensemble of WT sequence to those of the A2T and D23N variants. These mutations are particularly interesting as the protective Alzheimer's disease (AD) A2T mutation is known to decrease Aβ production, whereas the early onset AD D23N mutation does not affect Aβ production. We found noticeable differences in the structural ensembles of the three sequences. In particular, A2T varies from both WT and D23N by having long-range effects on the population of the extracellular justamembrane helix, the interface between the G29xxx-G33xxx-G37 motifs and the fluctuations of the transmembrane helical topologies.
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Affiliation(s)
- Yan Lu
- School of Physics, Xidian University, China
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19
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Sharma GP, Meyer AC, Habeeb S, Karbach M, Müller G. Free-energy landscapes and insertion pathways for peptides in membrane environment. Phys Rev E 2022; 106:014404. [PMID: 35974613 DOI: 10.1103/physreve.106.014404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Free-energy landscapes for short peptides-specifically for variants of the pH low insertion peptide (pHLIP)-in the heterogeneous environment of a lipid bilayer or cell membrane are constructed, taking into account a set of dominant interactions and the conformational preferences of the peptide backbone. Our methodology interprets broken internal H-bonds along the backbone of a polypeptide as statistically interacting quasiparticles, activated from the helix reference state. The favored conformation depends on the local environment (ranging from polar to nonpolar), specifically on the availability of external H-bonds (with H_{2}O molecules or lipid headgroups) to replace internal H-bonds. The dominant side-chain contribution is accounted for by residue-specific transfer free energies between polar and nonpolar environments. The free-energy landscape is sensitive to the level of pH in the aqueous environment surrounding the membrane. For high pH, we identify pathways of descending free energy that suggest a coexistence of membrane-adsorbed peptides with peptides in solution. A drop in pH raises the degree of protonation of negatively charged residues and thus increases the hydrophobicity of peptide segments near the C terminus. For low pH, we identify insertion pathways between the membrane-adsorbed state and a stable trans-membrane state with the C terminus having crossed the membrane.
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Affiliation(s)
- Ganga P Sharma
- Department of Physics, University of Rhode Island, Kingston, Rhode Island 02881, USA
| | - Aaron C Meyer
- Department of Physics, University of Rhode Island, Kingston, Rhode Island 02881, USA
| | - Suhail Habeeb
- Department of Physics, University of Rhode Island, Kingston, Rhode Island 02881, USA
| | - Michael Karbach
- Fachgruppe Physik, Bergische Universität Wuppertal, D-42097 Wuppertal, Germany
| | - Gerhard Müller
- Department of Physics, University of Rhode Island, Kingston, Rhode Island 02881, USA
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20
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Majumder A, Kwon S, Straub JE. On Computing Equilibrium Binding Constants for Protein-Protein Association in Membranes. J Chem Theory Comput 2022; 18:3961-3971. [PMID: 35580264 PMCID: PMC11260346 DOI: 10.1021/acs.jctc.2c00106] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein association in lipid membranes is fundamental to membrane protein function and of great biomedical relevance. All-atom and coarse-grained models have been extensively used to understand the protein-protein interactions in the membrane and to compute equilibrium association constants. However, slow translational and rotational diffusion of protein in membrane presents challenges to the effective sampling of conformations defining the ensembles of free and bound states contributing to the association equilibrium and the free energy of dimerization. We revisit the homodimerization equilibrium of the TM region of glycophorin A. Conformational sampling is performed using umbrella sampling along previously proposed one-dimensional collective variables and compared with sampling over a two-dimensional collective variable space using the MARTINI v2.2 force field. We demonstrate that the one-dimensional collective variables suffer from restricted sampling of the native homodimer conformations leading to a biased free energy landscape. Conversely, simulations along the two-dimensional collective variable effectively characterize the thermodynamically relevant native and non-native interactions contributing to the association equilibrium. These results demonstrate the challenges associated with accurately characterizing binding equilibria when multiple poses contribute to the bound state ensemble.
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Affiliation(s)
- Ayan Majumder
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Seulki Kwon
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - John E Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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21
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Nguyen PH, Derreumaux P. Computer Simulations Aimed at Exploring Protein Aggregation and Dissociation. Methods Mol Biol 2022; 2340:175-196. [PMID: 35167075 DOI: 10.1007/978-1-0716-1546-1_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein aggregation can lead to well-defined structures that are functional, but is also the cause of the death of neuron cells in many neurodegenerative diseases. The complexity of the molecular events involved in the aggregation kinetics of amyloid proteins and the transient and heterogeneous characters of all oligomers prevent high-resolution structural experiments. As a result, computer simulations have been used to determine the atomic structures of amyloid proteins at different association stages as well as to understand fibril dissociation. In this chapter, we first review the current computer simulation methods used for aggregation with some atomistic and coarse-grained results aimed at better characterizing the early formed oligomers and amyloid fibril formation. Then we present the applications of non-equilibrium molecular dynamics simulations to comprehend the dissociation of protein assemblies.
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Affiliation(s)
- Phuong H Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université de Paris, Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université de Paris, Paris, France.
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France.
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22
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Effect of cholesterol on the dimerization of C99-A molecular modeling perspective. Biointerphases 2021; 16:031002. [PMID: 34241229 DOI: 10.1116/6.0000985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
C99, a naturally occurring peptide, is a precursor of the amyloid β-peptide (Aβ) and plays an important role in the so-called amyloidogenic pathway of degradation of amyloid precursor protein. While the effect of C99's dimerization is not clearly determined, it has been hypothesized that the dimerization protects C99 from being cleaved further. Cholesterol (CHOL) is known to interact with C99 and its presence in high concentrations has been linked to an increase in the production of Aβ; however, to what extent this is correlated, and how, has not yet been determined. In this study, we systematically examine the effect of increasing cholesterol concentration on the homodimerization propensity of C99, combining unbiased atomistic molecular dynamics simulations with biased simulations using a coarse grained resolution. Through the use of umbrella sampling, we show how the presence of high levels of CHOL destabilizes the interaction between two C99 monomers. The interaction pattern between the two C99s has shifted several residues, from the N-terminal end of the transmembrane region toward the corresponding C-terminal in the presence of CHOL. The umbrella sampling shows that the presence of high levels of CHOL led to a decrease of the disassociation energy by approximately 3 kJ/mol. In conclusion, this suggests that increasing CHOL destabilizes the interaction between the two C99 monomers, which may possibly cause an increase in the production of Aβ42.
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23
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Structural Studies Providing Insights into Production and Conformational Behavior of Amyloid-β Peptide Associated with Alzheimer's Disease Development. MOLECULES (BASEL, SWITZERLAND) 2021; 26:molecules26102897. [PMID: 34068293 PMCID: PMC8153327 DOI: 10.3390/molecules26102897] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/06/2021] [Accepted: 05/11/2021] [Indexed: 12/18/2022]
Abstract
Alzheimer's disease is the most common type of neurodegenerative disease in the world. Genetic evidence strongly suggests that aberrant generation, aggregation, and/or clearance of neurotoxic amyloid-β peptides (Aβ) triggers the disease. Aβ accumulates at the points of contact of neurons in ordered cords and fibrils, forming the so-called senile plaques. Aβ isoforms of different lengths are found in healthy human brains regardless of age and appear to play a role in signaling pathways in the brain and to have neuroprotective properties at low concentrations. In recent years, different substances have been developed targeting Aβ production, aggregation, interaction with other molecules, and clearance, including peptide-based drugs. Aβ is a product of sequential cleavage of the membrane glycoprotein APP (amyloid precursor protein) by β- and γ-secretases. A number of familial mutations causing an early onset of the disease have been identified in the APP, especially in its transmembrane domain. The mutations are reported to influence the production, oligomerization, and conformational behavior of Aβ peptides. This review highlights the results of structural studies of the main proteins involved in Alzheimer's disease pathogenesis and the molecular mechanisms by which perspective therapeutic substances can affect Aβ production and nucleation.
