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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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2
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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: 5] [Impact Index Per Article: 1.3] [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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3
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Cuesta SA, Mora JR, Zambrano CH, Torres FJ, Rincón L. Comparative study of the nucleophilic attack step in the proteases catalytic activity: A theoretical study. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1705412] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Sebastián A. Cuesta
- Instituto de Simulación Computacional (ISM), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- Departamento de Ingeniería Química – Grupo de Química Computacional y Teórica (QCT), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - José R. Mora
- Instituto de Simulación Computacional (ISM), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- Departamento de Ingeniería Química – Grupo de Química Computacional y Teórica (QCT), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - Cesar H. Zambrano
- Instituto de Simulación Computacional (ISM), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- Departamento de Ingeniería Química – Grupo de Química Computacional y Teórica (QCT), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - F. Javier Torres
- Instituto de Simulación Computacional (ISM), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- Departamento de Ingeniería Química – Grupo de Química Computacional y Teórica (QCT), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - Luis Rincón
- Instituto de Simulación Computacional (ISM), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- Departamento de Ingeniería Química – Grupo de Química Computacional y Teórica (QCT), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
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4
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Hitzenberger M, Zacharias M. Uncovering the Binding Mode of γ -Secretase Inhibitors. ACS Chem Neurosci 2019; 10:3398-3403. [PMID: 31244051 DOI: 10.1021/acschemneuro.9b00272] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Knowledge of how transition state inhibitors bind to γ-secretase is of major importance for the design of new Alzheimer's disease therapies. On the basis of the known structure of γ-secretase in complex with a fragment of the amyloid precursor protein, we generated a structural model of γ-secretase in complex with the effective L-685,458 transition state inhibitor. The predicted binding mode is in excellent agreement with experimental data, mimicking all enzyme-substrate interactions at the active site and forming the relevant transition state geometry with the active site aspartate residues. The model also indicates the possible location and nature of the amino acid residues forming the proposed binding pockets S1', S2', and S3' near the active site that are occupied by chemical groups of the inhibitor. In addition, we found that the stability of the complex is very likely sensitive to the pH value. Comparative simulations on the binding of L-685,458 and the epimer L682,679 allowed us to explain the strongly reduced affinity of the epimer for γ-secretase. The structural model could form a valuable basis for the design of new or modified γ-secretase inhibitors.
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Affiliation(s)
- Manuel Hitzenberger
- Physics Department T38, Technical University of Munich, James-Frank-Strasse 1, 85748 Garching, Germany
| | - Martin Zacharias
- Physics Department T38, Technical University of Munich, James-Frank-Strasse 1, 85748 Garching, Germany
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5
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Petit D, Hitzenberger M, Lismont S, Zoltowska KM, Ryan NS, Mercken M, Bischoff F, Zacharias M, Chávez-Gutiérrez L. Extracellular interface between APP and Nicastrin regulates Aβ length and response to γ-secretase modulators. EMBO J 2019; 38:embj.2019101494. [PMID: 31109937 PMCID: PMC6576158 DOI: 10.15252/embj.2019101494] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 04/02/2019] [Accepted: 04/11/2019] [Indexed: 12/20/2022] Open
Abstract
γ-Secretase complexes (GSECs) are multimeric membrane proteases involved in a variety of physiological processes and linked to Alzheimer's disease (AD). Presenilin (PSEN, catalytic subunit), Nicastrin (NCT), Presenilin Enhancer 2 (PEN-2), and Anterior Pharynx Defective 1 (APH1) are the essential subunits of GSECs. Mutations in PSEN and the Amyloid Precursor Protein (APP) cause early-onset AD GSECs successively cut APP to generate amyloid-β (Aβ) peptides of various lengths. AD-causing mutations destabilize GSEC-APP/Aβn interactions and thus enhance the production of longer Aβs, which elicit neurotoxic events underlying pathogenesis. Here, we investigated the molecular strategies that anchor GSEC and APP/Aβn during the sequential proteolysis. Our studies reveal that a direct interaction between NCT ectodomain and APPC99 influences the stability of GSEC-Aβn assemblies and thereby modulates Aβ length. The data suggest a potential link between single-nucleotide variants in NCSTN and AD risk. Furthermore, our work indicates that an extracellular interface between the protease (NCT, PSEN) and the substrate (APP) represents the target for compounds (GSMs) modulating Aβ length. Our findings may guide future rationale-based drug discovery efforts.
