1
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Trilling CR, Weng JH, Sharma PK, Nolte V, Wu J, Ma W, Boassa D, Taylor SS, Herberg FW. RedOx regulation of LRRK2 kinase activity by active site cysteines. NPJ Parkinsons Dis 2024; 10:75. [PMID: 38570484 PMCID: PMC10991482 DOI: 10.1038/s41531-024-00683-5] [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: 10/20/2023] [Accepted: 03/12/2024] [Indexed: 04/05/2024] Open
Abstract
Mutations of the human leucine-rich repeat kinase 2 (LRRK2) have been associated with both, idiopathic and familial Parkinson's disease (PD). Most of these pathogenic mutations are located in the kinase domain (KD) or GTPase domain of LRRK2. In this study we describe a mechanism in which protein kinase activity can be modulated by reversible oxidation or reduction, involving a unique pair of adjacent cysteines, the "CC" motif. Among all human protein kinases, only LRRK2 contains this "CC" motif (C2024 and C2025) in the Activation Segment (AS) of the kinase domain. In an approach combining site-directed mutagenesis, biochemical analyses, cell-based assays, and Gaussian accelerated Molecular Dynamics (GaMD) simulations we could attribute a role for each of those cysteines. We employed reducing and oxidizing agents with potential clinical relevance to investigate effects on kinase activity and microtubule docking. We find that each cysteine gives a distinct contribution: the first cysteine, C2024, is essential for LRRK2 protein kinase activity, while the adjacent cysteine, C2025, contributes significantly to redox sensitivity. Implementing thiolates (R-S-) in GaMD simulations allowed us to analyse how each of the cysteines in the "CC" motif interacts with its surrounding residues depending on its oxidation state. From our studies we conclude that oxidizing agents can downregulate kinase activity of hyperactive LRRK2 PD mutations and may provide promising tools for therapeutic strategies.
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Affiliation(s)
| | - Jui-Hung Weng
- Department of Pharmacology, University of California, San Diego, CA, USA
| | | | - Viktoria Nolte
- Department of Biochemistry, University of Kassel, Kassel, Germany
| | - Jian Wu
- Department of Pharmacology, University of California, San Diego, CA, USA
| | - Wen Ma
- Department of Physics, University of Vermont, Burlington, VT, USA
| | - Daniela Boassa
- National Center for Microscopy and Imaging Research, University of California, San Diego, CA, USA
- Department of Neurosciences, University of California, San Diego, CA, USA
| | - Susan S Taylor
- Department of Pharmacology, University of California, San Diego, CA, USA
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA
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2
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Jiang Y, Chiu TP, Mitra R, Rohs R. Probing the role of the protonation state of a minor groove-linker histidine in Exd-Hox-DNA binding. Biophys J 2024; 123:248-259. [PMID: 38130056 PMCID: PMC10808038 DOI: 10.1016/j.bpj.2023.12.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 09/22/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023] Open
Abstract
DNA recognition and targeting by transcription factors (TFs) through specific binding are fundamental in biological processes. Furthermore, the histidine protonation state at the TF-DNA binding interface can significantly influence the binding mechanism of TF-DNA complexes. Nevertheless, the role of histidine in TF-DNA complexes remains underexplored. Here, we employed all-atom molecular dynamics simulations using AlphaFold2-modeled complexes based on previously solved co-crystal structures to probe the role of the His-12 residue in the Extradenticle (Exd)-Sex combs reduced (Scr)-DNA complex when binding to Scr and Ultrabithorax (Ubx) target sites. Our results demonstrate that the protonation state of histidine notably affected the DNA minor-groove width profile and binding free energy. Examining flanking sequences of various binding affinities derived from SELEX-seq experiments, we analyzed the relationship between binding affinity and specificity. We uncovered how histidine protonation leads to increased binding affinity but can lower specificity. Our findings provide new mechanistic insights into the role of histidine in modulating TF-DNA binding.
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Affiliation(s)
- Yibei Jiang
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California
| | - Tsu-Pei Chiu
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California
| | - Raktim Mitra
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California
| | - Remo Rohs
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California; Department of Chemistry, University of Southern California, Los Angeles, California; Department of Physics and Astronomy, University of Southern California, Los Angeles, California; Thomas Lord Department of Computer Science, University of Southern California, Los Angeles, California.
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3
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Rahman A, Saikia B, Gogoi CR, Baruah A. Advances in the understanding of protein misfolding and aggregation through molecular dynamics simulation. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 175:31-48. [PMID: 36044970 DOI: 10.1016/j.pbiomolbio.2022.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Aberrant protein folding known as protein misfolding is counted as one of the striking factors of neurodegenerative diseases. The extensive range of pathologies caused by protein misfolding, aggregation and subsequent accumulation are mainly classified into either gain of function diseases or loss of function diseases. In order to seek for novel strategies for treatment and diagnosis of neurodegenerative diseases, insights into the mechanism of misfolding and aggregation is essential. A comprehensive knowledge on the factors influencing misfolding and aggregation is required as well. An extensive experimental study on protein aggregation is somewhat challenging due to the insoluble and noncrystalline nature of amyloid fibrils. Thus there has been a growing use of computational approaches including Monte Carlo simulation, docking simulation, molecular dynamics simulation in the study of protein misfolding and aggregation. The review presents a discussion on molecular dynamics simulation alone as to how it has emerged as a promising tool in the understanding of protein misfolding and aggregation in general, detailing upon three different aspects considering four misfold prone proteins in particular. It is noticeable that all four proteins considered in this review i.e prion, superoxide dismutase1, huntingtin and amyloid β are linked to chronic neurodegenerative diseases with debilitating effects. Initially the review elaborates on the factors influencing the misfolding and aggregation. Next, it addresses our current understanding of the amyloid structures and the associated aggregation mechanisms, finally, summarizing the contribution of this computational tool in the search for therapeutic strategies against the respective protein-deposition diseases.
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Affiliation(s)
- Aziza Rahman
- Department of Chemistry, Dibrugarh University, Dibrugarh, 786004, Assam, India
| | - Bondeepa Saikia
- Department of Chemistry, Dibrugarh University, Dibrugarh, 786004, Assam, India
| | - Chimi Rekha Gogoi
- Department of Chemistry, Dibrugarh University, Dibrugarh, 786004, Assam, India
| | - Anupaul Baruah
- Department of Chemistry, Dibrugarh University, Dibrugarh, 786004, Assam, India.
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4
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Bhate SH, Udgaonkar JB, Das R. Destabilization of polar interactions in the prion protein triggers misfolding and oligomerization. Protein Sci 2021; 30:2258-2271. [PMID: 34558139 DOI: 10.1002/pro.4188] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 12/25/2022]
Abstract
The prion protein (PrP) misfolds and oligomerizes at pH 4 in the presence of physiological salt concentrations. Low pH and salt cause structural perturbations in the monomeric prion protein that lead to misfolding and oligomerization. However, the changes in stability within different regions of the PrP prior to oligomerization are poorly understood. In this study, we have characterized the local stability in PrP at high resolution using amide temperature coefficients (TC ) measured by nuclear magnetic resonance (NMR) spectroscopy. The local stability of PrP was investigated under native as well as oligomerizing conditions. We have also studied the rapidly oligomerizing PrP variant (Q216R) and the protective PrP variant (A6). We report that at low pH, salt destabilizes PrP at several polar residues, and the hydrogen bonds in helices α2 and α3 are weakened. In addition, salt changes the curvature of the α3 helix, which likely disrupts α2-α3 contacts and leads to oligomerization. These results are corroborated by the TC values of rapidly oligomerizing Q216R-PrP. The poly-alanine substitution in A6-PrP stabilizes α2, which prevents oligomerization. Altogether, these results highlight the importance of native polar interactions in determining the stability of PrP and reveal the structural disruptions in PrP that lead to misfolding and oligomerization.