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24
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Zhou S, He P, Dhindwal S, Grum-Tokars VL, Li Y, Parker K, Modica JA, Bleher R, Dos Reis R, Zuchniarz J, Dravid VP, Voth GA, Roux B, Mrksich M. Synthesis, Characterization, and Simulation of Four-Armed Megamolecules. Biomacromolecules 2021; 22:2363-2372. [PMID: 33979120 DOI: 10.1021/acs.biomac.1c00118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This paper describes the synthesis, characterization, and modeling of a series of molecules having four protein domains attached to a central core. The molecules were assembled with the "megamolecule" strategy, wherein enzymes react with their covalent inhibitors that are substituted on a linker. Three linkers were synthesized, where each had four oligo(ethylene glycol)-based arms terminated in a para-nitrophenyl phosphonate group that is a covalent inhibitor for cutinase. This enzyme is a serine hydrolase and reacts efficiently with the phosphonate to give a new ester linkage at the Ser-120 residue in the active site of the enzyme. Negative-stain transmission electron microscopy (TEM) images confirmed the architecture of the four-armed megamolecules. These cutinase tetramers were also characterized by X-ray crystallography, which confirmed the active-site serine-phosphonate linkage by electron-density maps. Molecular dynamics simulations of the tetracutinase megamolecules using three different force field setups were performed and compared with the TEM observations. Using the Amberff99SB-disp + pH7 force field, the two-dimensional projection distances of the megamolecules were found to agree with the measured dimensions from TEM. The study described here, which combines high-resolution characterization with molecular dynamics simulations, will lead to a comprehensive understanding of the molecular structures and dynamics for this new class of molecules.
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Affiliation(s)
- Shengwang Zhou
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, P. R. China
| | - Peng He
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Sonali Dhindwal
- Department of Materials Science, Northwestern University, Evanston, Illinois 60208, United States
| | - Valerie L Grum-Tokars
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Chicago, Illinois 60611, United States
| | - Ying Li
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Kelly Parker
- Department of Materials Science, Northwestern University, Evanston, Illinois 60208, United States
| | - Justin A Modica
- Departments of Chemistry and Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Reiner Bleher
- Department of Materials Science, Northwestern University, Evanston, Illinois 60208, United States
| | - Roberto Dos Reis
- Department of Materials Science, Northwestern University, Evanston, Illinois 60208, United States
| | - Joshua Zuchniarz
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Vinayak P Dravid
- Department of Materials Science, Northwestern University, Evanston, Illinois 60208, United States
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Milan Mrksich
- Departments of Chemistry and Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
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25
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Majumder A, Straub JE. Addressing the Excessive Aggregation of Membrane Proteins in the MARTINI Model. J Chem Theory Comput 2021; 17:2513-2521. [PMID: 33720709 DOI: 10.1021/acs.jctc.0c01253] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The MARTINI model is a widely used coarse-grained force field popular for its capacity to represent a diverse array of complex biomolecules. However, efforts to simulate increasingly realistic models of membranes, involving complex lipid mixtures and multiple proteins, suggest that membrane protein aggregates are overstabilized by the MARTINI v2.2 force field. In this study, we address this shortcoming of the MARTINI model. We determined the free energy of dimerization of four transmembrane protein systems using the nonpolarizable MARTINI model. Comparison with experimental FRET-based estimates of the dimerization free energy was used to quantify the significant overstabilization of each protein homodimer studied. To improve the agreement between simulation and experiment, a single uniform scaling factor, α, was used to enhance the protein-lipid Lennard-Jones interaction. A value of α = 1.04-1.045 was found to provide the best fit to the dimerization free energies for the proteins studied while maintaining the specificity of contacts at the dimer interface. To further validate the modified force field, we performed a multiprotein simulation using both MARTINI v2.2 and the reparameterized MARTINI model. While the original MARTINI model predicts oligomerization of protein into a single aggregate, the reparameterized MARTINI model maintains a dynamic equilibrium between monomers and dimers as predicted by experimental studies. The proposed reparameterization is an alternative to the standard MARTINI model for use in simulations of realistic models of a biological membrane containing diverse lipids and proteins.
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Affiliation(s)
- Ayan Majumder
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston 02215, Massachusetts, United States
| | - John E Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston 02215, Massachusetts, United States
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26
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Capone R, Tiwari A, Hadziselimovic A, Peskova Y, Hutchison JM, Sanders CR, Kenworthy AK. The C99 domain of the amyloid precursor protein resides in the disordered membrane phase. J Biol Chem 2021; 296:100652. [PMID: 33839158 PMCID: PMC8113881 DOI: 10.1016/j.jbc.2021.100652] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 04/02/2021] [Accepted: 04/07/2021] [Indexed: 12/11/2022] Open
Abstract
Processing of the amyloid precursor protein (APP) via the amyloidogenic pathway is associated with the etiology of Alzheimer's disease. The cleavage of APP by β-secretase to generate the transmembrane 99-residue C-terminal fragment (C99) and subsequent processing of C99 by γ-secretase to yield amyloid-β (Aβ) peptides are essential steps in this pathway. Biochemical evidence suggests that amyloidogenic processing of C99 occurs in cholesterol- and sphingolipid-enriched liquid-ordered phase membrane rafts. However, direct evidence that C99 preferentially associates with these rafts has remained elusive. Here, we tested this by quantifying the affinity of C99-GFP for raft domains in cell-derived giant plasma membrane vesicles (GPMVs). We found that C99 was essentially excluded from ordered domains in vesicles from HeLa cells, undifferentiated SH-SY5Y cells, or SH-SY5Y-derived neurons; instead, ∼90% of C99 partitioned into disordered domains. The strong association of C99 with disordered domains occurred independently of its cholesterol-binding activity or homodimerization, or of the presence of the familial Alzheimer disease Arctic mutation (APP E693G). Finally, through biochemical studies we confirmed previous results, which showed that C99 is processed in the plasma membrane by α-secretase, in addition to the well-known γ-secretase. These findings suggest that C99 itself lacks an intrinsic affinity for raft domains, implying that either i) amyloidogenic processing of the protein occurs in disordered regions of the membrane, ii) processing involves a marginal subpopulation of C99 found in rafts, or iii) as-yet-unidentified protein-protein interactions with C99 in living cells drive this protein into membrane rafts to promote its cleavage therein.
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Affiliation(s)
- Ricardo Capone
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA; Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Ajit Tiwari
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | | | - Yelena Peskova
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia, USA
| | - James M Hutchison
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Charles R Sanders
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA; Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Anne K Kenworthy
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA.
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Nguyen PH, Ramamoorthy A, Sahoo BR, Zheng J, Faller P, Straub JE, Dominguez L, Shea JE, Dokholyan NV, De Simone A, Ma B, Nussinov R, Najafi S, Ngo ST, Loquet A, Chiricotto M, Ganguly P, McCarty J, Li MS, Hall C, Wang Y, Miller Y, Melchionna S, Habenstein B, Timr S, Chen J, Hnath B, Strodel B, Kayed R, Lesné S, Wei G, Sterpone F, Doig AJ, Derreumaux P. Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis. Chem Rev 2021; 121:2545-2647. [PMID: 33543942 PMCID: PMC8836097 DOI: 10.1021/acs.chemrev.0c01122] [Citation(s) in RCA: 386] [Impact Index Per Article: 128.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein misfolding and aggregation is observed in many amyloidogenic diseases affecting either the central nervous system or a variety of peripheral tissues. Structural and dynamic characterization of all species along the pathways from monomers to fibrils is challenging by experimental and computational means because they involve intrinsically disordered proteins in most diseases. Yet understanding how amyloid species become toxic is the challenge in developing a treatment for these diseases. Here we review what computer, in vitro, in vivo, and pharmacological experiments tell us about the accumulation and deposition of the oligomers of the (Aβ, tau), α-synuclein, IAPP, and superoxide dismutase 1 proteins, which have been the mainstream concept underlying Alzheimer's disease (AD), Parkinson's disease (PD), type II diabetes (T2D), and amyotrophic lateral sclerosis (ALS) research, respectively, for many years.