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Affiliation(s)
- Dieter Petit
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,Department of Neurosciences, Leuven Research Institute for Neuroscience and Disease (LIND), KU Leuven, Leuven, Belgium
| | - Manuel Hitzenberger
- Physics Department, Theoretical Biophysics (T38), Technical University of Munich, München, Germany
| | - Sam Lismont
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,Department of Neurosciences, Leuven Research Institute for Neuroscience and Disease (LIND), KU Leuven, Leuven, Belgium
| | - Katarzyna Marta Zoltowska
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,Department of Neurosciences, Leuven Research Institute for Neuroscience and Disease (LIND), KU Leuven, Leuven, Belgium
| | - Natalie S Ryan
- Dementia Research Centre, Department of Neurodegenerative Disease UCL Queen Square Institute of Neurology, London, UK
| | - Marc Mercken
- Janssen Research & Development, Division of Janssen Pharmaceutica NV, Beerse, Belgium.,Janssen Research & Development, Neuroscience biology Turnhoutseweg, Beerse, Belgium
| | - François Bischoff
- Janssen Research & Development, Division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Martin Zacharias
- Physics Department, Theoretical Biophysics (T38), Technical University of Munich, München, Germany
| | - Lucía Chávez-Gutiérrez
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium .,Department of Neurosciences, Leuven Research Institute for Neuroscience and Disease (LIND), KU Leuven, Leuven, Belgium
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6
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Hitzenberger M, Zacharias M. Structural Modeling of γ-Secretase Aβ n Complex Formation and Substrate Processing. ACS Chem Neurosci 2019; 10:1826-1840. [PMID: 30638370 DOI: 10.1021/acschemneuro.8b00725] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The intramembrane aspartyl protease γ-secretase (GSEC) cleaves single-span transmembrane helices including the C-terminal fragment of the amyloid precursor protein (APP). This substrate is initially cleaved at the ϵ-site followed by successive processing (trimming) events mostly in steps of three amino acids. GSEC is responsible for the formation of N-terminal APP amyloid-β (Aβ) peptides of different length (e.g., Aβ42) that can form aggregates involved in Alzheimer's disease pathogenesis. The molecular mechanism of GSEC-APP substrate recognition is key for understanding how different peptide products are formed and could help in designing APP-selective modulators. Based on the known structure of apo GSEC and the APP-C99 fragment we have generated putative structural models of the initial binding in three different possible modes using extensive molecular dynamics (MD) simulations. The binding mode with the substrate helix located in a cleft between the transmembrane helices 2 and 3 of the presenilin subunit was identified as a most likely binding mode. Based on this arrangement, the processing steps were investigated using restraint MD simulations to pull the scissile bond (for each processing step) into a transition like (cleavable) state. This allowed us to analyze in detail the motions and energetic contributions of participating residues. The structural model agrees qualitatively well with the influence of many mutations in GSEC and C99. It also explains the effects of inhibitors, cross-linking, as well as spectroscopic data on GSEC substrate binding and can serve as working model for the future planning of structural and biochemical studies.
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Affiliation(s)
- M. Hitzenberger
- Physics Department T38, Technical University of Munich, James-Frank-Str. 1, 85748 Garching, Germany
| | - M. Zacharias
- Physics Department T38, Technical University of Munich, James-Frank-Str. 1, 85748 Garching, Germany
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Hitzenberger M, Zacharias M. γ-Secretase Studied by Atomistic Molecular Dynamics Simulations: Global Dynamics, Enzyme Activation, Water Distribution and Lipid Binding. Front Chem 2019; 6:640. [PMID: 30662893 PMCID: PMC6328467 DOI: 10.3389/fchem.2018.00640] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/07/2018] [Indexed: 11/14/2022] Open
Abstract
γ-secretase, an intramembrane-cleaving aspartyl protease is involved in the cleavage of a large number of intramembrane proteins. The most prominent substrate is the amyloid precursor protein, whose proteolytic processing leads to the production of different amyloid Aβ peptides. These peptides are known to form toxic aggregates and may play a key role in Alzheimer's disease (AD). Recently, the three-dimensional structure of γ-secretase has been determined via Cryo-EM, elucidating the spatial geometry of this enzyme complex in different functional states. We have used molecular dynamics (MD) simulations to study the global dynamics and conformational transitions of γ-secretase, as well as the water and lipid distributions in and around the transmembrane domains in atomic detail. Simulations were performed on the full enzyme complex and on the membrane embedded parts alone. The simulations revealed global motions compatible with the experimental enzyme structures and indicated little dependence of the dynamics of the transmembrane domains on the soluble extracellular subunits. During the simulation on the membrane spanning part a transition between an inactive conformation (with catalytic residues far apart) toward a putatively active form (with catalytic residues in close proximity) has been observed. This conformational change is associated with a distinct rearrangement of transmembrane helices, a global compaction of the catalytically active presenilin subunit a change in the water structure near the active site and a rigidification of the protein fold. The observed conformational rearrangement allows the interpretation of the effect of several mutations on the activity of γ-secretase. A number of long-lived lipid binding sites could be identified on the membrane spanning surface of γ-secretase which may coincide with association regions of hydrophobic membrane helices to form putative substrate binding exosites.
