1
|
Gu J, Xu Y, Nie Y. Role of distal sites in enzyme engineering. Biotechnol Adv 2023; 63:108094. [PMID: 36621725 DOI: 10.1016/j.biotechadv.2023.108094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 11/15/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023]
Abstract
The limitations associated with natural enzyme catalysis have triggered the rise of the field of protein engineering. Traditional rational design was based on the analysis of protein structural information and catalytic mechanisms to identify key active sites or ligand binding sites to reshape the substrate pocket. The role and significance of functional sites in the active center have been studied extensively. With a deeper understanding of the structure-catalysis relationship map, the entire protein molecule can be filled with residues that play a substantial role in its structure and function. However, the catalytic mechanism underlying distal mutations remains unclear. The aim of this review was to highlight the criticality of the distal site in enzyme engineering based on the following three aspects: What can distal mutations exert on function from mutability landscape? How do distal sites influence enzyme function? How to predict and design distal mutations? This review provides insights into the catalytic mechanism of enzymes from the global interaction network, knowledge from sequence-structure-dynamics-function relationships, and strategies for distal mutation-based protein engineering.
Collapse
Affiliation(s)
- Jie Gu
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yan Xu
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China; State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yao Nie
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China; Suqian Industrial Technology Research Institute of Jiangnan University, Suqian 223814, China.
| |
Collapse
|
2
|
Eraña H, Charco JM, Di Bari MA, Díaz-Domínguez CM, López-Moreno R, Vidal E, González-Miranda E, Pérez-Castro MA, García-Martínez S, Bravo S, Fernández-Borges N, Geijo M, D’Agostino C, Garrido J, Bian J, König A, Uluca-Yazgi B, Sabate R, Khaychuk V, Vanni I, Telling GC, Heise H, Nonno R, Requena JR, Castilla J. Development of a new largely scalable in vitro prion propagation method for the production of infectious recombinant prions for high resolution structural studies. PLoS Pathog 2019; 15:e1008117. [PMID: 31644574 PMCID: PMC6827918 DOI: 10.1371/journal.ppat.1008117] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 11/04/2019] [Accepted: 10/01/2019] [Indexed: 12/12/2022] Open
Abstract
The resolution of the three-dimensional structure of infectious prions at the atomic level is pivotal to understand the pathobiology of Transmissible Spongiform Encephalopathies (TSE), but has been long hindered due to certain particularities of these proteinaceous pathogens. Difficulties related to their purification from brain homogenates of disease-affected animals were resolved almost a decade ago by the development of in vitro recombinant prion propagation systems giving rise to highly infectious recombinant prions. However, lack of knowledge about the molecular mechanisms of the misfolding event and the complexity of systems such as the Protein Misfolding Cyclic Amplification (PMCA), have limited generating the large amounts of homogeneous recombinant prion preparations required for high-resolution techniques such as solid state Nuclear Magnetic Resonance (ssNMR) imaging. Herein, we present a novel recombinant prion propagation system based on PMCA that substitutes sonication with shaking thereby allowing the production of unprecedented amounts of multi-labeled, infectious recombinant prions. The use of specific cofactors, such as dextran sulfate, limit the structural heterogeneity of the in vitro propagated prions and makes possible, for the first time, the generation of infectious and likely homogeneous samples in sufficient quantities for studies with high-resolution structural techniques as demonstrated by the preliminary ssNMR spectrum presented here. Overall, we consider that this new method named Protein Misfolding Shaking Amplification (PMSA), opens new avenues to finally elucidate the three-dimensional structure of infectious prions.
Collapse
Affiliation(s)
- Hasier Eraña
- CIC bioGUNE, Derio (Bizkaia), Spain
- ATLAS Molecular Pharma S. L. Derio (Bizkaia), Spain
| | | | - Michele A. Di Bari
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | | | | | - Enric Vidal
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Barcelona, Spain
| | | | | | | | - Susana Bravo
- Proteomics Lab, IDIS, Santiago de Compostela, Spain
| | | | - Mariví Geijo
- Animal Health Department, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Derio (Bizkaia), Spain
| | - Claudia D’Agostino
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Joseba Garrido
- Animal Health Department, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Derio (Bizkaia), Spain
| | - Jifeng Bian
- Prion Research Center (PRC), Colorado State University, Fort Collins, Colorado, United States of America
| | - Anna König
- Institute of Complex Systems (ICS-6) and Jülich Center for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
- Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Boran Uluca-Yazgi
- Institute of Complex Systems (ICS-6) and Jülich Center for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
- Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Raimon Sabate
- Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Spain
| | - Vadim Khaychuk
- Prion Research Center (PRC), Colorado State University, Fort Collins, Colorado, United States of America
| | - Ilaria Vanni
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Glenn C. Telling
- Prion Research Center (PRC), Colorado State University, Fort Collins, Colorado, United States of America
| | - Henrike Heise
- Institute of Complex Systems (ICS-6) and Jülich Center for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
- Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Romolo Nonno
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Jesús R. Requena
- CIMUS Biomedical Research Institute, University of Santiago de Compostela-IDIS, Spain
| | - Joaquín Castilla
- CIC bioGUNE, Derio (Bizkaia), Spain
- IKERBasque, Basque Foundation for Science, Bilbao (Bizkaia), Spain
- * E-mail:
| |
Collapse
|
3
|
A Species-Correlated Transitional Residue D132 on Human FMRP Plays a Role in Nuclear Localization via an RNA-Dependent Interaction With PABP1. Neuroscience 2019; 404:282-296. [DOI: 10.1016/j.neuroscience.2019.01.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 12/16/2018] [Accepted: 01/17/2019] [Indexed: 11/22/2022]
|
4
|
Aucoin D, Xia Y, Theint T, Nadaud PS, Surewicz K, Surewicz WK, Jaroniec CP. Protein-solvent interfaces in human Y145Stop prion protein amyloid fibrils probed by paramagnetic solid-state NMR spectroscopy. J Struct Biol 2018; 206:36-42. [PMID: 29679649 DOI: 10.1016/j.jsb.2018.04.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 03/24/2018] [Accepted: 04/13/2018] [Indexed: 11/16/2022]
Abstract
The C-terminally truncated Y145Stop variant of prion protein (PrP23-144), which is associated with heritable PrP cerebral amyloid angiopathy in humans and also capable of triggering a transmissible prion disease in mice, serves as a useful in vitro model for investigating the molecular and structural basis of amyloid strains and cross-seeding specificities. Here, we determine the protein-solvent interfaces in human PrP23-144 amyloid fibrils generated from recombinant 13C,15N-enriched protein and incubated in aqueous solution containing paramagnetic Cu(II)-EDTA, by measuring residue-specific 15N longitudinal paramagnetic relaxation enhancements using two-dimensional magic-angle spinning solid-state NMR spectroscopy. To further probe the interactions of the amyloid core residues with solvent molecules we perform complementary measurements of amide hydrogen/deuterium exchange detected by solid-state NMR and solution NMR methods. The solvent accessibility data are evaluated in the context of the structural model for human PrP23-144 amyloid.