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Affiliation(s)
- Phuong H Nguyen
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Bikash R Sahoo
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jie Zheng
- Department of Chemical & Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Peter Faller
- Institut de Chimie, UMR 7177, CNRS-Université de Strasbourg, 4 rue Blaise Pascal, 67000 Strasbourg, France
| | - John E Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Laura Dominguez
- Facultad de Química, Departamento de Fisicoquímica, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Nikolay V Dokholyan
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
- Department of Chemistry, and Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K
- Molecular Biology, University of Naples Federico II, Naples 80138, Italy
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Saeed Najafi
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics & Faculty of Applied Sciences, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
| | - Antoine Loquet
- Institute of Chemistry & Biology of Membranes & Nanoobjects, (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600 Pessac, France
| | - Mara Chiricotto
- Department of Chemical Engineering and Analytical Science, University of Manchester, Manchester M13 9PL, U.K
| | - Pritam Ganguly
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - James McCarty
- Chemistry Department, Western Washington University, Bellingham, Washington 98225, United States
| | - Mai Suan Li
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Carol Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Yiming Wang
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Yifat Miller
- Department of Chemistry and The Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | | | - Birgit Habenstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects, (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600 Pessac, France
| | - Stepan Timr
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Jiaxing Chen
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Brianna Hnath
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases, and Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Sylvain Lesné
- Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Science, Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 200438, China
| | - Fabio Sterpone
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Andrew J Doig
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, U.K
| | - Philippe Derreumaux
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
- Laboratory of Theoretical Chemistry, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
- Faculty of Pharmacy, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
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Cholesterol content in the membrane promotes key lipid-protein interactions in a pentameric serotonin-gated ion channel. Biointerphases 2021; 15:061018. [PMID: 33397116 DOI: 10.1116/6.0000561] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs), embedded in the lipid membranes of nerve cells, mediate fast synaptic transmission and are major pharmaceutical targets. Because of their complexity and the limited knowledge of their structure, their working mechanisms have still to be fully unraveled at the molecular level. Over the past few years, evidence that the lipid membrane may modulate the function of membrane proteins, including pLGICs, has emerged. Here, we investigate, by means of molecular dynamics simulations, the behavior of the lipid membrane at the interface with the 5-HT3A receptor (5-HT3AR), a representative pLGIC which is the target of nausea-suppressant drugs, in a nonconductive state. Three lipid compositions are studied, spanning different concentrations of the phospholipids, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, and of cholesterol, hence a range of viscosities. A variety of lipid interactions and persistent binding events to different parts of the receptor are revealed in the investigated models, providing snapshots of the dynamical environment at the membrane-receptor interface. Some of these events result in lipid intercalation within the transmembrane domain, and others reach out to protein key sections for signal transmission and receptor activation, such as the Cys-loop and the M2-M3 loop. In particular, phospholipids, with their long hydrophobic tails, play an important role in these interactions, potentially providing a bridge between these two structures. A higher cholesterol content appears to promote lipid persistent binding to the receptor.
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In Silico Prediction of the Binding, Folding, Insertion, and Overall Stability of Membrane-Active Peptides. Methods Mol Biol 2021; 2315:161-182. [PMID: 34302676 DOI: 10.1007/978-1-0716-1468-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Membrane-active peptides (MAPs) are short-length peptides used for potential biomedical applications in diagnostic imaging of tissues, targeted drug delivery, gene delivery, and antimicrobials and antibiotics. The broad appeal of MAPs is that they are infinitely variable, relatively low cost, and biocompatible. However, experimentally characterizing the specific properties of a MAP or its many variants is a low-resolution and potentially time-consuming endeavor; molecular dynamics (MD) simulations have emerged as an invaluable tool in identifying the biophysical interactions that are fundamental to the function of MAPs. In this chapter, a step-by-step approach to discreetly model the binding, folding, and insertion of a membrane-active peptide to a model lipid bilayer using MD simulations is described. Detailed discussion is devoted to the critical aspects of running these types of simulations: prior knowledge of the system, understanding the strengths and weaknesses of molecular mechanics force fields, proper construction and equilibration of the system, realistically estimating both experimental and computational timescales, and leveraging analysis to make direct comparisons to experimental results as often as possible.
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Dimeric Transmembrane Orientations of APP/C99 Regulate γ-Secretase Processing Line Impacting Signaling and Oligomerization. iScience 2020; 23:101887. [PMID: 33367225 PMCID: PMC7749410 DOI: 10.1016/j.isci.2020.101887] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/21/2020] [Accepted: 11/25/2020] [Indexed: 12/22/2022] Open
Abstract
Amyloid precursor protein (APP) cleavage by the β-secretase produces the C99 transmembrane (TM) protein, which contains three dimerization-inducing Gly-x-x-x-Gly motifs. We demonstrate that dimeric C99 TM orientations regulate the precise cleavage lines by γ-secretase. Of all possible dimeric orientations imposed by a coiled-coil to the C99 TM domain, the dimer containing the 33Gly-x-x-x-Gly37 motif in the interface promoted the Aβ42 processing line and APP intracellular domain-dependent gene transcription, including the induction of BACE1 mRNA, enhancing amyloidogenic processing and signaling. Another orientation exhibiting the 25Gly-x-x-x-Gly29 motif in the interface favored processing to Aβ43/40. It induced significantly less gene transcription, while promoting formation of SDS-resistant "Aβ-like" oligomers, reminiscent of Aβ peptide oligomers. These required both Val24 of a pro-β motif and the 25Gly-x-x-x-Gly29 interface. Thus, crossing angles imposed by precise dimeric orientations control γ-secretase initial cleavage at Aβ48 or Aβ49, linking the former to enhanced signaling and Aβ42 production.
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31
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Pantelopulos GA, Panahi A, Straub JE. Impact of Cholesterol Concentration and Lipid Phase on Structure and Fluctuation of Amyloid Precursor Protein. J Phys Chem B 2020; 124:10173-10185. [PMID: 33135883 PMCID: PMC7958706 DOI: 10.1021/acs.jpcb.0c07615] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Elevated levels of cellular cholesterol have been identified as one factor contributing to the onset of Alzheimer's disease (AD). Specific interaction between cholesterol and the amyloid precursor protein (APP), investigated via NMR experiments and computational studies, has been proposed to play a critical role in the processing of APP by secretases and the biogenesis of amyloid-β (Aβ) protein. We present all-atom molecular dynamics simulations of the 40-residue congener of the C-terminal domain of APP, C9916-55 (C99), in cholesterol-enriched DMPC lipid bilayers. We investigated the effect of cholesterol concentration on the conformational ensemble of wild-type C99 and C99-cholesterol associations at the low pH of endosomal environments, at which residues E22 and D23 are neutral. C99 was also characterized in liquid ordered domains for Dutch (E22Q) and Iowa (D23N) Familial AD mutants at low pH and for the wild-type sequence using protonation states characteristic of neutral pH. Our results reproduce the equilibrium constant of past NMR characterizations of the C99-cholesterol interaction but are not consistent with the C99-cholesterol binding hypothesis. We find that the lifetimes of both DMPC and cholesterol complexed with C99 display a power-law distribution of residence lifetimes. Longer-lived C99-DMPC and C99-cholesterol complexes are primarily stabilized by salt bridges and hydrogen bonds of lysine amines to phosphate and hydroxyl groups. Nevertheless, specific interfaces for C99-cholesterol association which are not present for DMPC can be identified. Changes to C99-cholesterol interfaces are found to depend on C99 tilt angle and orientation of the juxtamembrane domain of C99 containing residues E22 and D23. These observations support a more nuanced view of the C99-cholesterol interaction than has previously been suggested. We propose that cholesterol modulates the conformation and activity of C99 and other small transmembrane proteins indirectly through induction of the liquid ordered phase and directly through hydrogen bonding. This suggests a critical role for membrane heterogeneity introduced by cholesterol in modulating the structural ensemble of C99 and the production of Aβ.