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Affiliation(s)
- Suhas H Bhate
- National Centre for Biological Sciences, TIFR, Bangalore, India
| | - Jayant B Udgaonkar
- National Centre for Biological Sciences, TIFR, Bangalore, India.,Indian Institute for Science Education and Research, Pune, India
| | - Ranabir Das
- National Centre for Biological Sciences, TIFR, Bangalore, India
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5
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Balogh RK, Németh E, Jones NC, Hoffmann SV, Jancsó A, Gyurcsik B. A study on the secondary structure of the metalloregulatory protein CueR: effect of pH, metal ions and DNA. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:491-500. [PMID: 33907862 DOI: 10.1007/s00249-021-01539-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/13/2021] [Accepted: 04/14/2021] [Indexed: 11/30/2022]
Abstract
The response of CueR towards environmental changes in solution was investigated. CueR is a bacterial metal ion selective transcriptional metalloregulator protein, which controls the concentration of copper ions in the cell. Although several articles have been devoted to the discussion of the structural and functional features of this protein, CueR has not previously been extensively characterized in solution. Here, we studied the effect of change in pH, temperature, and the presence of specific or non-specific binding partners on the secondary structure of CueR with circular dichroism (CD) spectroscopy. A rather peculiar reversible pH-dependent secondary structure transformation was observed, elucidated and supplemented with pKa estimation by PROPKA and CpHMD simulations suggesting an important role of His(76) and His(94) in this process. CD experiments revealed that the presence of DNA prevents this structural switch, suggesting that DNA locks CueR in the α-helical-rich form. In contrast to the non-cognate metal ions HgII, CdII and ZnII, the presence of the cognate AgI ion affects the secondary structure of CueR, most probably by stabilizing the metal ion and DNA-binding domains of the protein.
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Affiliation(s)
- Ria K Balogh
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, 6720, Hungary
| | - Eszter Németh
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, 6720, Hungary.,Institute of Enzymology, Genome Stability Research Group, Research Centre for Natural Sciences, Magyar tudósok körútja 2, Budapest, 1117, Hungary
| | - Nykola C Jones
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000, Aarhus C, Denmark
| | - Søren Vrønning Hoffmann
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000, Aarhus C, Denmark
| | - Attila Jancsó
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, 6720, Hungary
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, 6720, Hungary.
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6
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Myers R, Cembran A, Fernandez-Funez P. Insight From Animals Resistant to Prion Diseases: Deciphering the Genotype - Morphotype - Phenotype Code for the Prion Protein. Front Cell Neurosci 2020; 14:254. [PMID: 33013324 PMCID: PMC7461849 DOI: 10.3389/fncel.2020.00254] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 07/24/2020] [Indexed: 12/30/2022] Open
Abstract
Prion diseases are a group of neurodegenerative diseases endemic in humans and several ruminants caused by the misfolding of native prion protein (PrP) into pathological conformations. Experimental work and the mad-cow epidemic of the 1980s exposed a wide spectrum of animal susceptibility to prion diseases, including a few highly resistant animals: horses, rabbits, pigs, and dogs/canids. The variable susceptibility to disease offers a unique opportunity to uncover the mechanisms governing PrP misfolding, neurotoxicity, and transmission. Previous work indicates that PrP-intrinsic differences (sequence) are the main contributors to disease susceptibility. Several residues have been cited as critical for encoding PrP conformational stability in prion-resistant animals, including D/E159 in dog, S167 in horse, and S174 in rabbit and pig PrP (all according to human numbering). These amino acids alter PrP properties in a variety of assays, but we still do not clearly understand the structural correlates of PrP toxicity. Additional insight can be extracted from comparative structural studies, followed by molecular dynamics simulations of selected mutations, and testing in manipulable animal models. Our working hypothesis is that protective amino acids generate more compact and stable structures in a C-terminal subdomain of the PrP globular domain. We will explore this idea in this review and identify subdomains within the globular domain that may hold the key to unravel how conformational stability and disease susceptibility are encoded in PrP.
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Affiliation(s)
- Ryan Myers
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, United States
| | - Alessandro Cembran
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, United States
| | - Pedro Fernandez-Funez
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, United States
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7
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Xu Z, Liu H, Wang S, Zhang Q, Yao X, Zhou S, Liu H. Unraveling the Molecular Mechanism of Prion H2 C-Terminus Misfolding by Metadynamics Simulations. ACS Chem Neurosci 2020; 11:772-782. [PMID: 32023408 DOI: 10.1021/acschemneuro.9b00679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Conformational transition from the normal cellular form of prion protein (PrPC) to the pathogenic "scrapie" form (PrPSc) is considered to be a key event in the occurrence of prion disease. Additionally, the H2 C-terminus is widely considered to be a vital site for PrP conformational transition, which can be used as an important region to explore the potential mechanism of PrP misfolding. Therefore, to study the misfolding mechanism of PrP, 500 ns well-tempered metadynamics simulations were performed by focusing on the H2 C-terminus of PrP. For comparison, three systems were designed in total, including PrP in neutral and acidic conditions, as well as H187R mutant. The resulting free energy surfaces (FESs) obtained from metadynamics simulations reveal that acidic conditions and H187R mutation can facilitate PrP misfolding by decreasing free energy barriers for conformational transition and forming energy stable conformational states. Further analyses aimed at H2 C-terminus show that due to the increase of positive charge on residue 187 in both acidic and H187R systems, the electrostatic repulsion of residue 187 and R136/R156 increases greatly, which disrupts the electrostatic interaction network around H2 C-terminus and exposes the hydrophobic core to the solvent. Taken together, acidic conditions and H187R mutation can accelerate PrP misfolding mainly by forming more energetically stable metastable conformations with lower free energy barriers, and electrostatic network disruption involving residue 187 drives the initial misfolding of H2 C-terminus. This study provides quantitative insight into the related function of the H2 C-terminus in the PrP misfolding process, which may guide H2 C-terminus mediated drug design in the future.
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Affiliation(s)
- Zerong Xu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Hongli Liu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Shuo Wang
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Qianqian Zhang
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Xiaojun Yao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
| | - Shuangyan Zhou
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
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8
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Conceição RA, Ascari LM, Ferreira NC, Goes CF, Matos CO, Pinheiro AS, Alves MA, Souza AMT, Maia RC, Caughey B, Cordeiro Y, Barbosa MLC. Synthesis and in silico and in vitro evaluation of trimethoxy-benzamides designed as anti-prion derivatives. Med Chem Res 2019. [DOI: 10.1007/s00044-019-02441-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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9
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Mondal B, Reddy G. A Transient Intermediate Populated in Prion Folding Leads to Domain Swapping. Biochemistry 2019; 59:114-124. [DOI: 10.1021/acs.biochem.9b00621] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Balaka Mondal
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, Karnataka India, 560012
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, Karnataka India, 560012
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10
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Conformation and Domain Movement Analysis of Human Matrix Metalloproteinase-2: Role of Associated Zn 2+ and Ca 2+ Ions. Int J Mol Sci 2019; 20:ijms20174194. [PMID: 31461891 PMCID: PMC6747341 DOI: 10.3390/ijms20174194] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/20/2019] [Accepted: 08/26/2019] [Indexed: 12/23/2022] Open
Abstract
Matrix metaloproteinase-2 (MMP-2) is an extracellular Zn2+ protease specific to type I and IV collagens. Its expression is associated with several inflammatory, degenerative, and malignant diseases. Conformational properties, domain movements, and interactions between MMP-2 and its associated metal ions were characterized using a 1.0 µs molecular dynamics simulation. Dihedral principle component analysis revealed ten families of conformations with the greatest degree of variability occurring in the link region connecting the catalytic and hemopexin domains. Dynamic cross-correlation analysis indicated domain movements corresponding to the opening and closing of the hemopexin domain in relation to the fibronectin and catalytic domains facilitated by the link region. Interaction energies were calculated using the molecular mechanics Poisson Boltzman surface area-interaction entropy (MMPBSA-IE) analysis method and revealed strong binding energies for the catalytic Zn2+ ion 1, Ca2+ ion 1, and Ca2+ ion 3 with significant conformational stability at the binding sites of Zn2+ ion 1 and Ca2+ ion 1. Ca2+ ion 2 diffuses freely away from its crystallographically defined binding site. Zn2+ ion 2 plays a minor role in conformational stability of the catalytic domain while Ca2+ ion 3 is strongly attracted to the highly electronegative sidechains of the Asp residues around the central β-sheet core of the hemopexin domain; however, the interacting residue sidechain carboxyl groups are outside of Ca2+ ion 3′s coordination sphere.