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Affiliation(s)
| | - Martin Zacharias
- Physics Department T38, Technical University of Munich, Garching, Germany
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Geerts H, Hofmann-Apitius M, Anastasio TJ. Knowledge-driven computational modeling in Alzheimer's disease research: Current state and future trends. Alzheimers Dement 2017; 13:1292-1302. [PMID: 28917669 DOI: 10.1016/j.jalz.2017.08.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 07/05/2017] [Accepted: 08/01/2017] [Indexed: 11/24/2022]
Abstract
Neurodegenerative diseases such as Alzheimer's disease (AD) follow a slowly progressing dysfunctional trajectory, with a large presymptomatic component and many comorbidities. Using preclinical models and large-scale omics studies ranging from genetics to imaging, a large number of processes that might be involved in AD pathology at different stages and levels have been identified. The sheer number of putative hypotheses makes it almost impossible to estimate their contribution to the clinical outcome and to develop a comprehensive view on the pathological processes driving the clinical phenotype. Traditionally, bioinformatics approaches have provided correlations and associations between processes and phenotypes. Focusing on causality, a new breed of advanced and more quantitative modeling approaches that use formalized domain expertise offer new opportunities to integrate these different modalities and outline possible paths toward new therapeutic interventions. This article reviews three different computational approaches and their possible complementarities. Process algebras, implemented using declarative programming languages such as Maude, facilitate simulation and analysis of complicated biological processes on a comprehensive but coarse-grained level. A model-driven Integration of Data and Knowledge, based on the OpenBEL platform and using reverse causative reasoning and network jump analysis, can generate mechanistic knowledge and a new, mechanism-based taxonomy of disease. Finally, Quantitative Systems Pharmacology is based on formalized implementation of domain expertise in a more fine-grained, mechanism-driven, quantitative, and predictive humanized computer model. We propose a strategy to combine the strengths of these individual approaches for developing powerful modeling methodologies that can provide actionable knowledge for rational development of preventive and therapeutic interventions. Development of these computational approaches is likely to be required for further progress in understanding and treating AD.
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Affiliation(s)
- Hugo Geerts
- In Silico Biosciences, Berwyn, PA, USA; Perelman School of Medicine, Univ. of Pennsylvania.
| | - Martin Hofmann-Apitius
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany
| | - Thomas J Anastasio
- Department of Molecular and Integrative Physiology, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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9
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Gu K, Li Q, Lin H, Zhu J, Mo J, He S, Lu X, Jiang X, Sun H. Gamma secretase inhibitors: a patent review (2013 - 2015). Expert Opin Ther Pat 2017; 27:851-866. [PMID: 28350212 DOI: 10.1080/13543776.2017.1313231] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Gamma secretase (GS) is an intricate and multi-subunits complex, and it can cut various transmembrane proteins. Now it is a therapeutic target for a number of diseases. However, due to some side effects, the clinical development of GSI is not successful. Therefore, searching for effective GSIs has become a key point in drug discovery. Areas covered: This review discusses the structure and function of GS and various types of GSIs. And this article seeks to give an overview of the patents or applications published from 2013 to 2015 in which novel chemical classes are claimed to inhibit the GS. Expert opinion: Firstly, further understanding the structure and function of GS to elucidate the disease mechanism and develop AD therapies is urgent. Secondly, if the bioequivalence, pharmacokinetics and selectivity can be improved greatly, some failed clinical inhibitors still can become the promising compounds for clinical trials. Thirdly, some weaknesses are exposed during the development of GSI, especially the insufficient potency, low brain penetration and poor selectivity. Finally, to find potent and selective GSI is the major direction in future. Moreover, to find new indications and dosing regimens in a trial of GSIs also can be seen as new ways.
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Affiliation(s)
- Kai Gu
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Qi Li
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Hongzhi Lin
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Jie Zhu
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Jun Mo
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Siyu He
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Xin Lu
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Xueyang Jiang
- b Key Laboratory of Biomedical Functional Materials, School of Science , China Pharmaceutical University , Nanjing , China
| | - Haopeng Sun
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
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10
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Paul TJ, Barman A, Ozbil M, Bora RP, Zhang T, Sharma G, Hoffmann Z, Prabhakar R. Mechanisms of peptide hydrolysis by aspartyl and metalloproteases. Phys Chem Chem Phys 2016; 18:24790-24801. [DOI: 10.1039/c6cp02097f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptide hydrolysis has been involved in a wide range of biological, biotechnological, and industrial applications.
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Affiliation(s)
- Thomas J. Paul
- Department of Chemistry
- University of Miami
- Coral Gables
- USA
| | - Arghya Barman
- Department of Chemistry
- University of Miami
- Coral Gables
- USA
| | - Mehmet Ozbil
- Department of Chemistry
- University of Miami
- Coral Gables
- USA
| | | | - Tingting Zhang
- Department of Chemistry
- University of Miami
- Coral Gables
- USA
| | - Gaurav Sharma
- Department of Chemistry
- University of Miami
- Coral Gables
- USA
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11
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Lessard CB, Cottrell BA, Maruyama H, Suresh S, Golde TE, Koo EH. γ-Secretase Modulators and APH1 Isoforms Modulate γ-Secretase Cleavage but Not Position of ε-Cleavage of the Amyloid Precursor Protein (APP). PLoS One 2015; 10:e0144758. [PMID: 26678856 PMCID: PMC4683055 DOI: 10.1371/journal.pone.0144758] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 11/23/2015] [Indexed: 12/30/2022] Open
Abstract
The relative increase in Aβ42 peptides from familial Alzheimer disease (FAD) linked APP and PSEN mutations can be related to changes in both ε-cleavage site utilization and subsequent step-wise cleavage. Cleavage at the ε-site releases the amyloid precursor protein (APP) intracellular domain (AICD), and perturbations in the position of ε-cleavage are closely associated with changes in the profile of amyloid β-protein (Aβ) species that are produced and secreted. The mechanisms by which γ-secretase modulators (GSMs) or FAD mutations affect the various γ-secretase cleavages to alter the generation of Aβ peptides have not been fully elucidated. Recent studies suggested that GSMs do not modulate ε-cleavage of APP, but the data were derived principally from recombinant truncated epitope tagged APP substrate. Here, using full length APP from transfected cells, we investigated whether GSMs modify the ε-cleavage of APP under more native conditions. Our results confirmed the previous findings that ε-cleavage is insensitive to GSMs. In addition, fenofibrate, an inverse GSM (iGSM), did not alter the position or kinetics of ε-cleavage position in vitro. APH1A and APH1B, a subunit of the γ-secretase complex, also modulated Aβ42/Aβ40 ratio without any alterations in ε-cleavage, a result in contrast to what has been observed with PS1 and APP FAD mutations. Consequently, GSMs and APH1 appear to modulate γ-secretase activity and Aβ42 generation by altering processivity but not ε-cleavage site utilization.