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Affiliation(s)
- George A Pantelopulos
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Afra Panahi
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - John E Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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32
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Chen SY, Zacharias M. How Mutations Perturb γ-Secretase Active Site Studied by Free Energy Simulations. ACS Chem Neurosci 2020; 11:3321-3332. [PMID: 32960571 DOI: 10.1021/acschemneuro.0c00440] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
γ-Secretase is involved in processing of the amyloid precursor protein (APP) and generation of short Aβ peptides that may play a key role in neurodegenerative diseases such as Alzheimer's disease (AD). Several mutations in γ-secretase influence its activity, resulting in early AD onset (Familial AD or FAD mutations). The molecular details of how mutations, not located close to the active site, can affect enzyme activity is not understood. In molecular dynamics simulations of γ-secretase in the absence of substrate (apo), we identified two active site conformational states characterized by a direct contact between catalytic Asp residues (closed state) and an open water-bridged state. In the presence of substrate, only conformations compatible with the open active site geometry are accessible. Systematic free energy simulations on wild type and FAD mutations indicate a free energy difference between closed and open states that is significantly modulated by FAD mutations and correlates with the corresponding experimental activity. For mutations with reduced activity, an increased penalty for open-state transitions was found. Only for two mutations located at the active site a direct perturbation of the open-state geometry was observed that could directly explain the drop of enzyme activity. The simulations suggest that modulation of the closed/open equilibrium and perturbation of the open (active) catalytic geometry are possible mechanisms of how FAD mutations affect γ-secretase activity. The results also offer an explanation for the experimental finding that FAD mutations, although not located at the interface to the substrate, mainly destabilize the enzyme-substrate complex.
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Affiliation(s)
- Shu-Yu Chen
- Physik-Department T38,Techniche Universität München, James-Franck-Strasse 1, 85748 Garching, Germany
| | - Martin Zacharias
- Physik-Department T38,Techniche Universität München, James-Franck-Strasse 1, 85748 Garching, Germany
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33
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Hitzenberger M, Götz A, Menig S, Brunschweiger B, Zacharias M, Scharnagl C. The dynamics of γ-secretase and its substrates. Semin Cell Dev Biol 2020; 105:86-101. [DOI: 10.1016/j.semcdb.2020.04.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 04/09/2020] [Accepted: 04/15/2020] [Indexed: 12/18/2022]
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34
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Dehury B, Kepp KP. Membrane dynamics of γ-secretase with the anterior pharynx-defective 1B subunit. J Cell Biochem 2020; 122:69-85. [PMID: 32830360 DOI: 10.1002/jcb.29832] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/13/2020] [Indexed: 01/12/2023]
Abstract
The four-subunit protease complex γ-secretase cleaves many single-pass transmembrane (TM) substrates, including Notch and β-amyloid precursor protein to generate amyloid-β (Aβ), central to Alzheimer's disease. Two of the subunits anterior pharynx-defective 1 (APH-1) and presenilin (PS) exist in two homologous forms APH1-A and APH1-B, and PS1 and PS2. The consequences of these variations are poorly understood and could affect Aβ production and γ-secretase medicine. Here, we developed the first complete structural model of the APH-1B subunit using the published cryo-electron microscopy (cryo-EM) structures of APH1-A (Protein Data Bank: 5FN2, 5A63, and 6IYC). We then performed all-atom molecular dynamics simulations at 303 K in a realistic bilayer system to understand both APH-1B alone and in γ-secretase without and with substrate C83-bound. We show that APH-1B adopts a 7TM topology with a water channel topology similar to APH-1A. We demonstrate direct transport of water through this channel, mainly via Glu84, Arg87, His170, and His196. The apo and holo states closely resemble the experimental cryo-EM structures with APH-1A, however with subtle differences: The substrate-bound APH-1B γ-secretase was quite stable, but some TM helices of PS1 and APH-1B rearranged in the membrane consistent with the disorder seen in the cryo-EM data. This produces different accessibility of water molecules for the catalytic aspartates of PS1, critical for Aβ production. In particular, we find that the typical distance between the catalytic aspartates of PS1 and the C83 cleavage sites are shorter in APH-1B, that is, it represents a more closed state, due to interactions with the C-terminal fragment of PS1. Our structural-dynamic model of APH-1B alone and in γ-secretase suggests generally similar topology but some notable differences in water accessibility which may be relevant to the protein's existence in two forms and their specific function and location.
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Affiliation(s)
- Budheswar Dehury
- DTU Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kasper P Kepp
- DTU Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
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Dehury B, Tang N, Mehra R, Blundell TL, Kepp KP. Side-by-side comparison of Notch- and C83 binding to γ-secretase in a complete membrane model at physiological temperature. RSC Adv 2020; 10:31215-31232. [PMID: 35520661 PMCID: PMC9056423 DOI: 10.1039/d0ra04683c] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/15/2020] [Indexed: 12/29/2022] Open
Abstract
γ-Secretase cleaves the C99 fragment of the amyloid precursor protein, leading to formation of aggregated β-amyloid peptide central to Alzheimer's disease, and Notch, essential for cell regulation. Recent cryogenic electron microscopy (cryo-EM) structures indicate major changes upon substrate binding, a β-sheet recognition motif, and a possible helix unwinding to expose peptide bonds towards nucleophilic attack. Here we report side-by-side comparison of the 303 K dynamics of the two proteins in realistic membranes using molecular dynamics simulations. Our ensembles agree with the cryo-EM data (full-protein Cα-RMSD = 1.62–2.19 Å) but reveal distinct presenilin helix conformation states and thermal β-strand to coil transitions of C83 and Notch100. We identify distinct 303 K hydrogen bond dynamics and water accessibility of the catalytic sites. The RKRR motif (1758–1761) contributes significantly to Notch binding and serves as a “membrane anchor” that prevents Notch displacement. Water that transiently hydrogen bonds to G1753 and V1754 probably represents the catalytic nucleophile. At 303 K, Notch and C83 binding induce different conformation states, with Notch mostly present in a closed state with shorter Asp–Asp distance. This may explain the different outcome of Notch and C99 cleavage, as the latter is more imprecise with many products. Our identified conformation states may aid efforts to develop conformation-selective drugs that target C99 and Notch cleavage differently, e.g. Notch-sparing γ-secretase modulators. Distinct membrane dynamics and conformations of C83- and Notch-bound γ-secretase may aid the development of Notch-sparing treatments of Alzheimer's disease.![]()
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Affiliation(s)
- Budheswar Dehury
- Department of Chemistry, Technical University of Denmark DK-2800 Kongens Lyngby Denmark +45 45252409.,Department of Biochemistry, University of Cambridge Tennis Court Road CB2 1GA UK
| | - Ning Tang
- Department of Chemistry, Technical University of Denmark DK-2800 Kongens Lyngby Denmark +45 45252409
| | - Rukmankesh Mehra
- Department of Chemistry, Technical University of Denmark DK-2800 Kongens Lyngby Denmark +45 45252409
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge Tennis Court Road CB2 1GA UK
| | - Kasper P Kepp
- Department of Chemistry, Technical University of Denmark DK-2800 Kongens Lyngby Denmark +45 45252409
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36
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Hutchison JM, Shih KC, Scheidt HA, Fantin SM, Parson KF, Pantelopulos GA, Harrington HR, Mittendorf KF, Qian S, Stein RA, Collier SE, Chambers MG, Katsaras J, Voehler MW, Ruotolo BT, Huster D, McFeeters RL, Straub JE, Nieh MP, Sanders CR. Bicelles Rich in both Sphingolipids and Cholesterol and Their Use in Studies of Membrane Proteins. J Am Chem Soc 2020; 142:12715-12729. [PMID: 32575981 DOI: 10.1021/jacs.0c04669] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
How the distinctive lipid composition of mammalian plasma membranes impacts membrane protein structure is largely unexplored, partly because of the dearth of isotropic model membrane systems that contain abundant sphingolipids and cholesterol. This gap is addressed by showing that sphingomyelin and cholesterol-rich (SCOR) lipid mixtures with phosphatidylcholine can be cosolubilized by n-dodecyl-β-melibioside to form bicelles. Small-angle X-ray and neutron scattering, as well as cryo-electron microscopy, demonstrate that these assemblies are stable over a wide range of conditions and exhibit the bilayered-disc morphology of ideal bicelles even at low lipid-to-detergent mole ratios. SCOR bicelles are shown to be compatible with a wide array of experimental techniques, as applied to the transmembrane human amyloid precursor C99 protein in this medium. These studies reveal an equilibrium between low-order oligomer structures that differ significantly from previous experimental structures of C99, providing an example of how ordered membranes alter membrane protein structure.