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11
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Medina E, Villalobos P, Coñuecar R, Ramírez-Sarmiento CA, Babul J. The protonation state of an evolutionarily conserved histidine modulates domainswapping stability of FoxP1. Sci Rep 2019; 9:5441. [PMID: 30931977 PMCID: PMC6443806 DOI: 10.1038/s41598-019-41819-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 03/13/2019] [Indexed: 11/12/2022] Open
Abstract
Forkhead box P (FoxP) proteins are members of the versatile Fox transcription factors, which control the timing and expression of multiple genes for eukaryotic cell homeostasis. Compared to other Fox proteins, they can form domain-swapped dimers through their DNA-binding –forkhead– domains, enabling spatial reorganization of distant chromosome elements by tethering two DNA molecules together. Yet, domain swapping stability and DNA binding affinity varies between different FoxP proteins. Experimental evidence suggests that the protonation state of a histidine residue conserved in all Fox proteins is responsible for pH-dependent modulation of these interactions. Here, we explore the consequences of the protonation state of another histidine (H59), only conserved within FoxM/O/P subfamilies, on folding and dimerization of the forkhead domain of human FoxP1. Dimer dissociation kinetics and equilibrium unfolding experiments demonstrate that protonation of H59 leads to destabilization of the domain-swapped dimer due to an increase in free energy difference between the monomeric and transition states. This pH–dependence is abolished when H59 is mutated to alanine. Furthermore, anisotropy measurements and molecular dynamics evidence that H59 has a direct impact in the local stability of helix H3. Altogether, our results highlight the relevance of H59 in domain swapping and folding stability of FoxP1.
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Affiliation(s)
- Exequiel Medina
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, 7800003, Chile
| | - Pablo Villalobos
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, 7800003, Chile
| | - Ricardo Coñuecar
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, 7800003, Chile
| | - César A Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Santiago, 7820436, Chile.
| | - Jorge Babul
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, 7800003, Chile.
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12
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Moulick R, Goluguri RR, Udgaonkar JB. Ruggedness in the Free Energy Landscape Dictates Misfolding of the Prion Protein. J Mol Biol 2019; 431:807-824. [DOI: 10.1016/j.jmb.2018.12.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 11/15/2018] [Accepted: 12/16/2018] [Indexed: 12/12/2022]
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13
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Thompson HN, Thompson CE, Andrade Caceres R, Dardenne LE, Netz PA, Stassen H. Prion protein conversion triggered by acidic condition: a molecular dynamics study through different force fields. J Comput Chem 2018; 39:2000-2011. [DOI: 10.1002/jcc.25380] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 05/15/2018] [Accepted: 05/26/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Helen Nathalia Thompson
- Departamento de Físico-Química, Instituto de Química; Universidade Federal do Rio Grande do Sul; 91501-970 Porto Alegre Rio Grande do Sul Brazil
| | - Claudia Elizabeth Thompson
- Departamento de Farmacociências; Universidade Federal de Ciências da Saúde de Porto Alegre; 90050-170 Porto Alegre Rio Grande do Sul Brazil
| | - Rafael Andrade Caceres
- Departamento de Farmacociências; Universidade Federal de Ciências da Saúde de Porto Alegre; 90050-170 Porto Alegre Rio Grande do Sul Brazil
| | | | - Paulo Augusto Netz
- Departamento de Físico-Química, Instituto de Química; Universidade Federal do Rio Grande do Sul; 91501-970 Porto Alegre Rio Grande do Sul Brazil
| | - Hubert Stassen
- Departamento de Físico-Química, Instituto de Química; Universidade Federal do Rio Grande do Sul; 91501-970 Porto Alegre Rio Grande do Sul Brazil
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14
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Gao Y, Zhu T, Zhang C, Zhang JZ, Mei Y. Comparison of the unfolding and oligomerization of human prion protein under acidic and neutral environments by molecular dynamics simulations. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.07.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Unraveling the differential structural stability and dynamics features of T7 endolysin partially folded conformations. Biochim Biophys Acta Gen Subj 2018; 1862:924-935. [DOI: 10.1016/j.bbagen.2018.01.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 01/03/2018] [Accepted: 01/08/2018] [Indexed: 01/21/2023]
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16
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Bamdad K. Sequence-dependent dynamical instability of the human prion protein: a comparative simulation study. J Biomol Struct Dyn 2017; 36:3023-3033. [PMID: 28868991 DOI: 10.1080/07391102.2017.1375430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The present study aimed to explore the most probable regions of the human prion protein backbone for which the initial steps of conformational transitions as a result of intrinsic and extrinsic perturbing factors on the protein structure can be assigned. A total of 0.3-μs molecular dynamics simulations on several analog structures of the protein have been performed. To mimic the impact of the extrinsic and intrinsic destructive parameters on the dynamical characteristics of the protein, mild acidic conditions and R208H mutation have been simulated. The findings indicated that distribution of conformational flexibilities along the protein chain was almost independent of the induced perturbing factors, and was mostly centralized on certain distinct parts of the structure comprising residues 132-145 and 187-203. Analyses also revealed that the segment comprising residues 187-203 may be considered as a peptide sequence, possessing high potential to start the initial steps of conformational rearrangements due to the induced physicochemical alterations. Sequence alignment and molecular dynamics data also revealed that segment 178-203 prefers to accommodate in extended structures rather than α-helices. Region 178-203 may be considered as a peptide switch capable of initiating the conformational transitions due to the introduced modifications and perturbing parameters.
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Affiliation(s)
- Kourosh Bamdad
- a Department of Biology, Faculty of Science , Payame Noor University (PNU) , 19395-3697 , Iran
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17
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Malevanets A, Chong PA, Hansen DF, Rizk P, Sun Y, Lin H, Muhandiram R, Chakrabartty A, Kay LE, Forman-Kay JD, Wodak SJ. Interplay of buried histidine protonation and protein stability in prion misfolding. Sci Rep 2017; 7:882. [PMID: 28408762 PMCID: PMC5429843 DOI: 10.1038/s41598-017-00954-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 03/20/2017] [Indexed: 12/03/2022] Open
Abstract
Misofolding of mammalian prion proteins (PrP) is believed to be the cause of a group of rare and fatal neurodegenerative diseases. Despite intense scrutiny however, the mechanism of the misfolding reaction remains unclear. We perform nuclear Magnetic Resonance and thermodynamic stability measurements on the C-terminal domains (residues 90–231) of two PrP variants exhibiting different pH-induced susceptibilities to aggregation: the susceptible hamster prion (GHaPrP) and its less susceptible rabbit homolog (RaPrP). The pKa of histidines in these domains are determined from titration experiments, and proton-exchange rates are measured at pH 5 and pH 7. A single buried highly conserved histidine, H187/H186 in GHaPrP/RaPrP, exhibited a markedly down shifted pKa ~5 for both proteins. However, noticeably larger pH-induced shifts in exchange rates occur for GHaPrP versus RaPrP. Analysis of the data indicates that protonation of the buried histidine destabilizes both PrP variants, but produces a more drastic effect in the less stable GHaPrP. This interpretation is supported by urea denaturation experiments performed on both PrP variants at neutral and low pH, and correlates with the difference in disease susceptibility of the two species, as expected from the documented linkage between destabilization of the folded state and formation of misfolded and aggregated species.
