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Zaidi N, Ahmad O, Khursheed M, Nabi F, Uversky VN, Khan RH. Furosemide Derails Human Lysozyme Fibrillation by Interacting with Aggregation Hot Spots: A Biophysical Comprehension. J Phys Chem B 2024; 128:4283-4300. [PMID: 38683125 DOI: 10.1021/acs.jpcb.3c02613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Kidney-associated human lysozyme amyloidosis leads to renal impairments;thus, patients are often prescribed furosemide. Based on this fact, the effect of furosemide on induced human lysozyme fibrillation, in vitro, is evaluated by spectroscopic, calorimetric, computational, and cellular-based assays/methods. Results show that furosemide increases the lag phase and decreases the apparent rate of aggregation of human lysozyme, thereby decelerating the nucleation phase and amyloid fibril formation, as confirmed by the decrease in the level of Thioflavin-T fluorescence. Fewer entities of hydrodynamic radii of ∼171 nm instead of amyloid fibrils (∼412 nm) are detected in human lysozyme in the presence of furosemide by dynamic light scattering. Moreover, furosemide decreases the extent of conversion of the α/β structure of human lysozyme into a predominant β-sheet. The isothermal titration calorimetry established that furosemide forms a complex with human lysozyme, which was also confirmed through fluorescence quenching and computational studies. Also, human lysozyme lytic activity is inhibited competitively by furosemide due to the involvement of amino acid residues of the active site in catalysis, as well as complex formation. Conclusively, furosemide interacts with Gln58, Ile59, Asn60, Ala108, and Trp109 of aggregation-prone regions 2 and 4 of human lysozyme, thereby masking its sites of aggregation and generating only lower-order entities that are less toxic to red blood cells than the fibrils. Thus, furosemide slows the progression of amyloid fibrillation in human lysozyme.
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Affiliation(s)
- Nida Zaidi
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Owais Ahmad
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Maryam Khursheed
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Faisal Nabi
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
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2
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Ziaunys M, Mikalauskaite K, Sakalauskas A, Smirnovas V. Investigating lysozyme amyloid fibril formation and structural variability dependence on its initial folding state under different pH conditions. Protein Sci 2024; 33:e4888. [PMID: 38151910 PMCID: PMC10804668 DOI: 10.1002/pro.4888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/21/2023] [Accepted: 12/26/2023] [Indexed: 12/29/2023]
Abstract
Protein fibril formation and accumulation are associated with dozens of amyloidoses, including the widespread and yet-incurable Alzheimer's and Parkinson's diseases. Currently, there are still several aspects of amyloid aggregation that are not fully understood, which negatively contributes to the development of disease-altering drugs and treatments. One factor which requires a more in-depth analysis is the effect of the environment on both the initial state of amyloidogenic proteins and their aggregation process and resulting fibril characteristics. In this work, we examine how lysozyme's folding state influences its amyloid formation kinetics and resulting aggregate structural characteristics under several different pH conditions, ranging from acidic to neutral. We demonstrate that both the initial state of the protein and the solution's pH value have a significant combined effect on the variability of the resulting aggregate secondary structures, as well as their stabilities, interactions with amyloid-specific dye molecules, and self-replication properties.
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Affiliation(s)
- Mantas Ziaunys
- Institute of Biotechnology, Life Sciences Center, Vilnius UniversityVilniusLithuania
| | - Kamile Mikalauskaite
- Institute of Biotechnology, Life Sciences Center, Vilnius UniversityVilniusLithuania
| | - Andrius Sakalauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius UniversityVilniusLithuania
| | - Vytautas Smirnovas
- Institute of Biotechnology, Life Sciences Center, Vilnius UniversityVilniusLithuania
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3
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Holubová M, Kronek J, Datta S, Lobaz V, Hromádková J, Štěpánek P, Hrubý M. Amphiphilic (di-)gradient copoly(2-oxazoline)s are potent amyloid fibril formation inhibitors. Colloids Surf B Biointerfaces 2023; 230:113521. [PMID: 37634283 DOI: 10.1016/j.colsurfb.2023.113521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/07/2023] [Accepted: 08/19/2023] [Indexed: 08/29/2023]
Abstract
MOTIVATION Amyloidoses are diseases caused by the accumulation of normally soluble proteins in the form of insoluble amyloids, leading to the gradual dysfunction and failure of various organs and tissues. Inhibiting amyloid formation is therefore an important therapeutic target. HYPOTHESIS We hypothesized that mono- and di-gradient amphiphilic copolymers of hydrophilic 2-(m)ethyl-2-oxazoline and hydrophobic 2-aryl-2-oxazolines may inhibit amyloid fibril formation. EXPERIMENTS In the model system with hen egg white lysozyme (HEWL) as amyloidogenic protein we determined the effect of these polymers on the amyloid formation by making use of the thioflavin T fluorescence, transmission electron microscopy, isothermal titration calorimetry, and dynamic light scattering. FINDINGS We found that some gradient copolymers possess very potent concentration-dependent inhibitory effects on HEWL amyloid formation. Structure-activity relationship revealed that copolymers with higher ratios of aromatic monomeric units had stronger amyloid suppression effects, most plausibly due to the combination of hydrophobic and π-π interactions. The measurements also revealed that the polymers that inhibit amyloid formation most plausibly do so in the form of micelles that interact with the growing amyloid fibril ends, not with isolated HEWL molecules in solution. These findings suggest the potential use of these gradient copolymers as therapeutic agents for amyloidoses.