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Affiliation(s)
- James M Hutchison
- Chemical and Physical Biology Graduate Program and Center for Structural Biology, Vanderbilt University, Nashville 37240, Tennessee, United States
| | - Kuo-Chih Shih
- Polymer Program, Department of Chemical & Biomolecular Engineering, and Department of Biomedical Engineering, University of Connecticut, Storrs 06269, Connecticut, United States
| | - Holger A Scheidt
- Institute for Medical Physics and Biophysics, Leipzig University, Leipzig 16-18, 04107, Germany
| | - Sarah M Fantin
- Department of Chemistry, University of Michigan, Ann Arbor 48109, Michigan, United States
| | - Kristine F Parson
- Department of Chemistry, University of Michigan, Ann Arbor 48109, Michigan, United States
| | - George A Pantelopulos
- Department of Chemistry, Boston University, Boston 02215, Massachusetts, United States
| | - Haley R Harrington
- Center for Structural Biology and Department of Biochemistry, Vanderbilt University School of Medicine Basic Sciences, Nashville 37240, Tennessee, United States
| | - Kathleen F Mittendorf
- Center for Health Research, Kaiser Permanente, Portland 97227, Oregon, United States
| | - Shuo Qian
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge 37831, Tennessee, United States
| | - Richard A Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville37240, Tennessee, United States
| | - Scott E Collier
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland 97227, Oregon, United States
| | - Melissa G Chambers
- Center for Structural Biology, Vanderbilt University, Nashville 37240, Tennessee, United States
| | - John Katsaras
- Neutron Scattering Division and Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge 37831, Tennessee, United States
| | - Markus W Voehler
- Center for Structural Biology and Department of Chemistry, Vanderbilt University, Nashville 37240, Tennessee, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor 48109, Michigan, United States
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, Leipzig University, Leipzig 16-18, 04107, Germany
| | - Robert L McFeeters
- Department of Chemistry, University of Alabama, Huntsville 35899, Alabama, United States
| | - John E Straub
- Department of Chemistry, Boston University, Boston 02215, Massachusetts, United States
| | - Mu-Ping Nieh
- Polymer Program, Department of Chemical & Biomolecular Engineering, and Department of Biomedical Engineering, University of Connecticut, Storrs 06269, Connecticut, United States
| | - Charles R Sanders
- Center for Structural Biology, Department of Biochemistry, and Department of Medicine, Vanderbilt University School of Medicine, Nashville 37240, Tennessee, United States
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37
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Flanagan JC, Cardenas AE, Baiz CR. Ultrafast Spectroscopy of Lipid-Water Interfaces: Transmembrane Crowding Drives H-Bond Dynamics. J Phys Chem Lett 2020; 11:4093-4098. [PMID: 32364385 DOI: 10.1021/acs.jpclett.0c00783] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Biology takes place in crowded, heterogeneous environments, and it is therefore essential to account for crowding effects in our understanding of biophysical processes at the molecular level. Comparable to the cytosol, proteins occupy approximately 30% of the plasma membrane surface; thus, crowding should have an effect on the local structure and dynamics at the lipid-water interface. Using a combination of ultrafast two-dimensional infrared spectroscopy and molecular dynamics simulations, we quantify the effects of membrane peptide concentration on the picosecond interfacial H-bond dynamics. The measurements reveal a nonmonotonic dependence of water orientation and dynamics as a function of transmembrane peptide:lipid ratio. We observe three dynamical regimes: a "pure lipid-like" regime at low peptide concentrations, a bulk-like region at intermediate peptide concentrations where dynamics are faster by ∼20% compared to those of the pure lipid bilayer, and a crowded regime where high peptide concentrations slow dynamics by ∼50%.
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38
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Wang CR, Bubner ER, Jovcevski B, Mittal P, Pukala TL. Interrogating the higher order structures of snake venom proteins using an integrated mass spectrometric approach. J Proteomics 2020; 216:103680. [PMID: 32028038 DOI: 10.1016/j.jprot.2020.103680] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/20/2020] [Accepted: 02/02/2020] [Indexed: 12/20/2022]
Abstract
Snake venoms contain complex mixtures of proteins vital for the survival of venomous snakes. Aligned with their diverse pharmacological activities, the protein compositions of snake venoms are highly variable, and efforts to characterise the primary structures of such proteins are ongoing. Additionally, a significant knowledge gap exists in terms of the higher-order protein structures which modulate venom potency, posing a challenge for successful therapeutic applications. Here we use a multifaceted mass spectrometry approach to characterise proteins from venoms of Collett's snake Pseudechis colletti and the puff adder Bitis arietans. Following chromatographic fractionation and bottom-up proteomics analysis, native mass spectrometry identified, among other components, a non-covalent l-amino acid oxidase dimer in the P. colletti venom and a C-type lectin tetramer in the B. arietans venom. Furthermore, a covalently-linked phospholipase A2 (PLA2) dimer was identified in P. colletti venom, from which the PLA2 species were shown to adopt compact geometries using ion mobility measurements. Interestingly, we show that the dimeric PLA2 possesses greater bioactivity than the monomeric PLA2s. This work contributes to ongoing efforts cataloguing components of snake venoms, and notably, emphasises the importance of understanding higher-order venom protein interactions and the utility of a combined mass spectrometric approach for this task. SIGNIFICANCE: The protein constituents of snake venoms represent a sophisticated cocktail of biologically active molecules ideally suited for further exploration in drug design and development. Despite ongoing efforts to characterise the diverse protein components of such venoms there is still much work required in this area, particularly in moving from simply describing the protein primary sequence to providing an understanding of quaternary structure. The combined proteomic and native mass spectrometry workflow utilised here gives new insights into higher order protein structures in selected snake venoms, and can underpin further investigation into the protein interactions which govern snake venom specificity and potency.
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Affiliation(s)
- C Ruth Wang
- Department of Chemistry, School of Physical Sciences, University of Adelaide, Adelaide 5005, Australia
| | - Emily R Bubner
- Department of Chemistry, School of Physical Sciences, University of Adelaide, Adelaide 5005, Australia
| | - Blagojce Jovcevski
- Department of Chemistry, School of Physical Sciences, University of Adelaide, Adelaide 5005, Australia
| | - Parul Mittal
- Adelaide Proteomics Centre, University of Adelaide, Adelaide 5005, Australia
| | - Tara L Pukala
- Department of Chemistry, School of Physical Sciences, University of Adelaide, Adelaide 5005, Australia.