Collapse
Affiliation(s)
- Darryl Aucoin
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Yongjie Xia
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Theint Theint
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Philippe S Nadaud
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Krystyna Surewicz
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Witold K Surewicz
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Christopher P Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.
| |
Collapse
|
5
|
Ishibashi D, Nakagaki T, Ishikawa T, Atarashi R, Watanabe K, Cruz FA, Hamada T, Nishida N. Structure-Based Drug Discovery for Prion Disease Using a Novel Binding Simulation. EBioMedicine 2016; 9:238-249. [PMID: 27333028 PMCID: PMC4972544 DOI: 10.1016/j.ebiom.2016.06.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 05/25/2016] [Accepted: 06/06/2016] [Indexed: 12/22/2022] Open
Abstract
The accumulation of abnormal prion protein (PrP(Sc)) converted from the normal cellular isoform of PrP (PrP(C)) is assumed to induce pathogenesis in prion diseases. Therefore, drug discovery studies for these diseases have focused on the protein conversion process. We used a structure-based drug discovery algorithm (termed Nagasaki University Docking Engine: NUDE) that ran on an intensive supercomputer with a graphic-processing unit to identify several compounds with anti-prion effects. Among the candidates showing a high-binding score, the compounds exhibited direct interaction with recombinant PrP in vitro, and drastically reduced PrP(Sc) and protein-aggresomes in the prion-infected cells. The fragment molecular orbital calculation showed that the van der Waals interaction played a key role in PrP(C) binding as the intermolecular interaction mode. Furthermore, PrP(Sc) accumulation and microgliosis were significantly reduced in the brains of treated mice, suggesting that the drug candidates provided protection from prion disease, although further in vivo tests are needed to confirm these findings. This NUDE-based structure-based drug discovery for normal protein structures is likely useful for the development of drugs to treat other conformational disorders, such as Alzheimer's disease.
Collapse
Affiliation(s)
- Daisuke Ishibashi
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Japan.
| | - Takehiro Nakagaki
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Japan
| | - Takeshi Ishikawa
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Japan
| | - Ryuichiro Atarashi
- Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Japan
| | - Ken Watanabe
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Japan
| | - Felipe A Cruz
- Nagasaki Advanced Computing Center, Nagasaki University, Japan
| | - Tsuyoshi Hamada
- Nagasaki Advanced Computing Center, Nagasaki University, Japan
| | - Noriyuki Nishida
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Japan
| |
Collapse
|
6
|
Habenstein B, Loquet A. Solid-state NMR: An emerging technique in structural biology of self-assemblies. Biophys Chem 2016; 210:14-26. [DOI: 10.1016/j.bpc.2015.07.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 07/08/2015] [Indexed: 12/13/2022]
|
7
|
Goobes G. Past and Future Solid-State NMR Spectroscopy Studies at the Convergence Point between Biology and Materials Research. Isr J Chem 2014. [DOI: 10.1002/ijch.201300113] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
8
|
GhattyVenkataKrishna PK, Uberbacher EC, Cheng X. Effect of the amyloid β hairpin's structure on the handedness of helices formed by its aggregates. FEBS Lett 2013; 587:2649-55. [PMID: 23845280 DOI: 10.1016/j.febslet.2013.06.050] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 05/16/2013] [Accepted: 06/21/2013] [Indexed: 11/16/2022]
Abstract
Various structural models for amyloid β fibrils have been derived from a variety of experimental techniques. However, these models cannot differentiate between the relative position of the two arms of the β hairpin called the stagger. Amyloid fibrils of various hierarchical levels form left-handed helices composed of β sheets. However it is unclear if positive, negative and zero staggers all form the macroscopic left-handed helices. To address this issue we have conducted extensive molecular dynamics simulations of amyloid β sheets of various staggers and shown that only negative staggers lead to the experimentally observed left-handed helices while positive staggers generate the incorrect right-handed helices. This result suggests that the negative staggers are physiologically relevant structure of the amyloid β fibrils.
Collapse
|
9
|
Comellas G, Rienstra CM. Protein Structure Determination by Magic-Angle Spinning Solid-State NMR, and Insights into the Formation, Structure, and Stability of Amyloid Fibrils. Annu Rev Biophys 2013; 42:515-36. [DOI: 10.1146/annurev-biophys-083012-130356] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Chad M. Rienstra
- Center for Biophysics and Computational Biology,
- Department of Chemistry, and
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; ,
| |
Collapse
|
10
|
Emwas AHM, Al-Talla ZA, Guo X, Al-Ghamdi S, Al-Masri HT. Utilizing NMR and EPR spectroscopy to probe the role of copper in prion diseases. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2013; 51:255-268. [PMID: 23436479 DOI: 10.1002/mrc.3936] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 12/19/2012] [Accepted: 01/11/2013] [Indexed: 06/01/2023]
Abstract
Copper is an essential nutrient for the normal development of the brain and nervous system, although the hallmark of several neurological diseases is a change in copper concentrations in the brain and central nervous system. Prion protein (PrP) is a copper-binding, cell-surface glycoprotein that exists in two alternatively folded conformations: a normal isoform (PrP(C)) and a disease-associated isoform (PrP(Sc)). Prion diseases are a group of lethal neurodegenerative disorders that develop as a result of conformational conversion of PrP(C) into PrP(Sc). The pathogenic mechanism that triggers this conformational transformation with the subsequent development of prion diseases remains unclear. It has, however, been shown repeatedly that copper plays a significant functional role in the conformational conversion of prion proteins. In this review, we focus on current research that seeks to clarify the conformational changes associated with prion diseases and the role of copper in this mechanism, with emphasis on the latest applications of NMR and EPR spectroscopy to probe the interactions of copper with prion proteins.
Collapse
Affiliation(s)
- Abdul-Hamid M Emwas
- NMR Core Lab, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.
| | | | | | | | | |
Collapse
|
11
|
Abstract
Insulin is a hormone that is essential for regulating energy storage and glucose metabolism in the body. Insulin in liver, muscle, and fat tissues stimulates the cell to take up glucose from blood and store it as glycogen in liver and muscle. Failure of insulin control causes diabetes mellitus (DM). Insulin is the unique medicine to treat some forms of DM. The population of diabetics has dramatically increased over the past two decades, due to high absorption of carbohydrates (or fats and proteins), lack of physical exercise, and development of new diagnostic techniques. At present, the two largest developing countries (India and China) and the largest developed country (United States) represent the top three countries in terms of diabetic population. Insulin is a small protein, but contains almost all structural features typical of proteins: α-helix, β-sheet, β-turn, high order assembly, allosteric T®R-transition, and conformational changes in amyloidal fibrillation. More than ten years' efforts on studying insulin disulfide intermediates by NMR have enabled us to decipher the whole picture of insulin folding coupled to disulfide pairing, especially at the initial stage that forms the nascent peptide. Two structural switches are also known to regulate insulin binding to receptors and progress has been made to identify the residues involved in binding. However, resolving the complex structure of insulin and its receptor remains a challenge in insulin research. Nevertheless, the accumulated knowledge of insulin structure has allowed us to specifically design a new ultra-stable and active single-chain insulin analog (SCI-57), and provides a novel way to design super-stable, fast-acting and cheaper insulin formulations for DM patients. Continuing this long journey of insulin study will benefit basic research in proteins and in pharmaceutical therapy.