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Affiliation(s)
- Christian B. Lessard
- Department of Neurosciences, University of California San Diego, La Jolla, California, United States of America
| | - Barbara A. Cottrell
- Department of Neurosciences, University of California San Diego, La Jolla, California, United States of America
| | - Hiroko Maruyama
- Department of Neurosciences, University of California San Diego, La Jolla, California, United States of America
| | - Suraj Suresh
- Department of Neurosciences, University of California San Diego, La Jolla, California, United States of America
| | - Todd E. Golde
- Center for Translational Research in Neurodegenerative Disease, Department of Neuroscience, College of Medicine, University of Florida, Florida, United States of America
| | - Edward H. Koo
- Department of Neurosciences, University of California San Diego, La Jolla, California, United States of America
- Departments of Medicine and Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- * E-mail:
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12
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Ribeiro AJM, Santos-Martins D, Russo N, Ramos MJ, Fernandes PA. Enzymatic Flexibility and Reaction Rate: A QM/MM Study of HIV-1 Protease. ACS Catal 2015. [DOI: 10.1021/acscatal.5b00759] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- António J. M. Ribeiro
- UCBIO,
REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
- Dipartimento
di Chimica, Università della Calabria, 87036 Arcavacata
di Rende, Italia
| | - Diogo Santos-Martins
- UCBIO,
REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Nino Russo
- Dipartimento
di Chimica, Università della Calabria, 87036 Arcavacata
di Rende, Italia
| | - Maria J. Ramos
- UCBIO,
REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- UCBIO,
REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
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13
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Jang H, Arce FT, Ramachandran S, Kagan BL, Lal R, Nussinov R. Disordered amyloidogenic peptides may insert into the membrane and assemble into common cyclic structural motifs. Chem Soc Rev 2014; 43:6750-64. [PMID: 24566672 PMCID: PMC4143503 DOI: 10.1039/c3cs60459d] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Aggregation of disordered amyloidogenic peptides into oligomers is the causative agent of amyloid-related diseases. In solution, disordered protein states are characterized by heterogeneous ensembles. Among these, β-rich conformers self-assemble via a conformational selection mechanism to form energetically-favored cross-β structures, regardless of their precise sequences. These disordered peptides can also penetrate the membrane, and electrophysiological data indicate that they form ion-conducting channels. Based on these and additional data, including imaging and molecular dynamics simulations of a range of amyloid peptides, Alzheimer's amyloid-β (Aβ) peptide, its disease-related variants with point mutations and N-terminal truncated species, other amyloidogenic peptides, as well as a cytolytic peptide and a synthetic gel-forming peptide, we suggest that disordered amyloidogenic peptides can also present a common motif in the membrane. The motif consists of curved, moon-like β-rich oligomers associated into annular organizations. The motif is favored in the lipid bilayer since it permits hydrophobic side chains to face and interact with the membrane and the charged/polar residues to face the solvated channel pores. Such channels are toxic since their pores allow uncontrolled leakage of ions into/out of the cell, destabilizing cellular ionic homeostasis. Here we detail Aβ, whose aggregation is associated with Alzheimer's disease (AD) and for which there are the most abundant data. AD is a protein misfolding disease characterized by a build-up of Aβ peptide as senile plaques, neurodegeneration, and memory loss. Excessively produced Aβ peptides may directly induce cellular toxicity, even without the involvement of membrane receptors through Aβ peptide-plasma membrane interactions.