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39
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Ngo ST, Nguyen PH, Derreumaux P. Stability of Aβ11-40 Trimers with Parallel and Antiparallel β-Sheet Organizations in a Membrane-Mimicking Environment by Replica Exchange Molecular Dynamics Simulation. J Phys Chem B 2020; 124:617-626. [PMID: 31931566 DOI: 10.1021/acs.jpcb.9b10982] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The aggregation of the amyloid (Aβ) peptide of 39-43 amino acids into plaques is observed in the brain of Alzheimer's disease (AD) patients, but the mechanisms underlying the neurotoxicity of Aβ oligomers are still elusive. One suggested initial mechanism is related to the implications of amyloid membrane interactions, but characterization of these assemblies is challenging by experimental means. In this study, we have explored the stability of a trimer of Aβ11-40 in parallel and antiparallel β-sheet structures for the wild-type sequence and its F20W mutant in a dipalmitoylphosphatidylcholine membrane using atomistic replica exchange molecular dynamic simulations. We show that both the U-shape organization and the assembly of β-hairpins are maintained in the membrane and are resistant to the mutation F20W. In contrast the models are destabilized by the F19P mutation. Overall, our results indicate that these two assemblies represent minimal seeds or nuclei for the formation of either amyloid fibrils, a variety of β-barrel pores, or various aggregates for many Aβ sequences in a membrane-mimicking environment.
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Affiliation(s)
- Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics , Ton Duc Thang University , Ho Chi Minh City , Vietnam.,Faculty of Applied Sciences , Ton Duc Thang University , Ho Chi Minh City , Vietnam
| | - Phuong H Nguyen
- Laboratoire de Biochimie Théorique , UPR 9080, CNRS, Université de Paris , 13 rue Pierre et Marie Curie , 75005 , Paris , France.,Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University , 75005 Paris , France
| | - Philippe Derreumaux
- Laboratory of Theoretical Chemistry , Ton Duc Thang University , Ho Chi Minh City , Vietnam.,Faculty of Pharmacy , Ton Duc Thang University , Ho Chi Minh City , Vietnam
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40
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Computational analysis of Alzheimer-causing mutations in amyloid precursor protein and presenilin 1. Arch Biochem Biophys 2019; 678:108168. [DOI: 10.1016/j.abb.2019.108168] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/25/2019] [Accepted: 11/02/2019] [Indexed: 12/13/2022]
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41
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Mori T, Sugita Y. Implicit Micelle Model for Membrane Proteins Using Superellipsoid Approximation. J Chem Theory Comput 2019; 16:711-724. [DOI: 10.1021/acs.jctc.9b00783] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Takaharu Mori
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
- RIKEN Center for Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- RIKEN Center for Biosystems Dynamics Research, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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42
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Scharfenberg F, Armbrust F, Marengo L, Pietrzik C, Becker-Pauly C. Regulation of the alternative β-secretase meprin β by ADAM-mediated shedding. Cell Mol Life Sci 2019; 76:3193-3206. [PMID: 31201463 PMCID: PMC11105663 DOI: 10.1007/s00018-019-03179-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 05/23/2019] [Accepted: 05/29/2019] [Indexed: 12/12/2022]
Abstract
Alzheimer's Disease (AD) is the sixth-leading cause of death in industrialized countries. Neurotoxic amyloid-β (Aβ) plaques are one of the pathological hallmarks in AD patient brains. Aβ accumulates in the brain upon sequential, proteolytic processing of the amyloid precursor protein (APP) by β- and γ-secretases. However, so far disease-modifying drugs targeting β- and γ-secretase pathways seeking a decrease in the production of toxic Aβ peptides have failed in clinics. It has been demonstrated that the metalloproteinase meprin β acts as an alternative β-secretase, capable of generating truncated Aβ2-x peptides that have been described to be increased in AD patients. This indicates an important β-site cleaving enzyme 1 (BACE-1)-independent contribution of the metalloprotease meprin β within the amyloidogenic pathway and may lead to novel drug targeting avenues. However, meprin β itself is embedded in a complex regulatory network. Remarkably, the anti-amyloidogenic α-secretase a disintegrin and metalloproteinase domain-containing protein 10 (ADAM10) is a direct competitor for APP at the cell surface, but also a sheddase of inactive pro-meprin β. Overall, we highlight the current cellular, molecular and structural understanding of meprin β as alternative β-secretase within the complex protease web, regulating APP processing in health and disease.
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Affiliation(s)
- Franka Scharfenberg
- Unit for Degradomics of the Protease Web, Biochemical Institute, University of Kiel, Kiel, Germany
| | - Fred Armbrust
- Unit for Degradomics of the Protease Web, Biochemical Institute, University of Kiel, Kiel, Germany
| | - Liana Marengo
- Institute for Pathobiochemistry, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Claus Pietrzik
- Institute for Pathobiochemistry, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany.
| | - Christoph Becker-Pauly
- Unit for Degradomics of the Protease Web, Biochemical Institute, University of Kiel, Kiel, Germany.
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43
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Dehury B, Tang N, Blundell TL, Kepp KP. Structure and dynamics of γ-secretase with presenilin 2 compared to presenilin 1. RSC Adv 2019; 9:20901-20916. [PMID: 35515530 PMCID: PMC9065803 DOI: 10.1039/c9ra02623a] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/27/2019] [Indexed: 12/12/2022] Open
Abstract
Severe early-onset familial Alzheimer's disease (FAD) is caused by more than 200 different mutations in the genes coding for presenilin, the catalytic subunit of the 4-subunit protease complex γ-secretase, which cleaves the C99 fragment of the amyloid precursor protein (APP) to produce Aβ peptides. γ-Secretase exists with either of two homologues, PS1 and PS2. All cryo-electron microscopic structures and computational work has so far focused on γ-secretase with PS1, yet PS2 mutations also cause FAD. A central question is thus whether there are structural and dynamic differences between PS1 and PS2. To address this question, we use the cryo-electron microscopic data for PS1 to develop the first structural and dynamic model of PS2-γ-secretase in the catalytically relevant mature membrane-bound state at ambient temperature, equilibrated by three independent 500 ns molecular dynamics simulations. We find that the characteristic nicastrin extra-cellular domain breathing mode and major movements in the cytosolic loop between TM6 and TM7 occur in both PS2- and PS1-γ-secretase. The overall structures and conformational states are similar, suggesting similar catalytic activities. However, at the sequence level, charge-controlled membrane-anchoring is extracellular for PS1 and intracellular for PS2, which suggests different subcellular locations. The tilt angles of the TM2, TM6, TM7 and TM9 helices differ in the two forms of γ-secretase, suggesting that the two proteins have somewhat different substrate processing and channel sizes. Our MD simulations consistently indicated that PS2 retains several water molecules near the catalytic site at the bilayer, as required for catalysis. The possible reasons for the differences of PS1 and PS2 are discussed in relation to their location and function.