Collapse
Affiliation(s)
- Qingxin Hua
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106-4935, USA.
| |
Collapse
|
12
|
Molecular Structure of Amyloid Fibrils Formed by Residues 127 to 147 of the Human Prion Protein. Chemistry 2010; 16:5492-9. [DOI: 10.1002/chem.200903290] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
13
|
Scheinost JC, Witter DP, Boldt GE, Offer J, Wentworth P. Cholesterol secosterol adduction inhibits the misfolding of a mutant prion protein fragment that induces neurodegeneration. Angew Chem Int Ed Engl 2010; 48:9469-72. [PMID: 19899085 DOI: 10.1002/anie.200904524] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Johanna C Scheinost
- The Scripps-Oxford Laboratory, Department of Biochemistry, University of Oxford, South Parks Rd., Oxford OX13QU, UK
| | | | | | | | | |
Collapse
|
14
|
Colby DW, Wain R, Baskakov IV, Legname G, Palmer CG, Nguyen HOB, Lemus A, Cohen FE, DeArmond SJ, Prusiner SB. Protease-sensitive synthetic prions. PLoS Pathog 2010; 6:e1000736. [PMID: 20107515 PMCID: PMC2809756 DOI: 10.1371/journal.ppat.1000736] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Accepted: 12/21/2009] [Indexed: 11/19/2022] Open
Abstract
Prions arise when the cellular prion protein (PrPC) undergoes a self-propagating conformational change; the resulting infectious conformer is designated PrPSc. Frequently, PrPSc is protease-resistant but protease-sensitive (s) prions have been isolated in humans and other animals. We report here that protease-sensitive, synthetic prions were generated in vitro during polymerization of recombinant (rec) PrP into amyloid fibers. In 22 independent experiments, recPrP amyloid preparations, but not recPrP monomers or oligomers, transmitted disease to transgenic mice (n = 164), denoted Tg9949 mice, that overexpress N-terminally truncated PrP. Tg9949 control mice (n = 174) did not spontaneously generate prions although they were prone to late-onset spontaneous neurological dysfunction. When synthetic prion isolates from infected Tg9949 mice were serially transmitted in the same line of mice, they exhibited sPrPSc and caused neurodegeneration. Interestingly, these protease-sensitive prions did not shorten the life span of Tg9949 mice despite causing extensive neurodegeneration. We inoculated three synthetic prion isolates into Tg4053 mice that overexpress full-length PrP; Tg4053 mice are not prone to developing spontaneous neurological dysfunction. The synthetic prion isolates caused disease in 600–750 days in Tg4053 mice, which exhibited sPrPSc. These novel synthetic prions demonstrate that conformational changes in wild-type PrP can produce mouse prions composed exclusively of sPrPSc. Prions are infectious proteins that cause heritable, sporadic, and transmissible diseases in humans and other mammals. These infectious proteins arise when the normal form of the prion protein (PrP) adopts a self-perpetuating conformation. This disease-causing PrP form is frequently distinguished from normal PrP by its resistance to digestion by proteases although considerable evidence shows that protease-sensitive prions occur naturally in humans and sheep. Here we describe the generation of novel protease-sensitive synthetic prions. After producing recombinant PrP of the wild-type mouse sequence in Escherichia coli, we polymerized the protein into an amyloid fiber conformation. Mice inoculated with these amyloid fibers developed extensive neurodegeneration characteristic of prion disease, but did not generate protease-resistant PrP. Prions from sick animals were transmitted to healthy animals, which likewise developed neurodegeneration but not protease-resistant prions. These novel synthetic prions demonstrate that truncated wild-type PrP can undergo a conformational change that becomes infectious yet the protein remains protease sensitive.
Collapse
Affiliation(s)
- David W. Colby
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California, United States of America
| | - Rachel Wain
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California, United States of America
| | - Ilia V. Baskakov
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California, United States of America
| | - Giuseppe Legname
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California, United States of America
- Department of Neurology, University of California, San Francisco, California, United States of America
| | - Christina G. Palmer
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California, United States of America
| | - Hoang-Oanh B. Nguyen
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California, United States of America
| | - Azucena Lemus
- Department of Pathology, University of California, San Francisco, California, United States of America
| | - Fred E. Cohen
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California, United States of America
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
| | - Stephen J. DeArmond
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California, United States of America
- Department of Pathology, University of California, San Francisco, California, United States of America
| | - Stanley B. Prusiner
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California, United States of America
- Department of Neurology, University of California, San Francisco, California, United States of America
- * E-mail:
| |
Collapse
|
15
|
Ji HF, Zhang HY. beta-sheet constitution of prion proteins. Trends Biochem Sci 2010; 35:129-34. [PMID: 20060302 DOI: 10.1016/j.tibs.2009.12.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Revised: 12/07/2009] [Accepted: 12/09/2009] [Indexed: 11/19/2022]
Abstract
Structural information regarding normal prion protein (PrP(C)) and the scrapie isoform (PrP(Sc)) is of vital importance for elucidating the pathogenesis of prion diseases (PDs). Despite successful determination of the three-dimensional structures of PrP(C), the structural details of PrP(Sc) remain elusive. Nevertheless, accumulated evidence indicates that beta-sheets comprise the basic building blocks of PrP(Sc). Consensus has been reached about the beta-sheet constitution of the N-terminus of PrP, but the constitution of C-terminal beta-sheets is heavily debated. By evaluating the most recent observations regarding the dynamics and structures of PrP, we propose that helix 2 is more likely than helices 1 and 3 to participate in beta-sheet formation. This hypothesis also provides clues to explaining an intriguing phenomenon in prion biology-the lack of PDs in non-mammals.
Collapse
Affiliation(s)
- Hong-Fang Ji
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Center for Advanced Study, Shandong University of Technology, Zibo 255049, PR China.
| | | |
Collapse
|
16
|
Scheinost J, Witter D, Boldt G, Offer J, Wentworth P. Cholesterol Secosterol Adduction Inhibits the Misfolding of a Mutant Prion Protein Fragment that Induces Neurodegeneration. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200904524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
17
|
Maji SK, Wang L, Greenwald J, Riek R. Structure-activity relationship of amyloid fibrils. FEBS Lett 2009; 583:2610-7. [PMID: 19596006 DOI: 10.1016/j.febslet.2009.07.003] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 07/02/2009] [Accepted: 07/07/2009] [Indexed: 11/18/2022]
Abstract
Protein aggregation is a process in which proteins self-associate into imperfectly ordered macroscopic entities. Such aggregates are generally classified as either amorphous or highly ordered, the most common form of the latter being amyloid fibrils. Amyloid fibrils composed of cross-beta-sheet structure are the pathological hallmarks of several diseases including Alzheimer's disease, but are also associated with functional states such as the fungal HET-s prion. This review aims to summarize the recent high-resolution structural studies of amyloid fibrils in light of their (potential) activities. We propose that the repetitive nature of the cross-beta-sheet structure of amyloids is key for their multiple properties: the repeating motifs can translate a rather non-specific interaction into a specific one through cooperativity.