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Affiliation(s)
- Hyunbum Jang
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, U.S.A
| | - Fernando Teran Arce
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, U.S.A
| | - Srinivasan Ramachandran
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, U.S.A
| | - Bruce L. Kagan
- Department of Psychiatry, David Geffen School of Medicine, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, California 90024, U.S.A
| | - Ratnesh Lal
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, U.S.A
| | - Ruth Nussinov
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, U.S.A
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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14
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Barman A, Prabhakar R. Computational Insights into Substrate and Site Specificities, Catalytic Mechanism, and Protonation States of the Catalytic Asp Dyad of β -Secretase. SCIENTIFICA 2014; 2014:598728. [PMID: 25309776 PMCID: PMC4189502 DOI: 10.1155/2014/598728] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 06/21/2014] [Indexed: 06/04/2023]
Abstract
In this review, information regarding substrate and site specificities, catalytic mechanism, and protonation states of the catalytic Asp dyad of β-secretase (BACE1) derived from computational studies has been discussed. BACE1 catalyzes the rate-limiting step in the generation of Alzheimer amyloid beta peptide through the proteolytic cleavage of the amyloid precursor protein. Due to its biological functioning, this enzyme has been considered as one of the most important targets for finding the cure for Alzheimer's disease. Molecular dynamics (MD) simulations suggested that structural differences in the key regions (inserts A, D, and F and the 10s loop) of the enzyme are responsible for the observed difference in its activities towards the WT- and SW-substrates. The modifications in the flap, third strand, and insert F regions were found to be involved in the alteration in the site specificity of the glycosylphosphatidylinositol bound form of BACE1. Our QM and QM/MM calculations suggested that BACE1 hydrolyzed the SW-substrate more efficiently than the WT-substrate and that cleavage of the peptide bond occurred in the rate-determining step. The results from molecular docking studies showed that the information concerning a single protonation state of the Asp dyad is not enough to run an in silico screening campaign.
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Affiliation(s)
- Arghya Barman
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146, USA
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146, USA
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The Cleavage Domain of the Amyloid Precursor Protein Transmembrane Helix Does Not Exhibit Above-Average Backbone Dynamics. Chembiochem 2013; 14:1943-8. [DOI: 10.1002/cbic.201300322] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Indexed: 11/07/2022]
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Pester O, Barrett PJ, Hornburg D, Hornburg P, Pröbstle R, Widmaier S, Kutzner C, Dürrbaum M, Kapurniotu A, Sanders CR, Scharnagl C, Langosch D. The backbone dynamics of the amyloid precursor protein transmembrane helix provides a rationale for the sequential cleavage mechanism of γ-secretase. J Am Chem Soc 2013; 135:1317-29. [PMID: 23265086 PMCID: PMC3560327 DOI: 10.1021/ja3112093] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The etiology of Alzheimer's disease depends on the relative abundance of different amyloid-β (Aβ) peptide species. These peptides are produced by sequential proteolytic cleavage within the transmembrane helix of the 99 residue C-terminal fragment of the amyloid precursor protein (C99) by the intramembrane protease γ-secretase. Intramembrane proteolysis is thought to require local unfolding of the substrate helix, which has been proposed to be cleaved as a homodimer. Here, we investigated the backbone dynamics of the substrate helix. Amide exchange experiments of monomeric recombinant C99 and of synthetic transmembrane domain peptides reveal that the N-terminal Gly-rich homodimerization domain exchanges much faster than the C-terminal cleavage region. MD simulations corroborate the differential backbone dynamics, indicate a bending motion at a diglycine motif connecting dimerization and cleavage regions, and detect significantly different H-bond stabilities at the initial cleavage sites. Our results are consistent with the following hypotheses about cleavage of the substrate: First, the GlyGly hinge may precisely position the substrate within γ-secretase such that its catalytic center must start proteolysis at the known initial cleavage sites. Second, the ratio of cleavage products formed by subsequent sequential proteolysis could be influenced by differential extents of solvation and by the stabilities of H-bonds at alternate initial sites. Third, the flexibility of the Gly-rich domain may facilitate substrate movement within the enzyme during sequential proteolysis. Fourth, dimerization may affect substrate processing by decreasing the dynamics of the dimerization region and by increasing that of the C-terminal part of the cleavage region.
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Affiliation(s)
- Oxana Pester
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Paul J. Barrett
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee USA 37232-8725
| | - Daniel Hornburg
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Philipp Hornburg
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Rasmus Pröbstle
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Simon Widmaier
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Christoph Kutzner
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Milena Dürrbaum
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Aphrodite Kapurniotu
- Fachgebiet Peptidbiochemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
| | - Charles R. Sanders
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee USA 37232-8725
| | - Christina Scharnagl
- Fakultät für Physik E14, Technische Universität München, Maximus-von-Imhof-Forum 4, 85354 Freising, Germany
| | - Dieter Langosch
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
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Barman A, Prabhakar R. Elucidating the catalytic mechanism of β-secretase (BACE1): a quantum mechanics/molecular mechanics (QM/MM) approach. J Mol Graph Model 2013; 40:1-9. [PMID: 23337572 DOI: 10.1016/j.jmgm.2012.12.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 12/04/2012] [Accepted: 12/17/2012] [Indexed: 12/18/2022]
Abstract
In this quantum mechanics/molecular mechanics (QM/MM) study, the mechanisms of the hydrolytic cleavage of the Met2-Asp3 and Leu2-Asp3 peptide bonds of the amyloid precursor protein (WT-substrate) and its Swedish mutant (SW) respectively catalyzed by β-secretase (BACE1) have been investigated by explicitly including the electrostatic and steric effects of the protein environment in the calculations. BACE1 catalyzes the rate-determining step in the generation of Alzheimer amyloid beta peptides and is widely acknowledged as a promising therapeutic target. The general acid-base mechanism followed by the enzyme proceeds through the following two steps: (1) formation of the gem-diol intermediate and (2) cleavage of the peptide bond. The formation of the gem-diol intermediate occurs with the barriers of 19.6 and 16.1 kcal/mol for the WT- and SW-substrate respectively. The QM/MM energetics predict that with the barriers of 21.9 and 17.2 kcal/mol for the WT- and SW-substrate respectively the cleavage of the peptide bond occurs in the rate-determining step. The computed barriers are in excellent agreement with the measured barrier of ∼18.0 kcal/mol for the SW-substrate and in line with the experimental observation that the cleavage of this substrate is sixty times more efficient than the WT-substrate.