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Affiliation(s)
- Anatoly Malevanets
- Program in Molecular Structure and Function, Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1A8, Canada
| | - P Andrew Chong
- Program in Molecular Structure and Function, Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1A8, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - D Flemming Hansen
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,University College London, Division of Biosciences, London, WC1E 6BT, UK
| | - Paul Rizk
- Program in Molecular Structure and Function, Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1A8, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Yulong Sun
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 2M9, Canada
| | - Hong Lin
- Program in Molecular Structure and Function, Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1A8, Canada
| | - Ranjith Muhandiram
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Avi Chakrabartty
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 2M9, Canada
| | - Lewis E Kay
- Program in Molecular Structure and Function, Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1A8, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada
| | - Julie D Forman-Kay
- Program in Molecular Structure and Function, Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1A8, Canada. .,Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.
| | - Shoshana J Wodak
- Program in Molecular Structure and Function, Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1A8, Canada. .,Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada. .,VIB Structural Biology Research Center, VUB, Pleinlaan 2, 1050, Brussels, Belgium.
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18
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Moulick R, Udgaonkar JB. Identification and Structural Characterization of the Precursor Conformation of the Prion Protein which Directly Initiates Misfolding and Oligomerization. J Mol Biol 2017; 429:886-899. [DOI: 10.1016/j.jmb.2017.01.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/19/2017] [Accepted: 01/19/2017] [Indexed: 12/11/2022]
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19
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Chamachi NG, Chakrabarty S. Temperature-Induced Misfolding in Prion Protein: Evidence of Multiple Partially Disordered States Stabilized by Non-Native Hydrogen Bonds. Biochemistry 2017; 56:833-844. [DOI: 10.1021/acs.biochem.6b01042] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Neharika G. Chamachi
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Suman Chakrabarty
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
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20
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Singh RK, Chamachi NG, Chakrabarty S, Mukherjee A. Mechanism of Unfolding of Human Prion Protein. J Phys Chem B 2017; 121:550-564. [PMID: 28030950 DOI: 10.1021/acs.jpcb.6b11416] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Misfolding and aggregation of prion proteins are associated with several neurodegenerative diseases. Therefore, understanding the mechanism of the misfolding process is of enormous interest in the scientific community. It has been speculated and widely discussed that the native cellular prion protein (PrPC) form needs to undergo substantial unfolding to a more stable PrPC* state, which may further oligomerize into the toxic scrapie (PrPSc) form. Here, we have studied the mechanism of the unfolding of the human prion protein (huPrP) using a set of extensive well-tempered metadynamics simulations. Through multiple microsecond-long metadynamics simulations, we find several possible unfolding pathways. We show that each pathway leads to an unfolded state of lower free energy than the native state. Thus, our study may point to the signature of a PrPC* form that corresponds to a global minimum on the conformational free-energy landscape. Moreover, we find that these global minima states do not involve an increased β-sheet content, as was assumed to be a signature of PrPSc formation in previous simulation studies. We have further analyzed the origin of metastability of the PrPC form through free-energy surfaces of the chopped helical segments to show that the helices, particularly H2 and H3 of the prion protein, have the tendency to form either a random coil or a β-structure. Therefore, the secondary structural elements of the prion protein are only weakly stabilized by tertiary contacts and solvation forces so that relatively weak perturbations induced by temperature, pressure, pH, and so forth can lead to substantial unfolding with characteristics of intrinsically disordered proteins.
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Affiliation(s)
- Reman K Singh
- Department of Chemistry, Indian Institute of Science Education and Research , Pune 411008, Maharashtra, India
| | - Neharika G Chamachi
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Pune 411008, Maharashtra, India
| | - Suman Chakrabarty
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Pune 411008, Maharashtra, India
| | - Arnab Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research , Pune 411008, Maharashtra, India
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21
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Understanding the Effect of Disease-Related Mutations on Human Prion Protein Structure: Insights From NMR Spectroscopy. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2017; 150:83-103. [DOI: 10.1016/bs.pmbts.2017.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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22
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Structural Modeling of Human Prion Protein's Point Mutations. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2017; 150:105-122. [DOI: 10.1016/bs.pmbts.2017.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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23
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Awoonor-Williams E, Rowley CN. Evaluation of Methods for the Calculation of the pKa of Cysteine Residues in Proteins. J Chem Theory Comput 2016; 12:4662-73. [DOI: 10.1021/acs.jctc.6b00631] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ernest Awoonor-Williams
- Department of Chemistry, Memorial University of Newfoundland, St.
John’s, Newfoundland and Labrador A1B 3X9, Canada
| | - Christopher N. Rowley
- Department of Chemistry, Memorial University of Newfoundland, St.
John’s, Newfoundland and Labrador A1B 3X9, Canada
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24
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Singh J, Udgaonkar JB. Unraveling the Molecular Mechanism of pH-Induced Misfolding and Oligomerization of the Prion Protein. J Mol Biol 2016; 428:1345-1355. [PMID: 26854758 DOI: 10.1016/j.jmb.2016.01.030] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 01/27/2016] [Accepted: 01/28/2016] [Indexed: 12/31/2022]
Abstract
The misfolding of the prion protein (PrP) to aggregated forms is linked to several neurodegenerative diseases. Misfolded oligomeric forms of PrP are associated with neurotoxicity and/or infectivity, but the molecular mechanism by which they form is still poorly understood. A reduction in pH is known to be a key factor that triggers misfolded oligomer formation by PrP, but the residues whose protonation is linked with misfolding remain unidentified. The structural consequences of the protonation of these residues also remain to be determined. In the current study, amino acid residues whose protonation is critical for PrP misfolding and oligomerization have been identified using site-directed mutagenesis and misfolding/oligomerization assays. It is shown that the protonation of either H186 or D201, which mimics the effects of pathogenic mutations (H186R and D201N) at both residue sites, is critically linked to the stability, misfolding and oligomerization of PrP. Hydrogen-deuterium exchange studies coupled with mass spectrometry show that the protonation of either H186 or D201 leads to the same common structural change: increased structural dynamics in helix 1 and that in the loop between helix 1 and β-strand 2. It is shown that the protonation of either of these residues is sufficient for accelerating misfolded oligomer formation, most likely because the protonation of either residue causes the same structural perturbation. Hence, the increased structural dynamics in helix 1 and that in the loop between helix 1 and β-strand 2 appear to play an early critical role in acid-induced misfolding of PrP.
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Affiliation(s)
- Jogender Singh
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Jayant B Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India.