Collapse
Affiliation(s)
- Samir K Maji
- School of Bioscience and Bioengineering, IIT-Bombay, Powai, Mumbai, India.
| | | | | | | |
Collapse
|
18
|
Saracino GA, Villa A, Moro G, Cosentino U, Salmona M. Spontaneous β-helical fold in prion protein: The case of PrP(82-146). Proteins 2009; 75:964-76. [DOI: 10.1002/prot.22306] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
19
|
Boshuizen RS, Schulz V, Morbin M, Mazzoleni G, Meloen RH, Langedijk JPM. Heterologous stacking of prion protein peptides reveals structural details of fibrils and facilitates complete inhibition of fibril growth. J Biol Chem 2009; 284:12809-20. [PMID: 19304665 DOI: 10.1074/jbc.m809151200] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Fibrils play an important role in the pathogenesis of amyloidosis; however, the underlying mechanisms of the growth process and the structural details of fibrils are poorly understood. Crucial in the fibril formation of prion proteins is the stacking of PrP monomers. We previously proposed that the structure of the prion protein fibril may be similar as a parallel left-handed beta-helix. The beta-helix is composed of spiraling rungs of parallel beta-strands, and in the PrP model residues 105-143 of each PrP monomer can contribute two beta-helical rungs to the growing fibril. Here we report data to support this model. We show that two cyclized human PrP peptides corresponding to residues 105-124 and 125-143, based on two single rungs of the left-handed beta-helical core of the human PrP(Sc) fibril, show spontaneous cooperative fibril growth in vitro by heterologous stacking. Because the structural model must have predictive value, peptides were designed based on the structure rules of the left-handed beta-helical fold that could stack with prion protein peptides to stimulate or to block fibril growth. The stimulator peptide was designed as an optimal left-handed beta-helical fold that can serve as a template for fibril growth initiation. The inhibiting peptide was designed to bind to the exposed rung but frustrate the propagation of the fibril growth. The single inhibitory peptide hardly shows inhibition, but the combination of the inhibitory with the stimulatory peptide showed complete inhibition of the fibril growth of peptide huPrP-(106-126). Moreover, the unique strategy based on stimulatory and inhibitory peptides seems a powerful new approach to study amyloidogenic fibril structures in general and could prove useful for the development of therapeutics.
Collapse
|
20
|
Natalello A, Prokorov VV, Tagliavini F, Morbin M, Forloni G, Beeg M, Manzoni C, Colombo L, Gobbi M, Salmona M, Doglia SM. Conformational Plasticity of the Gerstmann–Sträussler–Scheinker Disease Peptide as Indicated by Its Multiple Aggregation Pathways. J Mol Biol 2008; 381:1349-61. [DOI: 10.1016/j.jmb.2008.06.063] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Revised: 06/17/2008] [Accepted: 06/21/2008] [Indexed: 10/21/2022]
|
21
|
Wasmer C, Soragni A, Sabaté R, Lange A, Riek R, Meier BH. Infectious and noninfectious amyloids of the HET-s(218-289) prion have different NMR spectra. Angew Chem Int Ed Engl 2008; 47:5839-41. [PMID: 18548467 DOI: 10.1002/anie.200704896] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Christian Wasmer
- Laboratorium für Physikalische Chemie, ETH Zurich, 8093 Zurich, Switzerland
| | | | | | | | | | | |
Collapse
|
22
|
Wasmer C, Soragni A, Sabaté R, Lange A, Riek R, Meier B. Infektiöse und nichtinfektiöse Amyloide des HET‐s(218‐289)‐Prions haben unterschiedliche NMR‐Spektren. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200704896] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
23
|
Dyukov MI, Grudinin MP, Sirotkin AK, Kiselev OI. Insulin fibrillogenesis in vitro. DOKL BIOCHEM BIOPHYS 2008; 419:79-81. [DOI: 10.1134/s1607672908020099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
24
|
Steric Zipper of the Amyloid Fibrils Formed by Residues 109–122 of the Syrian Hamster Prion Protein. J Mol Biol 2008; 378:1142-54. [DOI: 10.1016/j.jmb.2008.03.035] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2007] [Revised: 03/04/2008] [Accepted: 03/16/2008] [Indexed: 11/20/2022]
|
25
|
Andronesi OC, Bergen MV, Biernat J, Seidel K, Griesinger C, Mandelkow E, Baldus M. Characterization of Alzheimer’s-like Paired Helical Filaments from the Core Domain of Tau Protein Using Solid-State NMR Spectroscopy. J Am Chem Soc 2008; 130:5922-8. [DOI: 10.1021/ja7100517] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
26
|
Molecular conformation and dynamics of the Y145Stop variant of human prion protein in amyloid fibrils. Proc Natl Acad Sci U S A 2008; 105:6284-9. [PMID: 18436646 DOI: 10.1073/pnas.0711716105] [Citation(s) in RCA: 176] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A C-terminally truncated Y145Stop variant of the human prion protein (huPrP23-144) is associated with a hereditary amyloid disease known as PrP cerebral amyloid angiopathy. Previous studies have shown that recombinant huPrP23-144 can be efficiently converted in vitro to the fibrillar amyloid state, and that residues 138 and 139 play a critical role in the amyloidogenic properties of this protein. Here, we have used magic-angle spinning solid-state NMR spectroscopy to provide high-resolution insight into the protein backbone conformation and dynamics in fibrils formed by (13)C,(15)N-labeled huPrP23-144. Surprisingly, we find that signals from approximately 100 residues (i.e., approximately 80% of the sequence) are not detected above approximately -20 degrees C in conventional solid-state NMR spectra. Sequential resonance assignments revealed that signals, which are observed, arise exclusively from residues in the region 112-141. These resonances are remarkably narrow, exhibiting average (13)C and (15)N linewidths of approximately 0.6 and 1 ppm, respectively. Altogether, the present findings indicate the existence of a compact, highly ordered core of huPrP23-144 amyloid encompassing residues 112-141. Analysis of (13)C secondary chemical shifts identified likely beta-strand segments within this core region, including beta-strand 130-139 containing critical residues 138 and 139. In contrast to this relatively rigid, beta-sheet-rich amyloid core, the remaining residues in huPrP23-144 amyloid fibrils under physiologically relevant conditions are largely unordered, displaying significant conformational dynamics.
Collapse
|
27
|
|
28
|
Munishkina LA, Fink AL. Fluorescence as a method to reveal structures and membrane-interactions of amyloidogenic proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:1862-85. [PMID: 17493579 DOI: 10.1016/j.bbamem.2007.03.015] [Citation(s) in RCA: 219] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2006] [Revised: 03/11/2007] [Accepted: 03/13/2007] [Indexed: 10/23/2022]
Abstract
Amyloidogenesis is a characteristic feature of the 40 or so known protein deposition diseases, and accumulating evidence strongly suggests that self-association of misfolded proteins into either fibrils, protofibrils, or soluble oligomeric species is cytotoxic. The most likely mechanism for toxicity is through perturbation of membrane structure, leading to increased membrane permeability and eventual cell death. There have been a rather limited number of investigations of the interactions of amyloidogenic polypeptides and their aggregated states with membranes; these are briefly reviewed here. Amyloidogenic proteins discussed include A-beta from Alzheimer's disease, the prion protein, alpha-synuclein from Parkinson's disease, transthyretin (FAP, SSA amyloidosis), immunoglobulin light chains (primary (AL) amyloidosis), serum amyloid A (secondary (AA) amyloidosis), amylin or IAPP (Type 2 diabetes) and apolipoproteins. This review highlights the significant role played by fluorescence techniques in unraveling the nature of amyloid fibrils and their interactions and effects on membranes. Fluorescence spectroscopy is a valuable and versatile method for studying the complex mechanisms of protein aggregation, amyloid fibril formation and the interactions of amyloidogenic proteins with membranes. Commonly used fluorescent techniques include intrinsic and extrinsic fluorophores, fluorescent probes incorporated in the membrane, steady-state and lifetime measurements of fluorescence emission, fluorescence correlation spectroscopy, fluorescence anisotropy and polarization, fluorescence resonance energy transfer (FRET), fluorescence quenching, and fluorescence microscopy.