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Affiliation(s)
- Monika Holubová
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovský Sq. 2, 162 06 Prague 6, Czech Republic; Charles University in Prague, Faculty of Science, Albertov 6, 128 43 Prague 2, Czech Republic
| | - Juraj Kronek
- Department for Biomaterials Research, Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava 45, Slovak Republic
| | - Shubhashis Datta
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P. J. Safarik University in Kosice, Jesenna 5, 04154 Košice, Slovakia
| | - Volodymyr Lobaz
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovský Sq. 2, 162 06 Prague 6, Czech Republic
| | - Jiřina Hromádková
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovský Sq. 2, 162 06 Prague 6, Czech Republic
| | - Petr Štěpánek
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovský Sq. 2, 162 06 Prague 6, Czech Republic
| | - Martin Hrubý
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovský Sq. 2, 162 06 Prague 6, Czech Republic.
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4
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Hassan MN, Nabi F, Khan AN, Hussain M, Siddiqui WA, Uversky VN, Khan RH. The amyloid state of proteins: A boon or bane? Int J Biol Macromol 2022; 200:593-617. [PMID: 35074333 DOI: 10.1016/j.ijbiomac.2022.01.115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 11/05/2022]
Abstract
Proteins and their aggregation is significant field of research due to their association with various conformational maladies including well-known neurodegenerative diseases like Alzheimer's (AD), Parkinson's (PD), and Huntington's (HD) diseases. Amyloids despite being given negative role for decades are also believed to play a functional role in bacteria to humans. In this review, we discuss both facets of amyloid. We have shed light on AD, which is one of the most common age-related neurodegenerative disease caused by accumulation of Aβ fibrils as extracellular senile plagues. We also discuss PD caused by the aggregation and deposition of α-synuclein in form of Lewy bodies and neurites. Other amyloid-associated diseases such as HD and amyotrophic lateral sclerosis (ALS) are also discussed. We have also reviewed functional amyloids that have various biological roles in both prokaryotes and eukaryotes that includes formation of biofilm and cell attachment in bacteria to hormone storage in humans, We discuss in detail the role of Curli fibrils' in biofilm formation, chaplins in cell attachment to peptide hormones, and Pre-Melansomal Protein (PMEL) roles. The disease-related and functional amyloids are compared with regard to their structural integrity, variation in regulation, and speed of forming aggregates and elucidate how amyloids have turned from foe to friend.
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Affiliation(s)
- Md Nadir Hassan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Faisal Nabi
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Asra Nasir Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Murtaza Hussain
- Department of Biochemistry, Aligarh Muslim University, Aligarh 202002, India
| | - Waseem A Siddiqui
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Vladimir N Uversky
- Protein Research Group, Institute for Biological Instrumentation of the Russian Academy of Sciences, 10 Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy 11 of Sciences", Pushchino, Moscow Region 142290, Russia; Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College 13 of Medicine, University of South Florida, Tampa, FL 33612, United States
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India.