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Affiliation(s)
- Budheswar Dehury
- Department of Chemistry, Technical University of Denmark DK-2800 Kongens Lyngby Denmark +045 45252409
| | - Ning Tang
- Department of Chemistry, Technical University of Denmark DK-2800 Kongens Lyngby Denmark +045 45252409
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge Cambridge CB2 1GA UK
| | - Kasper P Kepp
- Department of Chemistry, Technical University of Denmark DK-2800 Kongens Lyngby Denmark +045 45252409
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44
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Castro MA, Hadziselimovic A, Sanders CR. The vexing complexity of the amyloidogenic pathway. Protein Sci 2019; 28:1177-1193. [PMID: 30897251 PMCID: PMC6566549 DOI: 10.1002/pro.3606] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 03/18/2019] [Accepted: 03/18/2019] [Indexed: 02/06/2023]
Abstract
The role of the amyloidogenic pathway in the etiology of Alzheimer's disease (AD), particularly the common sporadic late onset forms of the disease, is controversial. To some degree, this is a consequence of the failure of drug and therapeutic antibody trials based either on targeting the proteases in this pathway or its amyloid end products. Here, we explore the formidable complexity of the biochemistry and cell biology associated with this pathway. For example, we review evidence that the immediate precursor of amyloid-β, the C99 domain of the amyloid precursor protein (APP), may itself be toxic. We also review important new results that appear to finally establish a direct genetic link between mutations in APP and the sporadic forms of AD. Based on the complexity of amyloidogenesis, it seems possible that a major contributor to the failure of related drug trials is that we have an incomplete understanding of this pathway and how it is linked to Alzheimer's pathogenesis. If so, this highlights a need for further characterization of this pathway, not its abandonment.
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Affiliation(s)
- Manuel A. Castro
- Departments of Biochemistry and MedicineVanderbilt University School of MedicineNashvilleTennessee 37240
| | - Arina Hadziselimovic
- Departments of Biochemistry and MedicineVanderbilt University School of MedicineNashvilleTennessee 37240
| | - Charles R. Sanders
- Departments of Biochemistry and MedicineVanderbilt University School of MedicineNashvilleTennessee 37240
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45
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Götz A, Mylonas N, Högel P, Silber M, Heinel H, Menig S, Vogel A, Feyrer H, Huster D, Luy B, Langosch D, Scharnagl C, Muhle-Goll C, Kamp F, Steiner H. Modulating Hinge Flexibility in the APP Transmembrane Domain Alters γ-Secretase Cleavage. Biophys J 2019; 116:2103-2120. [PMID: 31130234 PMCID: PMC6554489 DOI: 10.1016/j.bpj.2019.04.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 02/14/2019] [Accepted: 04/15/2019] [Indexed: 01/27/2023] Open
Abstract
Intramembrane cleavage of the β-amyloid precursor protein C99 substrate by γ-secretase is implicated in Alzheimer's disease pathogenesis. Biophysical data have suggested that the N-terminal part of the C99 transmembrane domain (TMD) is separated from the C-terminal cleavage domain by a di-glycine hinge. Because the flexibility of this hinge might be critical for γ-secretase cleavage, we mutated one of the glycine residues, G38, to a helix-stabilizing leucine and to a helix-distorting proline. Both mutants impaired γ-secretase cleavage and also altered its cleavage specificity. Circular dichroism, NMR, and backbone amide hydrogen/deuterium exchange measurements as well as molecular dynamics simulations showed that the mutations distinctly altered the intrinsic structural and dynamical properties of the substrate TMD. Although helix destabilization and/or unfolding was not observed at the initial ε-cleavage sites of C99, subtle changes in hinge flexibility were identified that substantially affected helix bending and twisting motions in the entire TMD. These resulted in altered orientation of the distal cleavage domain relative to the N-terminal TMD part. Our data suggest that both enhancing and reducing local helix flexibility of the di-glycine hinge may decrease the occurrence of enzyme-substrate complex conformations required for normal catalysis and that hinge mobility can thus be conducive for productive substrate-enzyme interactions.
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Affiliation(s)
- Alexander Götz
- Physics of Synthetic Biological Systems (E14), Technical University of Munich, Freising, Germany
| | - Nadine Mylonas
- Biomedical Center (BMC), Metabolic Biochemistry, Ludwig-Maximilians-University, Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Philipp Högel
- Center for Integrated Protein Science Munich at the Lehrstuhl Chemie der Biopolymere, Technical University Munich, Freising, Germany
| | - Mara Silber
- Institute of Organic Chemistry and Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Hannes Heinel
- Institute for Medical Physics and Biophysics, Leipzig University, Leipzig, Germany
| | - Simon Menig
- Physics of Synthetic Biological Systems (E14), Technical University of Munich, Freising, Germany
| | - Alexander Vogel
- Institute for Medical Physics and Biophysics, Leipzig University, Leipzig, Germany
| | - Hannes Feyrer
- Institute of Organic Chemistry and Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, Leipzig University, Leipzig, Germany
| | - Burkhard Luy
- Institute of Organic Chemistry and Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Dieter Langosch
- Center for Integrated Protein Science Munich at the Lehrstuhl Chemie der Biopolymere, Technical University Munich, Freising, Germany
| | - Christina Scharnagl
- Physics of Synthetic Biological Systems (E14), Technical University of Munich, Freising, Germany.
| | - Claudia Muhle-Goll
- Institute of Organic Chemistry and Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Karlsruhe, Germany.
| | - Frits Kamp
- Biomedical Center (BMC), Metabolic Biochemistry, Ludwig-Maximilians-University, Munich, Germany
| | - Harald Steiner
- Biomedical Center (BMC), Metabolic Biochemistry, Ludwig-Maximilians-University, Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.
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46
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Minh Hung H, Dieu Hang T, Nguyen MT. Structural Investigation of Human Prolactin Receptor Transmembrane Domain Homodimerization in a Membrane Environment through Multiscale Simulations. J Phys Chem B 2019; 123:4858-4866. [PMID: 31099581 DOI: 10.1021/acs.jpcb.9b01986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
It is well established that prolactin (PRL) and its receptor (PRLR) are associated with hundreds of biological functions. They have been postulated to be linked to breast and prostate cancers, and PRLR signaling has attracted considerable medical and pharmaceutical interest in the development of compounds targeting PRLR. Dimerization of the receptor through its transmembrane (TM) domain is a key step for understanding its signaling and related issues. Our multiscale simulation results revealed that its TM domain can form dimers in a membrane environment with distinct states stabilized by different residue motifs. On the basis of the simulated data, an activation mechanism of PRL with the importance of two symmetrical tryptophan residues was proposed in detail to determine the conformational change of its receptor, which is essential for signal transduction. The better knowledge of PRLR structure and its protein-protein interaction can considerably contribute to a further understanding of PRLR signaling action and thereby help to develop some new PRLR signaling-based strategies for PRL-related diseases.
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Affiliation(s)
- Huynh Minh Hung
- Department of Chemistry , KU Leuven , Celestijnenlaan 200F , B-3001 Leuven , Belgium.,Department of Chemistry , Quy Nhon University , Quy Nhon 590000 , Vietnam
| | - Tran Dieu Hang
- Department of Chemistry , KU Leuven , Celestijnenlaan 200F , B-3001 Leuven , Belgium.,Department of Chemistry , Quy Nhon University , Quy Nhon 590000 , Vietnam
| | - Minh Tho Nguyen
- Computational Chemistry Research Group , Ton Duc Thang University , Ho Chi Minh City 700000 Vietnam.,Faculty of Applied Sciences , Ton Duc Thang University , Ho Chi Minh City 700000 Vietnam
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47
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De novo aggregation of Alzheimer's Aβ25-35 peptides in a lipid bilayer. Sci Rep 2019; 9:7161. [PMID: 31073226 PMCID: PMC6509337 DOI: 10.1038/s41598-019-43685-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/27/2019] [Indexed: 11/28/2022] Open
Abstract
A potential mechanism of cytotoxicity attributed to Alzheimer’s Aβ peptides postulates that their aggregation disrupts membrane structure causing uncontrollable permeation of Ca2+ ions. To gain molecular insights into these processes, we have performed all-atom explicit solvent replica exchange with solute tempering molecular dynamics simulations probing aggregation of the naturally occurring Aβ fragment Aβ25-35 within the DMPC lipid bilayer. To compare the impact produced on the bilayer by Aβ25-35 oligomers and monomers, we used as a control our previous simulations, which explored binding of Aβ25-35 monomers to the same bilayer. We found that compared to monomeric species aggregation results in much deeper insertion of Aβ25-35 peptides into the bilayer hydrophobic core causing more pronounced disruption in its structure. Aβ25-35 peptides aggregate by incorporating monomer-like structures with stable C-terminal helix. As a result the Aβ25-35 dimer features unusual helix head-to-tail topology supported by a parallel off-registry interface. Such topology affords further growth of an aggregate by recruiting additional peptides. Free energy landscape reveals that inserted dimers represent the dominant equilibrium state augmented by two metastable states associated with surface bound dimers and inserted monomers. Using the free energy landscape we propose the pathway of Aβ25-35 binding, aggregation, and insertion into the lipid bilayer.