Collapse
Affiliation(s)
- Larissa A Munishkina
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | | |
Collapse
|
29
|
Moro G, Bonati L, Bruschi M, Cosentino U, De Gioia L, Fantucci PC, Pandini A, Papaleo E, Pitea D, Saracino GA, Zampella G. Computational approaches to shed light on molecular mechanisms in biological processes. Theor Chem Acc 2007; 117:723-741. [PMID: 21415934 PMCID: PMC3057205 DOI: 10.1007/s00214-006-0203-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Computational approaches based on Molecular Dynamics simulations, Quantum Mechanical methods and 3D Quantitative Structure-Activity Relationships were employed by computational chemistry groups at the University of Milano-Bicocca to study biological processes at the molecular level. The paper reports the methodologies adopted and the results obtained on Aryl hydrocarbon Receptor and homologous PAS proteins mechanisms, the properties of prion protein peptides, the reaction pathway of hydrogenase and peroxidase enzymes and the defibrillogenic activity of tetracyclines.
Collapse
Affiliation(s)
- Giorgio Moro
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza, Milano 20126, Italy
| | - Laura Bonati
- Dipartimento di Scienze dell’Ambiente e del Territorio, Università di Milano-Bicocca, Piazza della Scienza, Milano 20126, Italy
| | - Maurizio Bruschi
- Dipartimento di Scienze dell’Ambiente e del Territorio, Università di Milano-Bicocca, Piazza della Scienza, Milano 20126, Italy
| | - Ugo Cosentino
- Dipartimento di Scienze dell’Ambiente e del Territorio, Università di Milano-Bicocca, Piazza della Scienza, Milano 20126, Italy
| | - Luca De Gioia
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza, Milano 20126, Italy
| | - Pier Carlo Fantucci
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza, Milano 20126, Italy
| | - Alessandro Pandini
- Dipartimento di Scienze dell’Ambiente e del Territorio, Università di Milano-Bicocca, Piazza della Scienza, Milano 20126, Italy
| | - Elena Papaleo
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza, Milano 20126, Italy
| | - Demetrio Pitea
- Dipartimento di Scienze dell’Ambiente e del Territorio, Università di Milano-Bicocca, Piazza della Scienza, Milano 20126, Italy
| | - Gloria A.A. Saracino
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza, Milano 20126, Italy
| | - Giuseppe Zampella
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza, Milano 20126, Italy
| |
Collapse
|
30
|
Vitrenko YA, Pavon ME, Stone SI, Liebman SW. Propagation of the [PIN+] prion by fragments of Rnq1 fused to GFP. Curr Genet 2007; 51:309-19. [PMID: 17415568 PMCID: PMC2597802 DOI: 10.1007/s00294-007-0127-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2007] [Revised: 03/08/2007] [Accepted: 03/09/2007] [Indexed: 11/30/2022]
Abstract
Prions are viewed as enigmatic infectious entities whose genetic properties are enciphered solely in an array of self-propagating protein aggregate conformations. Rnq1, a yeast protein with yet unknown function, forms a prion named [PIN+] for its ability to facilitate the de novo induction of another prion, [PSI+]. Here we investigate a set of RNQ1 truncations that were designed to cover major Rnq1 sequence elements similar to those important for the propagation of other yeast prions: a region rich in asparagines and glutamines and several types of oligopeptide repeats. Proteins encoded by these RNQ1 truncations were tested for their ability to (a) join (decorate) pre-existing [PIN+] aggregates made of wild-type Rnq1 and (b) maintain the heritable aggregated state in the absence of wild-type RNQ1. While the possible involvement of particular sequence elements in the propagation of [PIN+] is discussed, the major result is that the efficiency of transmission of [PIN+] from wild-type Rnq1 to a fragment decreased with the fragment's length.
Collapse
Affiliation(s)
- Yakov A Vitrenko
- Department of Biological Sciences, University of Illinois at Chicago, 900 S. Ashland M/C 567, Chicago, IL 60607, USA
| | | | | | | |
Collapse
|
31
|
Shewmaker F, Wickner RB, Tycko R. Amyloid of the prion domain of Sup35p has an in-register parallel beta-sheet structure. Proc Natl Acad Sci U S A 2006; 103:19754-9. [PMID: 17170131 PMCID: PMC1750918 DOI: 10.1073/pnas.0609638103] [Citation(s) in RCA: 260] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The [PSI(+)] prion of Saccharomyces cerevisiae is a self-propagating amyloid form of Sup35p, a subunit of the translation termination factor. Using solid-state NMR we have examined the structure of amyloid fibrils formed in vitro from purified recombinant Sup35(1-253), consisting of the glutamine- and asparagine-rich N-terminal 123-residue prion domain (N) and the adjacent 130-residue highly charged M domain. Measurements of magnetic dipole-dipole couplings among (13)C nuclei in a series of Sup35NM fibril samples, (13)C-labeled at backbone carbonyl sites of Tyr, Leu, or Phe residues or at side-chain methyl sites of Ala residues, indicate intermolecular (13)C-(13)C distances of approximately 0.5 nm for nearly all sites in the N domain. Certain sites in the M domain also exhibit intermolecular distances of approximately 0.5 nm. These results indicate that an in-register parallel beta-sheet structure underlies the [PSI(+)] prion phenomenon.
Collapse
Affiliation(s)
| | - Reed B. Wickner
- *Laboratory of Biochemistry and Genetics and
- To whom correspondence may be addressed at:
Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 8, Room 225, Bethesda, MD 20892-0830. E-mail:
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
- To whom correspondence may be addressed at:
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Room 112, Bethesda, MD 20892-0520. E-mail:
| |
Collapse
|
32
|
Langedijk JPM, Fuentes G, Boshuizen R, Bonvin AMJJ. Two-rung model of a left-handed beta-helix for prions explains species barrier and strain variation in transmissible spongiform encephalopathies. J Mol Biol 2006; 360:907-20. [PMID: 16782127 DOI: 10.1016/j.jmb.2006.05.042] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2006] [Revised: 05/12/2006] [Accepted: 05/17/2006] [Indexed: 11/22/2022]
Abstract
In this study, a new beta-helical model is proposed that explains the species barrier and strain variation in transmissible spongiform encephalopathies. The left-handed beta-helix serves as a structural model that can explain the seeded growth characteristics of beta-sheet structure in PrP(Sc) fibrils. Molecular dynamics simulations demonstrate that the left-handed beta-helix is structurally more stable than the right-handed beta-helix, with a higher beta-sheet content during the simulation and a better distributed network of inter-strand backbone-backbone hydrogen bonds between parallel beta-strands of different rungs. Multiple sequence alignments and homology modelling of prion sequences with different rungs of left-handed beta-helices illustrate that the PrP region with the highest beta-helical propensity (residues 105-143) can fold in just two rungs of a left-handed beta-helix. Even if no other flanking sequence participates in the beta-helix, the two rungs of a beta-helix can give the growing fibril enough elevation to accommodate the rest of the PrP protein in a tight packing at the periphery of a trimeric beta-helix. The folding of beta-helices is driven by backbone-backbone hydrogen bonding and stacking of side-chains in adjacent rungs. The sequence and structure of the last rung at the fibril end with unprotected beta-sheet edges selects the sequence of a complementary rung and dictates the folding of the new rung with optimal backbone hydrogen bonding and side-chain stacking. An important side-chain stack that facilitates the beta-helical folding is between methionine residues 109 and 129, which explains their importance in the species barrier of prions. Because the PrP sequence is not evolutionarily optimised to fold in a beta-helix, and because the beta-helical fold shows very little sequence preference, alternative alignments are possible that result in a different rung able to select for an alternative complementary rung. A different top rung results in a new strain with different growth characteristics. Hence, in the present model, sequence variation and alternative alignments clarify the basis of the species barrier and strain specificity in PrP-based diseases.