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Vettore N, Moray J, Brans A, Herman R, Charlier P, Kumita JR, Kerff F, Dobson CM, Dumoulin M. Characterisation of the structural, dynamic and aggregation properties of the W64R amyloidogenic variant of human lysozyme. Biophys Chem 2021; 271:106563. [PMID: 33640796 DOI: 10.1016/j.bpc.2021.106563] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 02/05/2021] [Accepted: 02/06/2021] [Indexed: 10/22/2022]
Abstract
The accumulation in vital organs of amyloid fibrils made of mutational variants of lysozyme (HuL) is associated with a human systemic amyloid disease. The detailed comparison of the in vitro properties of the I56T and D67H amyloidogenic variants to those of the T70N non-amyloidogenic variant and the wild-type (WT) protein suggested that the deposition of large amounts of aggregated disease-related lysozyme variants is initiated by the formation of transient intermediate species. The ability to populate such intermediates is essentially due to the destabilisation of the protein and the loss of the global structural cooperativity under physiologically relevant conditions. Here, we report the characterisation of a third naturally occurring amyloidogenic lysozyme variant, W64R, in comparison with the I56T and WT proteins. The X-ray crystal structure of the W64R variant at 1.15 Å resolution is very similar to that of the WT protein; a few interactions within the β-domain and at the interface between the α- and β-domains differ, however, from those in the WT protein. Consequently, the W64R mutation destabilizes the protein to an extent that is similar to that observed for the I56T and D67H mutations. The ΔG°NU(H2O) is reduced by 24 kJ·mol-1 and the Tm is about 12 °C lower than that of the WT protein. Under native conditions, the W64R and I56T proteins are readily digested by proteinase K, while the WT protein remains intact. These results suggest that the two variant proteins transiently populate similar partially unfolded states in which proteinase K cleavage sites are accessible to the protease. Moreover, the in vitro aggregation properties of the W64R protein are similar to those of the I56T variant. Altogether, these results indicate that the properties of the W64R protein are astonishingly similar to those of the I56T variant. They further corroborate the idea that HuL variants associated with the disease are those whose stability and global structural cooperativity are sufficiently reduced to allow the formation of aggregation prone partially folded intermediates under physiological conditions.
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Affiliation(s)
- Nicola Vettore
- Centre for Protein Engineering, InBioS, Department of Life Sciences, University of Liège, (Sart-Tilman) 4000 Liège, Belgium
| | - Joël Moray
- Centre for Protein Engineering, InBioS, Department of Life Sciences, University of Liège, (Sart-Tilman) 4000 Liège, Belgium
| | - Alain Brans
- Centre for Protein Engineering, InBioS, Department of Life Sciences, University of Liège, (Sart-Tilman) 4000 Liège, Belgium
| | - Raphaël Herman
- Centre for Protein Engineering, InBioS, Department of Life Sciences, University of Liège, (Sart-Tilman) 4000 Liège, Belgium
| | - Paulette Charlier
- Centre for Protein Engineering, InBioS, Department of Life Sciences, University of Liège, (Sart-Tilman) 4000 Liège, Belgium
| | - Janet R Kumita
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Frédéric Kerff
- Centre for Protein Engineering, InBioS, Department of Life Sciences, University of Liège, (Sart-Tilman) 4000 Liège, Belgium
| | - Christopher M Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Mireille Dumoulin
- Centre for Protein Engineering, InBioS, Department of Life Sciences, University of Liège, (Sart-Tilman) 4000 Liège, Belgium.
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Kim SK, Goughnour PC, Lee EJ, Kim MH, Chae HJ, Yun GY, Kim YR, Choi JW. Identification of drug combinations on the basis of machine learning to maximize anti-aging effects. PLoS One 2021; 16:e0246106. [PMID: 33507975 PMCID: PMC7843016 DOI: 10.1371/journal.pone.0246106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 01/13/2021] [Indexed: 11/19/2022] Open
Abstract
Aging is a multifactorial process that involves numerous genetic changes, so identifying anti-aging agents is quite challenging. Age-associated genetic factors must be better understood to search appropriately for anti-aging agents. We utilized an aging-related gene expression pattern-trained machine learning system that can implement reversible changes in aging by linking combinatory drugs. In silico gene expression pattern-based drug repositioning strategies, such as connectivity map, have been developed as a method for unique drug discovery. However, these strategies have limitations such as lists that differ for input and drug-inducing genes or constraints to compare experimental cell lines to target diseases. To address this issue and improve the prediction success rate, we modified the original version of expression profiles with a stepwise-filtered method. We utilized a machine learning system called deep-neural network (DNN). Here we report that combinational drug pairs using differential expressed genes (DEG) had a more enhanced anti-aging effect compared with single independent treatments on leukemia cells. This study shows potential drug combinations to retard the effects of aging with higher efficacy using innovative machine learning techniques.