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Affiliation(s)
- Arghya Barman
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146, USA
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Brás NF, Ramos MJ, Fernandes PA. The catalytic mechanism of mouse renin studied with QM/MM calculations. Phys Chem Chem Phys 2012; 14:12605-13. [PMID: 22796659 DOI: 10.1039/c2cp41422h] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hypertension is a chronic condition that affects nearly 25% of adults worldwide. As the Renin-Angiotensin-Aldosterone System is implicated in the control of blood pressure and body fluid homeostasis, its combined blockage is an attractive therapeutic strategy currently in use for the treatment of several cardiovascular conditions. We have performed QM/MM calculations to study the mouse renin catalytic mechanism in atomistic detail, using the N-terminal His6-Asn14 segment of angiotensinogen as substrate. The enzymatic reaction (hydrolysis of the peptidic bond between residues in the 10th and 11th positions) occurs through a general acid/base mechanism and, surprisingly, it is characterized by three mechanistic steps: it begins with the creation of a first very stable tetrahedral gem-diol intermediate, followed by protonation of the peptidic bond nitrogen, giving rise to a second intermediate. In a final step the peptidic bond is completely cleaved and both gem-diol hydroxyl protons are transferred to the catalytic dyad (Asp32 and Asp215). The final reaction products are two separate peptides with carboxylic acid and amine extremities. The activation energy for the formation of the gem-diol intermediate was calculated as 23.68 kcal mol(-1), whereas for the other steps the values were 15.51 kcal mol(-1) and 14.40 kcal mol(-1), respectively. The rate limiting states were the reactants and the first transition state. The associated barrier (23.68 kcal mol(-1)) is close to the experimental values for the angiotensinogen substrate (19.6 kcal mol(-1)). We have also tested the influence of the density functional on the activation and reaction energies. All eight density functionals tested (B3LYP, B3LYP-D3, X3LYP, M06, B1B95, BMK, mPWB1K and B2PLYP) gave very similar results.
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Affiliation(s)
- Natércia F Brás
- REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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Barman A, Prabhakar R. Protonation states of the catalytic dyad of β-secretase (BACE1) in the presence of chemically diverse inhibitors: a molecular docking study. J Chem Inf Model 2012; 52:1275-87. [PMID: 22545704 DOI: 10.1021/ci200611t] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In this molecular docking study, the protonation states of the catalytic Asp dyad of the beta-secretase (BACE1) enzyme in the presence of eight chemically diverse inhibitors have been predicted. BACE1 catalyzes the rate-determining step in the generation of Alzheimer amyloid beta peptides and is widely considered as a promising therapeutic target. All the inhibitors were redocked into their corresponding X-ray structures using a combination of eight different protonation states of the Asp dyad for each inhibitor. Five inhibitors were primarily found to favor two different monoprotonated states, and the remaining three favor a dideprotonated state. In addition, five of them exhibited secondary preference for a diprotonated state. These results show that the knowledge of a single protonation state of the Asp dyad is not sufficient to search for the novel inhibitors of BACE1 and the most plausible state for each inhibitor must be determined prior to conducting in-silico screening.
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Affiliation(s)
- Arghya Barman
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146, USA
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Zhu Y, Obregon D, Hou H, Giunta B, Ehrhart J, Fernandez F, Mori T, Nikolic W, Zhao Y, Morgan D, Town T, Tan J. Mutant presenilin-1 deregulated peripheral immunity exacerbates Alzheimer-like pathology. J Cell Mol Med 2012; 15:327-38. [PMID: 19900216 PMCID: PMC2891003 DOI: 10.1111/j.1582-4934.2009.00962.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Mutations in the presenilin-1 (PS1) gene are independent causes of familial Alzheimer's disease (AD). AD patients have dysregulated immunity, and PS1 mutant mice exhibit abnormal systemic immune responses. To test whether immune function abnormality caused by a mutant human PS1 gene (mhPS1) could modify AD-like pathology, we reconstituted immune systems of AD model mice carrying a mutant human amyloid precursor protein gene (mhAPP; Tg2576 mice) or both mhAPP and mhPS1 genes (PSAPP mice) with allo-geneic bone marrow cells. Here, we report a marked reduction in amyloid-β (Aβ) levels, β-amyloid plaques and brain inflammatory responses in PSAPP mice following strain-matched wild-type PS1 bone marrow reconstitution. These effects occurred with immune switching from pro-inflammatory T helper (Th) 1 to anti-inflammatory Th2 immune responses in the periphery and in the brain, which likely instructed microglia to phagocytose and clear Aβ in an ex vivo assay. Conversely, Tg2576 mice displayed accelerated AD-like pathology when reconstituted with mhPS1 bone marrow. These data show that haematopoietic cells bearing the mhPS1 transgene exacerbate AD-like pathology, suggesting a novel therapeutic strategy for AD based on targeting PS1 in peripheral immune cells.