Collapse
|
33
|
Kruppa M, Imperato G, König B. Synthesis of chiral amino acids with metal ion chelating side chains from l-serine using Negishi cross-coupling reaction. Tetrahedron 2006. [DOI: 10.1016/j.tet.2005.11.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
34
|
Lim KH, Nguyen TN, Damo SM, Mazur T, Ball HL, Prusiner SB, Pines A, Wemmer DE. Solid-state NMR structural studies of the fibril form of a mutant mouse prion peptide PrP89-143(P101L). SOLID STATE NUCLEAR MAGNETIC RESONANCE 2006; 29:183-90. [PMID: 16256316 DOI: 10.1016/j.ssnmr.2005.09.017] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2005] [Revised: 09/07/2005] [Indexed: 05/05/2023]
Abstract
The peptide fragment 89-143 of the prion protein (carrying a P101L mutation) is biologically active in transgenic mice when in a fibrillar form. Injection of these fibrils into transgenic mice (expressing full length PrP with the P101L mutation) induces a neurodegenerative prion disease (Kaneko et al., J. Mol. Biol. 295 (2000) 997). Here we present solid-state NMR studies of PrP(89-143)(P101L) fibrils, probing the conformation of residues in the hydrophobic segment 112-124 with chemical shifts. The conformations of glycine residues were analyzed using doubly (13)C=O labeled peptides by two-dimensional (2D) double-quantum correlation, and double-quantum filtered dephasing distance measurements. MQ-NMR experiments were carried out to probe the relative alignment of the individual peptides fibrils. These NMR studies indicate that the 112-124 segment adopts an extended beta-sheet conformation, though not in a parallel, in register alignment. There is evidence for conformational variability at Gly 113. DQ correlation experiments provide useful information in regions with conformational heterogeneity.
Collapse
Affiliation(s)
- Kwang Hun Lim
- Department of Chemistry, University of California, USA
| | | | | | | | | | | | | | | |
Collapse
|
35
|
Petkova AT, Yau WM, Tycko R. Experimental constraints on quaternary structure in Alzheimer's beta-amyloid fibrils. Biochemistry 2006; 45:498-512. [PMID: 16401079 PMCID: PMC1435828 DOI: 10.1021/bi051952q] [Citation(s) in RCA: 898] [Impact Index Per Article: 49.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We describe solid-state nuclear magnetic resonance (NMR) measurements on fibrils formed by the 40-residue beta-amyloid peptide associated with Alzheimer's disease (Abeta(1-40)) that place constraints on the identity and symmetry of contacts between in-register, parallel beta-sheets in the fibrils. We refer to these contacts as internal and external quaternary contacts, depending on whether they are within a single molecular layer or between molecular layers. The data include (1) two-dimensional 13C-13C NMR spectra that indicate internal quaternary contacts between side chains of L17 and F19 and side chains of I32, L34, and V36, as well as external quaternary contacts between side chains of I31 and G37; (2) two-dimensional 15N-13C NMR spectra that indicate external quaternary contacts between the side chain of M35 and the peptide backbone at G33; (3) measurements of magnetic dipole-dipole couplings between the side chain carboxylate group of D23 and the side chain amine group of K28 that indicate salt bridge interactions. Isotopic dilution experiments allow us to make distinctions between intramolecular and intermolecular contacts. On the basis of these data and previously determined structural constraints from solid-state NMR and electron microscopy, we construct full molecular models using restrained molecular dynamics simulations and restrained energy minimization. These models apply to Abeta(1-40) fibrils grown with gentle agitation. We also present evidence for different internal quaternary contacts in Abeta(1-40) fibrils grown without agitation, which are morphologically distinct.
Collapse
Affiliation(s)
- Aneta T Petkova
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| | | | | |
Collapse
|
36
|
Tycko R. Characterization of amyloid structures at the molecular level by solid state nuclear magnetic resonance spectroscopy. Methods Enzymol 2006; 413:103-22. [PMID: 17046393 PMCID: PMC1633711 DOI: 10.1016/s0076-6879(06)13006-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Solid state nuclear magnetic resonance (NMR) spectroscopy is particularly useful in structural studies of amyloid fibrils because solid state NMR techniques have unique capabilities as site-specific, molecular-level structural probes of noncrystalline materials. These techniques provide experimental data that strongly constrain the secondary, tertiary, and quaternary structures of amyloid fibrils, permitting the development of experimentally based structural models. Examples of techniques that are applicable to amyloid samples prepared with isotopic labeling of specific sites and to samples prepared with uniform isotopic labeling of selected residues are presented, illustrating the utility of the various techniques and labeling schemes. Information regarding the preparation of amyloid samples for solid state NMR measurements is also included.
Collapse
Affiliation(s)
- Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Room 112, Bethesda, Maryland 20892-0520, e-mail: , phone: 301-402-8272, fax: 301-496-0825
| |
Collapse
|
37
|
Abstract
Solid state nuclear magnetic resonance (NMR) has developed into one of the most informative and direct experimental approaches to the characterization of the molecular structures of amyloid fibrils, including those associated with Alzheimer's disease. In this article, essential aspects of solid state NMR methods are described briefly and results obtained to date regarding the supramolecular organization of amyloid fibrils and the conformations of peptides within amyloid fibrils are reviewed.
Collapse
Affiliation(s)
- Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA.
| |
Collapse
|
38
|
Cegelski L, Schaefer J. Glycine metabolism in intact leaves by in vivo 13C and 15N labeling. J Biol Chem 2005; 280:39238-45. [PMID: 16159873 DOI: 10.1074/jbc.m507053200] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Solid-state (13)C NMR measurements of intact soybean leaves labeled by (13)CO(2) (at subambient concentrations) show that excess glycine from the photorespiratory C(2) cycle (i.e. glycine not part of the production of glycerate in support of photosynthesis) is either fully decarboxylated or inserted as (13)C-labeled glycyl residues in proteins. This (13)C incorporation in leaf protein, which is uniformly (15)N labeled by (15)NH(4)(15)NO(3), occurs as soon as 2 min after the start of (13)CO(2) labeling. In those leaves with lower levels of available nitrogen (as measured by leaf nitrate and glutamine-glutamate concentrations), the excess glycine is used primarily as glycyl residues in protein.