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25
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Moulick R, Das R, Udgaonkar JB. Partially Unfolded Forms of the Prion Protein Populated under Misfolding-promoting Conditions: CHARACTERIZATION BY HYDROGEN EXCHANGE MASS SPECTROMETRY AND NMR. J Biol Chem 2015; 290:25227-40. [PMID: 26306043 DOI: 10.1074/jbc.m115.677575] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Indexed: 12/16/2022] Open
Abstract
The susceptibility of the cellular prion protein (PrP(C)) to convert to an alternative misfolded conformation (PrP(Sc)), which is the key event in the pathogenesis of prion diseases, is indicative of a conformationally flexible native (N) state. In the present study, hydrogen-deuterium exchange (HDX) in conjunction with mass spectrometry and nuclear magnetic resonance spectroscopy were used for the structural and energetic characterization of the N state of the full-length mouse prion protein, moPrP(23-231), under conditions that favor misfolding. The kinetics of HDX of 34 backbone amide hydrogens in the N state were determined at pH 4. In contrast to the results of previous HDX studies on the human and Syrian hamster prion proteins at a higher pH, various segments of moPrP were found to undergo different extents of subglobal unfolding events at pH 4, a pH at which the protein is known to be primed to misfold to a β-rich conformation. No residual structure around the disulfide bond was observed for the unfolded state at pH 4. The N state of the prion protein was observed to be at equilibrium with at least two partially unfolded forms (PUFs). These PUFs, which are accessed by stochastic fluctuations of the N state, have altered surface area exposure relative to the N state. One of these PUFs resembles a conformation previously implicated to be an initial intermediate in the conversion of monomeric protein into misfolded oligomer at pH 4.
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Affiliation(s)
- Roumita Moulick
- From the National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Ranabir Das
- From the National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Jayant B Udgaonkar
- From the National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
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26
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Singh J, Udgaonkar JB. Molecular Mechanism of the Misfolding and Oligomerization of the Prion Protein: Current Understanding and Its Implications. Biochemistry 2015; 54:4431-42. [PMID: 26171558 DOI: 10.1021/acs.biochem.5b00605] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Prion diseases, also known as transmissible spongiform encephalopathies, make up a group of fatal neurodegenerative disorders linked with the misfolding and aggregation of the prion protein (PrP). Although it is not yet understood how the misfolding of PrP induces neurodegeneration, it is widely accepted that the formation of misfolded prion protein (termed PrP(Sc)) is both the triggering event in the disease and the main component of the infectious agent responsible for disease transmission. Despite the clear involvement of PrP(Sc) in prion diseases, the exact composition of PrP(Sc) is not yet well-known. Recent studies show that misfolded oligomers of PrP could, however, be responsible for neurotoxicity and/or infectivity in the prion diseases. Hence, understanding the molecular mechanism of formation of the misfolded oligomers of PrP is critical for developing an understanding about the prion diseases and for developing anti-prion therapeutics. This review discusses recent advances in understanding the molecular mechanism of misfolded oligomer formation by PrP and its implications for the development of anti-prion therapeutics.
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Affiliation(s)
- Jogender Singh
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Jayant B Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
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27
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Flannelly DF, Aoki TG, Aristilde L. Short-time dynamics of pH-dependent conformation and substrate binding in the active site of beta-glucosidases: A computational study. J Struct Biol 2015; 191:352-64. [PMID: 26160737 DOI: 10.1016/j.jsb.2015.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 06/17/2015] [Accepted: 07/03/2015] [Indexed: 12/25/2022]
Abstract
The complete degradation of cellulose to glucose is essential to carbon turnover in terrestrial ecosystems and to engineered biofuel production. A rate-limiting step in this pathway is catalyzed by beta-glucosidase (BG) enzymes, which convert cellulobiose into two glucose molecules. The activity of these enzymes has been shown to vary with solution pH. However, it is not well understood how pH influences the enzyme conformation required for catalytic action on the substrate. A structural understanding of this pH effect is important for predicting shifts in BG activity in bioreactors and environmental matrices, in addition to informing targeted protein engineering. Here we applied molecular dynamics simulations to explore conformational and substrate binding dynamics in two well-characterized BGs of bacterial (Clostridium cellulovorans) and fungal (Trichoderma reesei) origins as a function of pH. The enzymes were simulated in an explicit solvated environment, with NaCl as electrolytes, at their prominent ionization states obtained at pH 5, 6, 7, and 7.5. Our findings indicated that pH-dependent changes in the ionization states of non-catalytic residues localized outside of the immediate active site led to pH-dependent disruption of the active site conformation. This disruption interferes with favorable H-bonding interactions with catalytic residues required to initiate catalysis on the substrate. We also identified specific non-catalytic residues that are involved in stabilizing the substrate at the optimal pH for enzyme activity. The simulations further revealed the dynamics of water-bridging interactions both outside and inside the substrate binding cleft during structural changes in the enzyme-substrate complex. These findings provide new structural insights into the pH-dependent substrate binding specificity in BGs.
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Affiliation(s)
- David F Flannelly
- The Institute for Comparative and Environmental Toxicology, College of Agricultural and Life Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Thalia G Aoki
- Department of Biological and Environmental Engineering, College of Agricultural and Life Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Ludmilla Aristilde
- The Institute for Comparative and Environmental Toxicology, College of Agricultural and Life Sciences, Cornell University, Ithaca, NY 14853, USA; Department of Biological and Environmental Engineering, College of Agricultural and Life Sciences, Cornell University, Ithaca, NY 14853, USA.
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28
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Hadži S, Ondračka A, Jerala R, Hafner‐Bratkovič I. Pathological mutations H187R and E196K facilitate subdomain separation and prion protein conversion by destabilization of the native structure. FASEB J 2014; 29:882-93. [DOI: 10.1096/fj.14-255646] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- San Hadži
- Department of BiotechnologyNational Institute of ChemistryLjubljanaSlovenia
| | - Andrej Ondračka
- Department of BiotechnologyNational Institute of ChemistryLjubljanaSlovenia
| | - Roman Jerala
- Department of BiotechnologyNational Institute of ChemistryLjubljanaSlovenia
- EN‐FIST Centre of ExcellenceLjubljanaSlovenia
| | - Iva Hafner‐Bratkovič
- Department of BiotechnologyNational Institute of ChemistryLjubljanaSlovenia
- EN‐FIST Centre of ExcellenceLjubljanaSlovenia
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29
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Structural and dynamic properties of the human prion protein. Biophys J 2014; 106:1152-63. [PMID: 24606939 DOI: 10.1016/j.bpj.2013.12.053] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 12/11/2013] [Accepted: 12/26/2013] [Indexed: 11/23/2022] Open
Abstract
Prion diseases involve the conformational conversion of the cellular prion protein (PrP(C)) to its misfolded pathogenic form (PrP(Sc)). To better understand the structural mechanism of this conversion, we performed extensive all-atom, explicit-solvent molecular-dynamics simulations for three structures of the wild-type human PrP (huPrP) at different pH values and temperatures. Residue 129 is polymorphic, being either Met or Val. Two of the three structures have Met in position 129 and the other has Val. Lowering the pH or raising the temperature induced large conformational changes of the C-terminal globular domain and increased exposure of its hydrophobic core. In some simulations, HA and its preceding S1-HA loop underwent large displacements. The C-terminus of HB was unstable and sometimes partially unfolded. Two hydrophobic residues, Phe-198 and Met-134, frequently became exposed to solvent. These conformational changes became more dramatic at lower pH or higher temperature. Furthermore, Tyr-169 and the S2-HB loop, or the X-loop, were different in the starting structures but converged to common conformations in the simulations for the Met-129, but not the Val-129, protein. α-Strands and β-strands formed in the initially unstructured N-terminus. α-Strand propensity in the N-terminus was different between the Met-129 and Val129 proteins, but β-strand propensity was similar. This study reveals detailed structural and dynamic properties of huPrP, providing insight into the mechanism of the conversion of PrP(C) to PrP(Sc).