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Affiliation(s)
- Yuyan Zhu
- Rashid Laboratory for Developmental Neurobiology, Silver Child Development Center, College of Medicine, University of South Florida, Tampa, FL 33613, USA
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Mishra S, Caflisch A. Dynamics in the Active Site of β-Secretase: A Network Analysis of Atomistic Simulations. Biochemistry 2011; 50:9328-39. [DOI: 10.1021/bi2011948] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
| | - Amedeo Caflisch
- Department
of Biochemistry, University of Zurich, Zurich, Switzerland
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Zhu X, Barman A, Ozbil M, Zhang T, Li S, Prabhakar R. Mechanism of peptide hydrolysis by co-catalytic metal centers containing leucine aminopeptidase enzyme: a DFT approach. J Biol Inorg Chem 2011; 17:209-22. [PMID: 21918843 DOI: 10.1007/s00775-011-0843-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 08/30/2011] [Indexed: 11/28/2022]
Abstract
In this density functional theory study, reaction mechanisms of a co-catalytic binuclear metal center (Zn1-Zn2) containing enzyme leucine aminopeptidase for two different metal bridging nucleophiles (H(2)O and -OH) have been investigated. In addition, the effects of the substrate (L-leucine-p-nitroanilide → L-leucyl-p-anisidine) and metal (Zn1 → Mg and Zn2 → Co, i.e., Mg1-Zn2 and Mg1-Co2 variants) substitutions on the energetics of the mechanism have been investigated. The general acid/base mechanism utilizing a bicarbonate ion followed by this enzyme is divided into two steps: (1) the formation of the gem-diolate intermediate, and (2) the cleavage of the peptide bond. With the computed barrier of 17.8 kcal/mol, the mechanism utilizing a hydroxyl nucleophile was found to be in excellent agreement with the experimentally measured barrier of 18.7 kcal/mol. The rate-limiting step for reaction with L-leucine-p-nitroanilide is the cleavage of the peptide bond with a barrier of 17.8 kcal/mol. However, for L-leucyl-p-anisidine all steps of the mechanism were found to occur with similar barriers (18.0-19.0 kcal/mol). For the metallovariants, cleavage of the peptide bond occurs in the rate-limiting step with barriers of 17.8, 18.0, and 24.2 kcal/mol for the Zn1-Zn2, Mg1-Zn2, and Mg1-Co2 enzymes, respectively. The nature of the metal ion was found to affect only the creation of the gem-diolate intermediate, and after that all three enzymes follow essentially the same energetics. The results reported in this study have elucidated specific roles of both metal centers, the nucleophile, indirect ligands, and substrates in the catalytic functioning of this important class of binuclear metallopeptidases.
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Affiliation(s)
- Xiaoxia Zhu
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146, USA
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Computational insights into the development of novel therapeutic strategies for Alzheimer's disease. Future Med Chem 2011; 1:119-35. [PMID: 21426072 DOI: 10.4155/fmc.09.10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND β-amyloidosis and oxidative stress have been implicated as root causes of Alzheimer's disease (AD). Current potential therapeutic strategies for the treatment of AD include inhibition of amyloid β (Aβ) production, stimulation of Aβ degradation and prevention of Aβ oligomerization. However, efforts in this direction are hindered by the lack of understanding of the biochemical processes occurring at the atomic level in AD. DISCUSSION A radically different approach to achieve this goal would be the application of comprehensive theoretical and computational techniques such as molecular dynamics, quantum mechanics, hybrid quantum mechanics/molecular mechanics, bioinformatics and rotational spectroscopy to investigate complex chemical and physical processes in β-amyloidosis and the oxidative stress mechanism. CONCLUSION Results obtained from these studies will provide an atomic level understanding of biochemical processes occurring in AD and advance efforts to develop effective therapeutic strategies for this disease.