Collapse
Affiliation(s)
- Lynette Cegelski
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, USA
| | | |
Collapse
|
39
|
Heise H, Hoyer W, Becker S, Andronesi OC, Riedel D, Baldus M. Molecular-level secondary structure, polymorphism, and dynamics of full-length alpha-synuclein fibrils studied by solid-state NMR. Proc Natl Acad Sci U S A 2005; 102:15871-6. [PMID: 16247008 PMCID: PMC1276071 DOI: 10.1073/pnas.0506109102] [Citation(s) in RCA: 511] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The 140-residue protein alpha-synuclein (AS) is able to form amyloid fibrils and as such is the main component of protein inclusions involved in Parkinson's disease. We have investigated the structure and dynamics of full-length AS fibrils by high-resolution solid-state NMR spectroscopy. Homonuclear and heteronuclear 2D and 3D spectra of fibrils grown from uniformly (13)C/(15)N-labeled AS and AS reverse-labeled for two of the most abundant amino acids, K and V, were analyzed. (13)C and (15)N signals exhibited linewidths of <0.7 ppm. Sequential assignments were obtained for 48 residues in the hydrophobic core region. We identified two different types of fibrils displaying chemical-shift differences of up to 13 ppm in the (15)N dimension and up to 5 ppm for backbone and side-chain (13)C chemical shifts. EM studies suggested that molecular structure is correlated with fibril morphology. Investigation of the secondary structure revealed that most amino acids of the core region belong to beta-strands with similar torsion angles in both conformations. Selection of regions with different mobility indicated the existence of monomers in the sample and allowed the identification of mobile segments of the protein within the fibril in the presence of monomeric protein. At least 35 C-terminal residues were mobile and lacked a defined secondary structure, whereas the N terminus was rigid starting from residue 22. Our findings agree well with the overall picture obtained with other methods and provide insight into the amyloid fibril structure and dynamics with residue-specific resolution.
Collapse
Affiliation(s)
- Henrike Heise
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
| | | | | | | | | | | |
Collapse
|
40
|
Heise H, Luca S, de Groot BL, Grubmüller H, Baldus M. Probing conformational disorder in neurotensin by two-dimensional solid-state NMR and comparison to molecular dynamics simulations. Biophys J 2005; 89:2113-20. [PMID: 15994900 PMCID: PMC1366713 DOI: 10.1529/biophysj.105.059964] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An approach is introduced to characterize conformational ensembles of intrinsically unstructured peptides on the atomic level using two-dimensional solid-state NMR data and their combination with molecular dynamics simulations. For neurotensin, a peptide that binds with high affinity to a G-protein coupled receptor, this method permits the investigation of the changes in conformational preferences of a neurotransmitter transferred from a frozen aqueous solution via a lipid model phase to the receptor-bound form. The results speak against a conformational pre-organization of the ligand in detergents in which the receptor has been shown to be functional. Further extensions to the study of protein folding are possible.
Collapse
Affiliation(s)
- Henrike Heise
- Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | | | | | | | | |
Collapse
|
41
|
Ritter C, Maddelein ML, Siemer AB, Lührs T, Ernst M, Meier BH, Saupe SJ, Riek R. Correlation of structural elements and infectivity of the HET-s prion. Nature 2005; 435:844-8. [PMID: 15944710 PMCID: PMC1567094 DOI: 10.1038/nature03793] [Citation(s) in RCA: 359] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2005] [Accepted: 05/12/2005] [Indexed: 11/08/2022]
Abstract
Prions are believed to be infectious, self-propagating polymers of otherwise soluble, host-encoded proteins. This concept is now strongly supported by the recent findings that amyloid fibrils of recombinant prion proteins from yeast, Podospora anserina and mammals can induce prion phenotypes in the corresponding hosts. However, the structural basis of prion infectivity remains largely elusive because acquisition of atomic resolution structural properties of amyloid fibrils represents a largely unsolved technical challenge. HET-s, the prion protein of P. anserina, contains a carboxy-terminal prion domain comprising residues 218-289. Amyloid fibrils of HET-s(218-289) are necessary and sufficient for the induction and propagation of prion infectivity. Here, we have used fluorescence studies, quenched hydrogen exchange NMR and solid-state NMR to determine the sequence-specific positions of amyloid fibril secondary structure elements of HET-s(218-289). This approach revealed four beta-strands constituted by two pseudo-repeat sequences, each forming a beta-strand-turn-beta-strand motif. By using a structure-based mutagenesis approach, we show that this conformation is the functional and infectious entity of the HET-s prion. These results correlate distinct structural elements with prion infectivity.
Collapse
Affiliation(s)
- Christiane Ritter
- The Salk Institute, 10010 North Torrey Pines Road, La Jolla, California 92037, USA
| | | | | | | | | | | | | | | |
Collapse
|
42
|
Siemer AB, Ritter C, Ernst M, Riek R, Meier BH. High-Resolution Solid-State NMR Spectroscopy of the Prion Protein HET-s in Its Amyloid Conformation. Angew Chem Int Ed Engl 2005; 44:2441-4. [PMID: 15770629 DOI: 10.1002/anie.200462952] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ansgar B Siemer
- Laboratory of Physical Chemistry, ETH Zurich, ETH-Hönggerberg, Switzerland
| | | | | | | | | |
Collapse
|
43
|
Siemer AB, Ritter C, Ernst M, Riek R, Meier BH. Hochauflösende Festkörper-NMR-Spektroskopie am Prionprotein HET-s in seiner amyloiden Form. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200462952] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
44
|
Havlin RH, Walls JD, Pines A. Isotropic proton-detected local-field nuclear magnetic resonance in solids. J Chem Phys 2005; 122:074507. [PMID: 15743254 DOI: 10.1063/1.1844296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
A nuclear magnetic resonance method is presented which produces linear, isotropic proton-detected local-field spectra for INS spin systems in powdered samples. The method, heteronuclear isotropic evolution (HETIE), refocuses the anisotropic portion of the heteronuclear dipolar coupling frequencies by evolving the system under a series of specially designed Hamiltonians and evolution pathways. The theory behind HETIE is presented along with experimental studies conducted on a powdered sample of ferrocene, demonstrating the methodology outlined in this paper. Applications of HETIE for use in structure determination in the solid state are discussed.
Collapse
Affiliation(s)
- Robert H Havlin
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | | | | |
Collapse
|
45
|
DeMarco ML, Daggett V. From conversion to aggregation: protofibril formation of the prion protein. Proc Natl Acad Sci U S A 2004; 101:2293-8. [PMID: 14983003 PMCID: PMC356944 DOI: 10.1073/pnas.0307178101] [Citation(s) in RCA: 265] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2003] [Indexed: 01/08/2023] Open
Abstract
The ability to diagnose and treat prion diseases is limited by our current understanding of the conversion process of the protein from healthy to harmful isoform. Whereas the monomeric, benign species is well characterized, the misfolded conformations responsible for infectivity and neurodegeneration remain elusive. There is mounting evidence that fibrillization intermediates, or protofibrils, but not mature fibrils or plaques, are the pathogenic species in amyloid diseases. Here, we use molecular dynamics to simulate the conversion of the prion protein. Molecular dynamics simulation produces a scrapie prion protein-like conformation enriched in beta-structure that is in good agreement with available experimental data. The converted conformation was then used to model a protofibril by means of the docking of hydrophobic patches of the template structure to form hydrogen-bonded sheets spanning adjacent subunits. The resulting protofibril model provides a non-branching aggregate with a 3(1) axis of symmetry that is in good agreement with a wide variety of experimental data; importantly, it was derived from realistic simulation of the conversion process.