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48
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Corradi V, Sejdiu BI, Mesa-Galloso H, Abdizadeh H, Noskov SY, Marrink SJ, Tieleman DP. Emerging Diversity in Lipid-Protein Interactions. Chem Rev 2019; 119:5775-5848. [PMID: 30758191 PMCID: PMC6509647 DOI: 10.1021/acs.chemrev.8b00451] [Citation(s) in RCA: 260] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Indexed: 02/07/2023]
Abstract
Membrane lipids interact with proteins in a variety of ways, ranging from providing a stable membrane environment for proteins to being embedded in to detailed roles in complicated and well-regulated protein functions. Experimental and computational advances are converging in a rapidly expanding research area of lipid-protein interactions. Experimentally, the database of high-resolution membrane protein structures is growing, as are capabilities to identify the complex lipid composition of different membranes, to probe the challenging time and length scales of lipid-protein interactions, and to link lipid-protein interactions to protein function in a variety of proteins. Computationally, more accurate membrane models and more powerful computers now enable a detailed look at lipid-protein interactions and increasing overlap with experimental observations for validation and joint interpretation of simulation and experiment. Here we review papers that use computational approaches to study detailed lipid-protein interactions, together with brief experimental and physiological contexts, aiming at comprehensive coverage of simulation papers in the last five years. Overall, a complex picture of lipid-protein interactions emerges, through a range of mechanisms including modulation of the physical properties of the lipid environment, detailed chemical interactions between lipids and proteins, and key functional roles of very specific lipids binding to well-defined binding sites on proteins. Computationally, despite important limitations, molecular dynamics simulations with current computer power and theoretical models are now in an excellent position to answer detailed questions about lipid-protein interactions.
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Affiliation(s)
- Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Besian I. Sejdiu
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Haydee Mesa-Galloso
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Haleh Abdizadeh
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Sergei Yu. Noskov
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - 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
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
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49
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Molecular dynamics of C99-bound γ-secretase reveal two binding modes with distinct compactness, stability, and active-site retention: implications for Aβ production. Biochem J 2019; 476:1173-1189. [PMID: 30910800 DOI: 10.1042/bcj20190023] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/20/2019] [Accepted: 03/22/2019] [Indexed: 12/11/2022]
Abstract
The membrane protease γ-secretase cleaves the C99 fragment of the amyloid precursor protein, thus producing the Aβ peptides central to Alzheimer's disease. Cryo-electron microscopy has provided the topology but misses the membrane and loop parts that contribute to substrate binding. We report here an essentially complete atomic model of C99 within wild-type γ-secretase that respects all the experimental constraints and additionally describes loop, helix, and C99 substrate dynamics in a realistic all-atom membrane. Our model represents the matured auto-cleaved state required for catalysis. From two independent 500-ns molecular dynamic simulations, we identify two conformation states of C99 in equilibrium, a compact and a loose state. Our simulations provide a basis for C99 processing and Aβ formation and explain the production of longer and shorter Aβ, as the compact state retains C99 for longer and thus probably trims to shorter Aβ peptides. We expect pathogenic presenilin mutations to stabilize the loose over the compact state. The simulations detail the role of the Lys53-Lys54-Lys55 anchor for C99 binding, a loss of helicity of bound C99, and positioning of Thr48 and Leu49 leading to alternative trimming pathways on opposite sides of the C99 helix in three amino acid steps. The C99 binding topology resembles that of C83-bound γ-secretase without membrane but lacks a presenilin 1-C99 β-sheet, which could be induced by C83's stronger binding. The loose state should be selectively disfavored by γ-secretase modulators to increase C99 trimming and reduce the formation of longer Aβ, a strategy that is currently much explored but has lacked a structural basis.
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50
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Götz A, Högel P, Silber M, Chaitoglou I, Luy B, Muhle-Goll C, Scharnagl C, Langosch D. Increased H-Bond Stability Relates to Altered ε-Cleavage Efficiency and Aβ Levels in the I45T Familial Alzheimer's Disease Mutant of APP. Sci Rep 2019; 9:5321. [PMID: 30926830 PMCID: PMC6440955 DOI: 10.1038/s41598-019-41766-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 02/27/2019] [Indexed: 12/15/2022] Open
Abstract
Cleavage of the amyloid precursor protein's (APP) transmembrane domain (TMD) by γ-secretase is a crucial step in the aetiology of Alzheimer's Disease (AD). Mutations in the APP TMD alter cleavage and lead to familial forms of AD (FAD). The majority of FAD mutations shift the preference of initial cleavage from ε49 to ε48, thus raising the AD-related Aβ42/Aβ40 ratio. The I45T mutation is among the few FAD mutations that do not alter ε-site preference, while it dramatically reduces the efficiency of ε-cleavage. Here, we investigate the impact of the I45T mutation on the backbone dynamics of the substrate TMD. Amide exchange experiments and molecular dynamics simulations in solvent and a lipid bilayer reveal an increased stability of amide hydrogen bonds at the ζ- and γ-cleavage sites. Stiffening of the H-bond network is caused by an additional H-bond between the T45 side chain and the TMD backbone, which alters dynamics within the cleavage domain. In particular, the increased H-bond stability inhibits an upward movement of the ε-sites in the I45T mutant. Thus, an altered presentation of ε-sites to the active site of γ-secretase as a consequence of restricted local flexibility provides a rationale for reduced ε-cleavage efficiency of the I45T mutant.
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Grants
- Deutsche Forschungsgemeinschaft (German Research Foundation)
- Helmholtz-Gemeinschaft (Helmholtz Association)
- Leibniz Supercomputing Centre: Leibniz-Rechenzentrum der Bayerischen Akademie der Wissenschaften, Boltzmannstraße 1, 85748 Garching bei München, Germany, WEB: https://www.lrz.de Gauss Centre for Supercomputing: GCS-Geschäftsstelle Bonn, Ahrstrasse 45, 53175 Bonn, Germany, WEB: http://www.gauss-centre.eu
- Center for Integrated Protein Science: Munich Center For Integrated Protein Science (CIPSM), Butenandtstr. 5 - 13, 81377 Munich, Germany, WEB: http://www.cipsm.de/ Leibniz Supercomputing Centre: Leibniz-Rechenzentrum der Bayerischen Akademie der Wissenschaften, Boltzmannstraße 1, 85748 Garching bei München, Germany, WEB: https://www.lrz.de
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Affiliation(s)
- Alexander Götz
- Lehrstuhl für Physik synthetischer Biosysteme (E14), Technische Universität München, Maximus-von-Imhof Forum 4, 85354, Freising, Germany
| | - Philipp Högel
- Center for Integrated Protein Science Munich (CIPSM) at the Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Mara Silber
- Institute of Organic Chemistry and Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Iro Chaitoglou
- Center for Integrated Protein Science Munich (CIPSM) at the Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Burkhard Luy
- Institute of Organic Chemistry and Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Claudia Muhle-Goll
- Institute of Organic Chemistry and Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Christina Scharnagl
- Lehrstuhl für Physik synthetischer Biosysteme (E14), Technische Universität München, Maximus-von-Imhof Forum 4, 85354, Freising, Germany.
| | - Dieter Langosch
- Center for Integrated Protein Science Munich (CIPSM) at the Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany.
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