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30
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Yamamoto N. Hot Spot of Structural Ambivalence in Prion Protein Revealed by Secondary Structure Principal Component Analysis. J Phys Chem B 2014; 118:9826-33. [DOI: 10.1021/jp5034245] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Norifumi Yamamoto
- Department of Life and Environmental
Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino 275-0016, Japan
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31
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Pagadala NS, Perez-Pineiro R, Wishart DS, Tuszynski JA. In silico studies and fluorescence binding assays of potential anti-prion compounds reveal an important binding site for prion inhibition from PrP(C) to PrP(Sc). Eur J Med Chem 2014; 91:118-31. [PMID: 25042003 DOI: 10.1016/j.ejmech.2014.07.045] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 07/09/2014] [Accepted: 07/14/2014] [Indexed: 01/28/2023]
Abstract
To understand the pharmacophore properties of 2-aminothiazoles and design novel inhibitors against the prion protein, a highly predictive 3D quantitative structure-activity relationship (QSAR) has been developed by performing comparative molecular field analysis (CoMFA) and comparative similarity analysis (CoMSIA). Both CoMFA and CoMSIA maps reveal the presence of the oxymethyl groups in meta and para positions on the phenyl ring of compound 17 (N-[4-(3,4-dimethoxyphenyl)-1,3-thiazol-2-yl]quinolin-2-amine), is necessary for activity while electro-negative nitrogen of quinoline is highly favorable to enhance activity. The blind docking results for these compounds show that the compound with quinoline binds with higher affinity than isoquinoline and naphthalene groups. Out of 150 novel compounds retrieved using finger print analysis by pharmacophoric model predicted based on five test sets of compounds, five compounds with diverse scaffolds were selected for biological evaluation as possible PrP inhibitors. Molecular docking combined with fluorescence quenching studies show that these compounds bind to pocket-D of SHaPrP near Trp145. The new antiprion compounds 3 and 6, which bind with the interaction energies of -12.1 and -13.2 kcal/mol, respectively, show fluorescence quenching with binding constant (Kd) values of 15.5 and 44.14 μM, respectively. Further fluorescence binding assays with compound 5, which is similar to 2-aminothiazole as a positive control, also show that the molecule binds to the pocket-D with the binding constant (Kd) value of 84.7 μM. Finally, both molecular docking and a fluorescence binding assay of noscapine as a negative control reveals the same binding site on the surface of pocket-A near a rigid loop between β2 and α2 interacting with Arg164. This high level of correlation between molecular docking and fluorescence quenching studies confirm that these five compounds are likely to act as inhibitors for prion propagation while noscapine might act as a prion accelerator from PrP(C) to PrP(Sc).
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Affiliation(s)
- Nataraj S Pagadala
- Department of Medical Microbiology and Immunology, 6-020 Katz Group Centre, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Rolando Perez-Pineiro
- Departments of Biological Sciences, and Computing Science, University of Alberta, Edmonton, Alberta T6G 2E8, Canada
| | - David S Wishart
- Departments of Biological Sciences, and Computing Science, University of Alberta, Edmonton, Alberta T6G 2E8, Canada
| | - Jack A Tuszynski
- Department of Physics, University of Alberta, Edmonton, Alberta T6G 2J1, Canada.
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32
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The role of Cys179–Cys214 disulfide bond in the stability and folding of prion protein: insights from molecular dynamics simulations. J Mol Model 2014; 20:2106. [DOI: 10.1007/s00894-014-2106-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Accepted: 12/07/2013] [Indexed: 01/23/2023]
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33
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Lu X, Zeng J, Gao Y, Zhang JZH, Zhang D, Mei Y. The intrinsic helical propensities of the helical fragments in prion protein under neutral and low pH conditions: a replica exchange molecular dynamics study. J Mol Model 2013; 19:4897-908. [DOI: 10.1007/s00894-013-1985-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 08/22/2013] [Indexed: 11/29/2022]
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34
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Garrec J, Tavernelli I, Rothlisberger U. Two misfolding routes for the prion protein around pH 4.5. PLoS Comput Biol 2013; 9:e1003057. [PMID: 23696721 PMCID: PMC3656106 DOI: 10.1371/journal.pcbi.1003057] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2012] [Accepted: 03/27/2013] [Indexed: 11/18/2022] Open
Abstract
Using molecular dynamics simulations, we show that the prion protein (PrP) exhibits a dual behavior, with two possible transition routes, upon protonation of H187 around pH 4.5, which mimics specific conditions encountered in endosomes. Our results suggest a picture in which the protonated imidazole ring of H187 experiences an electrostatic repulsion with the nearby guanidinium group of R136, to which the system responds by pushing either H187 or R136 sidechains away from their native cavities. The regions to which H187 and R136 are linked, namely the C-terminal part of H2 and the loop connecting S1 to H1, respectively, are affected in a different manner depending on which pathway is taken. Specific in vivo or in vitro conditions, such as the presence of molecular chaperones or a particular experimental setup, may favor one transition pathway over the other, which can result in very different [Formula: see text] monomers. This has some possible connections with the observation of various fibril morphologies and the outcome of prion strains. In addition, the finding that the interaction of H187 with R136 is a weak point in mammalian PrP is supported by the absence of the [Formula: see text] residue pair in non-mammalian species that are known to be resistant to prion diseases.
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Affiliation(s)
- Julian Garrec
- Laboratory of Computational Chemistry and Biochemistry - Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Ivano Tavernelli
- Laboratory of Computational Chemistry and Biochemistry - Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry - Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- * E-mail:
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35
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Nicolini P, Frezzato D, Gellini C, Bizzarri M, Chelli R. Toward quantitative estimates of binding affinities for protein-ligand systems involving large inhibitor compounds: a steered molecular dynamics simulation route. J Comput Chem 2013; 34:1561-76. [PMID: 23620471 DOI: 10.1002/jcc.23286] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Revised: 03/01/2013] [Accepted: 03/05/2013] [Indexed: 11/09/2022]
Abstract
Understanding binding mechanisms between enzymes and potential inhibitors and quantifying protein-ligand affinities in terms of binding free energy is of primary importance in drug design studies. In this respect, several approaches based on molecular dynamics simulations, often combined with docking techniques, have been exploited to investigate the physicochemical properties of complexes of pharmaceutical interest. Even if the geometric properties of a modeled protein-ligand complex can be well predicted by computational methods, it is still challenging to rank with chemical accuracy a series of ligand analogues in a consistent way. In this article, we face this issue calculating relative binding free energies of a focal adhesion kinase, an important target for the development of anticancer drugs, with pyrrolopyrimidine-based ligands having different inhibitory power. To this aim, we employ steered molecular dynamics simulations combined with nonequilibrium work theorems for free energy calculations. This technique proves very powerful when a series of ligand analogues is considered, allowing one to tackle estimation of protein-ligand relative binding free energies in a reasonable time. In our cases, the calculated binding affinities are comparable with those recovered from experiments by exploiting the Michaelis-Menten mechanism with a competitive inhibitor.
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Affiliation(s)
- Paolo Nicolini
- Departament de Física i Enginyeria Nuclear, Universitat Politècnica de Catalunya, Campus Nord B4-B5, E-08034 Barcelona, Spain
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36
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Chakroun N, Fornili A, Prigent S, Kleinjung J, Dreiss CA, Rezaei H, Fraternali F. Decrypting Prion Protein Conversion into a β-Rich Conformer by Molecular Dynamics. J Chem Theory Comput 2013; 9:2455-2465. [PMID: 23700393 PMCID: PMC3656828 DOI: 10.1021/ct301118j] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Indexed: 01/08/2023]
Abstract
Prion diseases are fatal neurodegenerative diseases characterized by the formation of β-rich oligomers and the accumulation of amyloid fibrillar deposits in the central nervous system. Understanding the conversion of the cellular prion protein into its β-rich polymeric conformers is fundamental to tackling the early stages of the development of prion diseases. In this paper, we have identified unfolding and refolding steps critical to the conversion into a β-rich conformer for different constructs of the ovine prion protein by molecular dynamics simulations. By combining our results with in vitro experiments, we show that the folded C-terminus of the ovine prion protein is able to recurrently undergo a drastic conformational change by displacement of the H1 helix, uncovering of the H2H3 domain, and formation of persistent β-sheets between H2 and H3 residues. The observed β-sheets refold toward the C-terminus exposing what we call a "bending region" comprising residues 204-214. This is strikingly coincident with the region harboring mutations determining the fate of the prion oligomerization process. The β-rich intermediate is used here for the construction of a putative model for the assembly into an oligomeric aggregate. The results presented here confirm the importance of the H2H3 domain for prion oligomer formation and therefore its potential use as molecular target in the design of novel prion inhibitors.