Collapse
Affiliation(s)
- Mari L DeMarco
- Biomolecular Structure and Design Program, Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195-7610, USA
| | | |
Collapse
|
46
|
Jaroniec CP, MacPhee CE, Bajaj VS, McMahon MT, Dobson CM, Griffin RG. High-resolution molecular structure of a peptide in an amyloid fibril determined by magic angle spinning NMR spectroscopy. Proc Natl Acad Sci U S A 2004; 101:711-6. [PMID: 14715898 PMCID: PMC321745 DOI: 10.1073/pnas.0304849101] [Citation(s) in RCA: 386] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Amyloid fibrils are self-assembled filamentous structures associated with protein deposition conditions including Alzheimer's disease and the transmissible spongiform encephalopathies. Despite the immense medical importance of amyloid fibrils, no atomic-resolution structures are available for these materials, because the intact fibrils are insoluble and do not form diffraction-quality 3D crystals. Here we report the high-resolution structure of a peptide fragment of the amyloidogenic protein transthyretin, TTR(105-115), in its fibrillar form, determined by magic angle spinning NMR spectroscopy. The structure resolves not only the backbone fold but also the precise conformation of the side chains. Nearly complete (13)C and (15)N resonance assignments for TTR(105-115) formed the basis for the extraction of a set of distance and dihedral angle restraints. A total of 76 self-consistent experimental measurements, including 41 restraints on 19 backbone dihedral angles and 35 (13)C-(15)N distances between 3 and 6 A were obtained from 2D and 3D NMR spectra recorded on three fibril samples uniformly (13)C, (15)N-labeled in consecutive stretches of four amino acids and used to calculate an ensemble of peptide structures. Our results indicate that TTR(105-115) adopts an extended beta-strand conformation in the amyloid fibrils such that both the main- and side-chain torsion angles are close to their optimal values. Moreover, the structure of this peptide in the fibrillar form has a degree of long-range order that is generally associated only with crystalline materials. These findings provide an explanation of the unusual stability and characteristic properties of this form of polypeptide assembly.
Collapse
Affiliation(s)
- Christopher P Jaroniec
- Department of Chemistry and Center for Magnetic Resonance, Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | | | | | | | |
Collapse
|
47
|
Kuwata K, Matumoto T, Cheng H, Nagayama K, James TL, Roder H. NMR-detected hydrogen exchange and molecular dynamics simulations provide structural insight into fibril formation of prion protein fragment 106-126. Proc Natl Acad Sci U S A 2003; 100:14790-5. [PMID: 14657385 PMCID: PMC299804 DOI: 10.1073/pnas.2433563100] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PrP106-126, a peptide corresponding to residues 107-127 of the human prion protein, induces neuronal cell death by apoptosis and causes proliferation and hypertrophy of glia, reproducing the main neuropathological features of prion-related transmissible spongiform encephalopathies, such as bovine spongiform encephalopathy and Creutzfeldt-Jakob disease. Although PrP106-126 has been shown to form amyloid-like fibrils in vitro, their structural properties have not been elucidated. Here, we investigate the conformational characteristics of a fibril-forming fragment of the mouse prion protein, MoPrP106-126, by using electron microscopy, CD spectroscopy, NMR-detected hydrogen-deuterium exchange measurements, and molecular dynamics simulations. The fibrils contain approximately 50% beta-sheet structure, and strong amide exchange protection is limited to the central portion of the peptide spanning the palindromic sequence VAGAAAAGAV. Molecular dynamics simulations indicate that MoPrP106-126 in water assumes a stable structure consisting of two four-stranded parallel beta-sheets that are tightly packed against each other by methyl-methyl interactions. Fibril formation involving polyalanine stacking is consistent with the experimental observations.
Collapse
Affiliation(s)
- Kazuo Kuwata
- Department of Biochemistry and Biophysics, School of Medicine, Gifu University, 40 Tsukasa-machi, Gifu 500-8705, Japan.
| | | | | | | | | | | |
Collapse
|
48
|
Luca S, White JF, Sohal AK, Filippov DV, van Boom JH, Grisshammer R, Baldus M. The conformation of neurotensin bound to its G protein-coupled receptor. Proc Natl Acad Sci U S A 2003; 100:10706-11. [PMID: 12960362 PMCID: PMC196868 DOI: 10.1073/pnas.1834523100] [Citation(s) in RCA: 200] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2003] [Indexed: 11/18/2022] Open
Abstract
G protein-coupled receptors (GPCRs) mediate the perception of smell, light, taste, and pain. They are involved in signal recognition and cell communication and are some of the most important targets for drug development. Because currently no direct structural information on high-affinity ligands bound to GPCRs is available, rational drug design is limited to computational prediction combined with mutagenesis experiments. Here, we present the conformation of a high-affinity peptide agonist (neurotensin, NT) bound to its GPCR NTS-1, determined by direct structural methods. Functional receptors were expressed in Escherichia coli, purified in milligram amounts by using optimized procedures, and subsequently reconstituted into lipid vesicles. Solid-state NMR experiments were tailored to allow for the unequivocal detection of microgram quantities of 13C,15N-labeled NT(8-13) in complex with functional NTS-1. The NMR data are consistent with a disordered state of the ligand in the absence of receptor. Upon receptor binding, the peptide undergoes a linear rearrangement, adopting a beta-strand conformation. Our results provide a viable structural template for further pharmacological investigations.
Collapse
Affiliation(s)
- Sorin Luca
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | | | | | | | | | | | | |
Collapse
|
49
|
Antzutkin ON, Balbach JJ, Tycko R. Site-specific identification of non-beta-strand conformations in Alzheimer's beta-amyloid fibrils by solid-state NMR. Biophys J 2003; 84:3326-35. [PMID: 12719262 PMCID: PMC1302893 DOI: 10.1016/s0006-3495(03)70057-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The most well-established structural feature of amyloid fibrils is the cross-beta motif, an extended beta-sheet structure formed by beta-strands oriented perpendicular to the long fibril axis. Direct experimental identification of non-beta-strand conformations in amyloid fibrils has not been reported previously. Here we report the results of solid-state NMR measurements on amyloid fibrils formed by the 40-residue beta-amyloid peptide associated with Alzheimer's disease (Abeta(1-40)), prepared synthetically with pairs of (13)C labels at consecutive backbone carbonyl sites. The measurements probe the peptide backbone conformation in residues 24-30, a segment where a non-beta-strand conformation has been suggested by earlier sequence analysis, cross-linking experiments, and molecular modeling. Data obtained with the fpRFDR-CT, DQCSA, and 2D MAS exchange solid-state NMR techniques, which provide independent constraints on the phi and psi backbone torsion angles between the labeled carbonyl sites, indicate non-beta-strand conformations at G25, S26, and G29. These results represent the first site-specific identification and characterization of non-beta-strand peptide conformations in an amyloid fibril.
Collapse
Affiliation(s)
- Oleg N Antzutkin
- Department of Inorganic Chemistry, Luleå University of Technology, Luleå, Sweden
| | | | | |
Collapse
|
50
|
Abstract
The Monte Carlo technique is used to simulate the energy landscape and the folding kinetics of a minimal prion-like protein model. We show that the competition between hydrogen-bonding and hydrophobic interactions yields two energetically favored secondary structures, an alpha-helix and a beta-hairpin. Folding simulations indicate that the probability of reaching the alpha-helix form from a denatured random conformation is much higher than the probability of reaching the beta-sheet form, even though the beta-sheet has a lower energy. The existence of a lower energy beta-sheet state gives the possibility for the normal alpha-helix structure to take a structural transformation into the beta-sheet structure under external influences.
Collapse
Affiliation(s)
- Jeff Z Y Chen
- Department of Physics, University of Waterloo, Waterloo, Ontario, Canada.
| | | | | | | |
Collapse
|