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Barman A, Schürer S, Prabhakar R. Computational modeling of substrate specificity and catalysis of the β-secretase (BACE1) enzyme. Biochemistry 2011; 50:4337-49. [PMID: 21500768 DOI: 10.1021/bi200081h] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
In this combined MD simulation and DFT study, interactions of the wild-type (WT) amyloid precursor protein (APP) and its Swedish variant (SW), Lys670 → Asn and Met671 → Leu, with the beta-secretase (BACE1) enzyme and their cleavage mechanisms have been investigated. BACE1 catalyzes the rate-limiting step in the generation of 40-42 amino acid long Alzheimer amyloid beta (Aβ) peptides. All key structural parameters such as position of the flap, volume of the active site, electrostatic binding energy, structures, and positions of the inserts A, D, and F and 10s loop obtained from the MD simulations show that, in comparison to the WT-substrate, BACE1 exhibits greater affinity for the SW-substrate and orients it in a more reactive conformation. The enzyme-substrate models derived from the MD simulations were further utilized to investigate the general acid/base mechanism used by BACE1 to hydrolytically cleave these substrates. This mechanism proceeds through the following two steps: (1) formation of the gem-diol intermediate and (2) cleavage of the peptide bond. For the WT-substrate, the overall barrier of 22.4 kcal/mol for formation of the gem-diol intermediate is 3.3 kcal/mol higher than for the SW-substrate (19.1 kcal/mol). This process is found to be the rate-limiting in the entire mechanism. The computed barrier is in agreement with the measured barrier of ca. 18.00 kcal/mol for the WT-substrate and supports the experimental observation that the cleavage of the SW-substrate is 60 times more efficient than the WT-substrate.
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Affiliation(s)
- Arghya Barman
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146, USA
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Ni Z, Jin X, Zhou P, Wu Q, Lin XF. A Combination of Computational and Experimental Approaches to Investigate the Binding Behavior of B.sub Lipase A Mutants with Substrate pNPP. Mol Inform 2011; 30:359-67. [PMID: 27466952 DOI: 10.1002/minf.201000110] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 01/29/2011] [Indexed: 11/09/2022]
Affiliation(s)
- Zhong Ni
- Department of Chemistry, Zhejiang University, Hangzhou 31002, P. R. China tel: +86 571 87952618, fax: +86 571 87951588
| | - Xin Jin
- Department of Chemistry, Zhejiang University, Hangzhou 31002, P. R. China tel: +86 571 87952618, fax: +86 571 87951588
| | - Peng Zhou
- Department of Chemistry, Zhejiang University, Hangzhou 31002, P. R. China tel: +86 571 87952618, fax: +86 571 87951588
| | - Qi Wu
- Department of Chemistry, Zhejiang University, Hangzhou 31002, P. R. China tel: +86 571 87952618, fax: +86 571 87951588
| | - Xian-Fu Lin
- Department of Chemistry, Zhejiang University, Hangzhou 31002, P. R. China tel: +86 571 87952618, fax: +86 571 87951588.
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Jang H, Teran Arce F, Ramachandran S, Capone R, Lal R, Nussinov R. Structural convergence among diverse, toxic beta-sheet ion channels. J Phys Chem B 2010; 114:9445-51. [PMID: 20608696 PMCID: PMC2908347 DOI: 10.1021/jp104073k] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Revised: 06/22/2010] [Indexed: 12/11/2022]
Abstract
Recent studies show that an array of beta-sheet peptides, including N-terminally truncated Abeta peptides (Abeta(11-42/17-42)), K3 (a beta(2)-microglobulin fragment), and protegrin-1 (PG-1) peptides form ion channel-like structures and elicit single channel ion conductance when reconstituted in lipid bilayers and induce cell damage through cell calcium overload. Striking similarities are observed in the dimensions of these toxic channels irrespective of their amino acid sequences. However, the intriguing question of preferred channel sizes is still unresolved. Here, exploiting ssNMR-based, U-shaped, beta-strand-turn-beta-strand coordinates, we modeled truncated Abeta peptide (p3) channels with different sizes (12- to 36-mer). Molecular dynamics (MD) simulations show that optimal channel sizes of the ion channels presenting toxic ionic flux range between 16- and 24-mer. This observation is in good agreement with channel dimensions imaged by AFM for Abeta(9-42), K3 fragment, and PG-1 channels and highlights the bilayer-supported preferred toxic beta-channel sizes and organization, regardless of the peptide sequence.
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Affiliation(s)
| | | | | | | | - Ratnesh Lal
- Corresponding authors. (R.N.) Phone: 301-846-5579. Fax: 301-846-5598. E-mail: . (R.L.) E-mail:
| | - Ruth Nussinov
- Corresponding authors. (R.N.) Phone: 301-846-5579. Fax: 301-846-5598. E-mail: . (R.L.) E-mail:
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Bora RP, Barman A, Zhu X, Ozbil M, Prabhakar R. Which One Among Aspartyl Protease, Metallopeptidase, and Artificial Metallopeptidase is the Most Efficient Catalyst in Peptide Hydrolysis? J Phys Chem B 2010; 114:10860-75. [DOI: 10.1021/jp104294x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Ram Prasad Bora
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Arghya Barman
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Xiaoxia Zhu
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Mehmet Ozbil
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
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Bora RP, Ozbil M, Prabhakar R. Elucidation of insulin degrading enzyme catalyzed site specific hydrolytic cleavage of amyloid β peptide: a comparative density functional theory study. J Biol Inorg Chem 2009; 15:485-95. [DOI: 10.1007/s00775-009-0617-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Accepted: 12/14/2009] [Indexed: 01/29/2023]
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Kreft AF, Martone R, Porte A. Recent advances in the identification of gamma-secretase inhibitors to clinically test the Abeta oligomer hypothesis of Alzheimer's disease. J Med Chem 2009; 52:6169-88. [PMID: 19694467 DOI: 10.1021/jm900188z] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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