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Affiliation(s)
- Nesrine Chakroun
- Institute of Pharmaceutical Science, King's College London, 150 Stamford Street, London, SE1 9NH, United Kingdom ; Randall Division of Cell and Molecular Biophysics, King's College London, Guy's Campus, London, SE1 1UL, United Kingdom
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37
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Arena G, La Mendola D, Pappalardo G, Sóvágó I, Rizzarelli E. Interactions of Cu2+ with prion family peptide fragments: Considerations on affinity, speciation and coordination. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2012.03.038] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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38
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Biljan I, Ilc G, Giachin G, Plavec J, Legname G. Structural Rearrangements at Physiological pH: Nuclear Magnetic Resonance Insights from the V210I Human Prion Protein Mutant. Biochemistry 2012; 51:7465-74. [DOI: 10.1021/bi3009856] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ivana Biljan
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000
Ljubljana, Slovenia
| | - Gregor Ilc
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000
Ljubljana, Slovenia
- EN→FIST Centre of Excellence, Dunajska 156, SI-1001 Ljubljana,
Slovenia
| | - Gabriele Giachin
- Laboratory of Prion
Biology, Department
of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), via Bonomea 265, Trieste, Italy
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000
Ljubljana, Slovenia
- EN→FIST Centre of Excellence, Dunajska 156, SI-1001 Ljubljana,
Slovenia
- Faculty of Chemistry and Chemical
Technology, University of Ljubljana, Aškerčeva
cesta 5, SI-1000 Ljubljana, Slovenia
| | - Giuseppe Legname
- Laboratory of Prion
Biology, Department
of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), via Bonomea 265, Trieste, Italy
- ELETTRA Laboratory, Sincrotrone Trieste S.C.p.A., I-34149 Basovizza, Trieste,
Italy
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Vila-Viçosa D, Campos SRR, Baptista AM, Machuqueiro M. Reversibility of prion misfolding: insights from constant-pH molecular dynamics simulations. J Phys Chem B 2012; 116:8812-21. [PMID: 22803931 DOI: 10.1021/jp3034837] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The prion protein (PrP) is the cause of a group of diseases known as transmissible spongiform encephalopathies (TSEs). Creutzfeldt-Jakob disease and bovine spongiform encephalopathy are examples of TSEs. Although the normal form of PrP (PrP(C)) is monomeric and soluble, it can misfold into a pathogenic form (PrP(Sc)) that has a high content of β-structure and can aggregate forming amyloid fibrils. The mechanism of conversion of PrP(C) into PrP(Sc) is not known but different triggers have been proposed. It can be catalyzed by a PrP(Sc) sample, or it can be induced by an external factor, such as low pH. The pH effect on the structure of PrP was recently studied by computational methods [Campos et al. J. Phys. Chem. B 2010, 114, 12692-12700], and an evident trend of loss of helical structure was observed with pH decrease, together with a gain of β-structures. In particular, one simulation at pH 2 showed an evident misfolding transition. The main goal of the present work was to study the effects of a change in pH to 7 in several transient conformations of this simulation, in order to draw some conclusions about the reversibility of PrP misfolding. Although the most significant effect caused by the change of pH to 7 was a global stabilization of the protein structure, we could also observe that some conformational transitions induced by pH 2 were reversible in many of our simulations, namely those started from the early moments of the misfolding transition. This observation is in good agreement with experiments showing that, even at pH as low as 1.7, it is possible to revert the misfolding process [Bjorndahl et al. Biochemistry 2011, 50, 1162-1173].
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Affiliation(s)
- Diogo Vila-Viçosa
- Centro de Química e Bioquímica e Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
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40
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Achilonu I, Fanucchi S, Cross M, Fernandes M, Dirr HW. Role of individual histidines in the pH-dependent global stability of human chloride intracellular channel 1. Biochemistry 2012; 51:995-1004. [PMID: 22242893 DOI: 10.1021/bi201541w] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chloride intracellular channel proteins exist in both a soluble cytosolic form and a membrane-bound form. The mechanism of conversion between the two forms is not properly understood, although one of the contributing factors is believed to be the variation in pH between the cytosol (~7.4) and the membrane (~5.5). We systematically mutated each of the three histidine residues in CLIC1 to an alanine at position 74 and a phenylalanine at positions 185 and 207. We examined the effect of the histidine-mediated pH dependence on the structure and global stability of CLIC1. None of the mutations were found to alter the global structure of the protein. However, the stability of H74A-CLIC1 and H185F-CLIC1, as calculated from the equilibrium unfolding data, is no longer dependent on pH because similar trends are observed at pH 7.0 and 5.5. The crystal structures show that the mutations result in changes in the local hydrogen bond coordination. Because the mutant total free energy change upon unfolding is not different from that of the wild type at pH 7.0, despite the presence of intermediates that are not seen in the wild type, we propose that it may be the stability of the intermediate state rather than the native state that is dependent on pH. On the basis of the lower stability of the intermediate in the H74A and H185F mutants compared to that of the wild type, we conclude that both His74 and His185 are involved in triggering the pH changes to the conformational stability of wild-type CLIC1 via their protonation, which stabilizes the intermediate state.
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Affiliation(s)
- Ikechukwu Achilonu
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2050, South Africa
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41
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Foam fractionation of protein: Correlation of protein adsorption onto bubbles with a pH-induced conformational transition. Anal Biochem 2011; 419:173-9. [DOI: 10.1016/j.ab.2011.08.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2011] [Revised: 08/10/2011] [Accepted: 08/11/2011] [Indexed: 11/21/2022]
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42
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Nam KY, Chang BH, No KT. Conformational Study of N-terminal Prion Peptides by Molecular Dynamics Simulations. B KOREAN CHEM SOC 2011. [DOI: 10.5012/bkcs.2011.32.10.3553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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43
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NMR structure and CD titration with metal cations of human prion alpha2-helix-related peptides. Bioinorg Chem Appl 2011:10720. [PMID: 18274605 PMCID: PMC2216051 DOI: 10.1155/2007/10720] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2007] [Revised: 06/04/2007] [Accepted: 07/11/2007] [Indexed: 11/17/2022] Open
Abstract
The 173–195 segment corresponding to the helix 2 of the C-globular prion protein domain could be one of several “spots” of intrinsic conformational flexibility. In fact, it possesses chameleon conformational behaviour and gathers several disease-associated point mutations. We have performed spectroscopic studies on the wild-type fragment 173–195 and on its D178N mutant dissolved in trifluoroethanol to mimic the in vivo system, both in the presence and in the absence of metal cations. NMR data showed that the structure of the D178N mutant is characterized by two short helices separated by a kink, whereas the wild-type peptide is fully helical. Both peptides retained these structural organizations, as monitored by CD, in the presence of metal cations. NMR spectra were however not in favour of the formation of definite ion-peptide complexes. This agrees with previous evidence that other regions of the prion protein are likely the natural target of metal cation binding.
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44
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Santo KP, Berjanskii M, Wishart DS, Stepanova M. Comparative analysis of essential collective dynamics and NMR-derived flexibility profiles in evolutionarily diverse prion proteins. Prion 2011; 5:188-200. [PMID: 21869604 DOI: 10.4161/pri.5.3.16097] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Collective motions on ns-μs time scales are known to have a major impact on protein folding, stability, binding and enzymatic efficiency. It is also believed that these motions may have an important role in the early stages of prion protein misfolding and prion disease. In an effort to accurately characterize these motions and their potential influence on the misfolding and prion disease transmissibility we have conducted a combined analysis of molecular dynamic simulations and NMR-derived flexibility measurements over a diverse range of prion proteins. Using a recently developed numerical formalism, we have analyzed the essential collective dynamics (ECD) for prion proteins from 8 different species including human, cow, elk, cat, hamster, chicken, turtle and frog. We also compared the numerical results with flexibility profiles generated by the random coil index (RCI) from NMR chemical shifts. Prion protein backbone flexibility derived from experimental NMR data and from theoretical computations show strong agreement with each other, demonstrating that it is possible to predict the observed RCI profiles employing the numerical ECD formalism. Interestingly, flexibility differences in the loop between second beta strand (S2) and the second alpha helix (HB) appear to distinguish prion proteins from species that are susceptible to prion disease and those that are resistant. Our results show that the different levels of flexibility in the S2-HB loop in various species are predictable via the ECD method, indicating that ECD may be used to identify disease resistant variants of prion proteins, as well as the influence of prion proteins mutations on disease susceptibility or misfolding propensity.
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45
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van der Kamp MW, Daggett V. Molecular dynamics as an approach to study prion protein misfolding and the effect of pathogenic mutations. Top Curr Chem (Cham) 2011; 305:169-97. [PMID: 21526434 DOI: 10.1007/128_2011_158] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Computer simulation of protein dynamics offers unique high-resolution information that complements experiment. Using experimentally derived structures of the natively folded prion protein (PrP), physically realistic dynamics and conformational changes can be simulated, including the initial steps of misfolding. By introducing mutations in silico, the effect of pathogenic mutations on PrP conformation and dynamics can be assessed. Here, we briefly introduce molecular dynamics methods and review the application of molecular dynamics simulations to obtain insight into various aspects of the PrP, including the mechanism of misfolding, the response to changes in the environment, and the influence of disease-related mutations.
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Affiliation(s)
- Marc W van der Kamp
- Department of Bioengineering, University of Washington, Seattle, WA 98195-5013, USA
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46
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Zhong L. Exposure of Hydrophobic Core in Human Prion Protein Pathogenic Mutant H187R. J Biomol Struct Dyn 2010; 28:355-61. [DOI: 10.1080/07391102.2010.10507365] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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47
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Campos SRR, Machuqueiro M, Baptista AM. Constant-pH Molecular Dynamics Simulations Reveal a β-Rich Form of the Human Prion Protein. J Phys Chem B 2010; 114:12692-700. [DOI: 10.1021/jp104753t] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Sara R. R. Campos
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157 Oeiras, Portugal
| | - Miguel Machuqueiro
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157 Oeiras, Portugal
| | - António M. Baptista
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157 Oeiras, Portugal
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48
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Blinov N, Dorosh L, Wishart D, Kovalenko A. Association thermodynamics and conformational stability of beta-sheet amyloid beta(17-42) oligomers: effects of E22Q (Dutch) mutation and charge neutralization. Biophys J 2010; 98:282-96. [PMID: 20338850 DOI: 10.1016/j.bpj.2009.09.062] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2008] [Revised: 09/16/2009] [Accepted: 09/17/2009] [Indexed: 12/21/2022] Open
Abstract
Amyloid fibrils are associated with many neurodegenerative diseases. It was found that amyloidogenic oligomers, not mature fibrils, are neurotoxic agents related to these diseases. Molecular mechanisms of infectivity, pathways of aggregation, and molecular structure of these oligomers remain elusive. Here, we use all-atom molecular dynamics, molecular mechanics combined with solvation analysis by statistical-mechanical, three-dimensional molecular theory of solvation (also known as 3D-RISM-KH) in a new MM-3D-RISM-KH method to study conformational stability, and association thermodynamics of small wild-type Abeta(17-42) oligomers with different protonation states of Glu(22), as well the E22Q (Dutch) mutants. The association free energy of small beta-sheet oligomers shows near-linear trend with the dimers being thermodynamically more stable relative to the larger constructs. The linear (within statistical uncertainty) dependence of the association free energy on complex size is a consequence of the unilateral stacking of monomers in the beta-sheet oligomers. The charge reduction of the wild-type Abeta(17-42) oligomers upon protonation of the solvent-exposed Glu(22) at acidic conditions results in lowering the association free energy compared to the wild-type oligomers at neutral pH and the E22Q mutants. The neutralization of the peptides because of the E22Q mutation only marginally affects the association free energy, with the reduction of the direct electrostatic interactions mostly compensated by the unfavorable electrostatic solvation effects. For the wild-type oligomers at acidic conditions such compensation is not complete, and the electrostatic interactions, along with the gas-phase nonpolar energetic and the overall entropic effects, contribute to the lowering of the association free energy. The differences in the association thermodynamics between the wild-type Abeta(17-42) oligomers at neutral pH and the Dutch mutants, on the one hand, and the Abeta(17-42) oligomers with protonated Glu(22), on the other, may be explained by destabilization of the inter- and intrapeptide salt bridges between Asp(23) and Lys(28). Peculiarities in the conformational stability and the association thermodynamics for the different models of the Abeta(17-42) oligomers are rationalized based on the analysis of the local physical interactions and the microscopic solvation structure.
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Affiliation(s)
- Nikolay Blinov
- National Institute for Nanotechnology, National Research Council of Canada, Edmonton, Alberta, Canada
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49
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Chakroun N, Prigent S, Dreiss CA, Noinville S, Chapuis C, Fraternali F, Rezaei H. The oligomerization properties of prion protein are restricted to the H2H3 domain. FASEB J 2010; 24:3222-31. [PMID: 20410442 DOI: 10.1096/fj.09-153924] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The propensity of the prion protein (PrP) to adopt different structures is a clue to its pathological behavior. The determination of the region involved in the PrP(C) to PrP(Sc) conversion is fundamental for the understanding of the mechanisms underlying this process at the molecular level. In this paper, the polymerization of the helical H2H3 domain of ovine PrP (OvPrP) was compared to the full-length construct (using chromatography and light scattering). We show that the oligomerization patterns are identical, although the H2H3 domain has a higher polymerization rate. Furthermore, the depolymerization kinetics of purified H2H3 oligomers compared to those purified from the full-length PrP reveal that regions outside H2H3 do not significantly contribute to the oligomerization process. By combining rational mutagenesis and molecular dynamics to investigate the early stages of H2H3 oligomerization, we observe a conformationally stable beta-sheet structure that we propose as a possible nucleus for oligomerization; we also show that single point mutations in H2 and H3 present structural polymorphisms and oligomerization properties that could constitute the basis of species or strain variability.
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Affiliation(s)
- Nesrine Chakroun
- Institut National de la Recherche Agronomique, Virologie et Immunologie Moléculaires, INRA, F-78352 Jouy-en-Josas, France
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50
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Watanabe Y, Hiraoka W, Igarashi M, Ito K, Shimoyama Y, Horiuchi M, Yamamori T, Yasui H, Kuwabara M, Inagaki F, Inanami O. A novel copper(II) coordination at His186 in full-length murine prion protein. Biochem Biophys Res Commun 2010; 394:522-8. [DOI: 10.1016/j.bbrc.2010.03.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Accepted: 03/02/2010] [Indexed: 10/19/2022]
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