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Affiliation(s)
- Sun Kyung Kim
- College of Pharmacy, Kyung Hee University, Seoul, Republic of Korea
| | | | - Eui Jin Lee
- College of Pharmacy, Kyung Hee University, Seoul, Republic of Korea
| | - Myeong Hyun Kim
- Center for Research and Development, Oncocross Ltd., Seoul, Republic of Korea
| | - Hee Jin Chae
- Center for Research and Development, Oncocross Ltd., Seoul, Republic of Korea
| | - Gwang Yeul Yun
- Center for Research and Development, Oncocross Ltd., Seoul, Republic of Korea
| | - Yi Rang Kim
- Center for Research and Development, Oncocross Ltd., Seoul, Republic of Korea
- Department of Hematology/Oncology, Yuseong Sun Hospital, Daejeon, Republic of Korea
- * E-mail: (YRK); (JWC)
| | - Jin Woo Choi
- College of Pharmacy, Kyung Hee University, Seoul, Republic of Korea
- Department of Life and Nano-pharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea
- * E-mail: (YRK); (JWC)
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7
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Griffin JWD, Bradshaw PC. In silico prediction of novel residues involved in amyloid primary nucleation of human I56T and D67H lysozyme. BMC STRUCTURAL BIOLOGY 2018; 18:9. [PMID: 30029603 PMCID: PMC6053722 DOI: 10.1186/s12900-018-0088-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 07/09/2018] [Indexed: 11/30/2022]
Abstract
Background Amyloidogenic proteins are most often associated with neurodegenerative diseases such as Alzheimer’s disease, Parkinson’s disease, and Huntington’s disease, but there are more than two dozen human proteins known to form amyloid fibrils associated with disease. Lysozyme is an antimicrobial protein that is used as a general model to study amyloid fibril formation. Studies aimed at elucidating the process of amyloid formation of lysozyme tend to focus on partial unfolding of the native state due to the relative instability of mutant amyloidogenic variants. While this is well supported, the data presented here suggest the native structure of the variants may also play a role in primary nucleation. Results Three-dimensional structural analysis identified lysozyme residues 21, 62, 104, and 122 as displaced in both amyloidogenic variants compared to wild type lysozyme. Residue interaction network (RIN) analysis found greater clustering of residues 112–117 in amyloidogenic variants of lysozyme compared to wild type. An analysis of the most energetically favored predicted dimers and trimers provided further evidence for a role for residues 21, 62, 104, 122, and 112–117 in amyloid formation. Conclusions This study used lysozyme as a model to demonstrate the utility of combining 3D structural analysis with RIN analysis for studying the general process of amyloidogenesis. Results indicated that binding of two or more amyloidogenic lysozyme mutants may be involved in amyloid nucleation by placing key residues (21, 62, 104, 122, and 112–117) in proximity before partial unfolding occurs. Identifying residues in the native state that may be involved in amyloid formation could provide novel drug targets to prevent a range of amyloidoses.
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Affiliation(s)
- Jeddidiah W D Griffin
- Department of Biomedical Sciences, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA.
| | - Patrick C Bradshaw
- Department of Biomedical Sciences, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
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8
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Application of Lysine-specific Labeling to Detect Transient Interactions Present During Human Lysozyme Amyloid Fibril Formation. Sci Rep 2017; 7:15018. [PMID: 29101328 PMCID: PMC5670245 DOI: 10.1038/s41598-017-14739-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 10/16/2017] [Indexed: 11/08/2022] Open
Abstract
Populating transient and partially unfolded species is a crucial step in the formation and accumulation of amyloid fibrils formed from pathogenic variants of human lysozyme linked with a rare but fatal hereditary systemic amyloidosis. The partially unfolded species possess an unstructured β-domain and C-helix with the rest of the α-domain remaining native-like. Here we use paramagnetic relaxation enhancement (PRE) measured by NMR spectroscopy to study the transient intermolecular interactions between such intermediate species. Nitroxide spin labels, introduced specifically at three individual lysine residues, generate distinct PRE profiles, indicating the presence of intermolecular interactions between residues within the unfolded β-domain. This study describes the applicability to PRE NMR measurements of selective lysine labeling, at different sites within a protein, as an alternative to the introduction of spin labels via engineered cysteine residues. These results reveal the importance of the β-sheet region of lysozyme for initiating self-assembly into amyloid fibrils.
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9
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Ahn M, Hagan CL, Bernardo-Gancedo A, De Genst E, Newby FN, Christodoulou J, Dhulesia A, Dumoulin M, Robinson CV, Dobson CM, Kumita JR. The Significance of the Location of Mutations for the Native-State Dynamics of Human Lysozyme. Biophys J 2017; 111:2358-2367. [PMID: 27926837 PMCID: PMC5153563 DOI: 10.1016/j.bpj.2016.10.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 09/09/2016] [Accepted: 10/19/2016] [Indexed: 11/27/2022] Open
Abstract
The conversion of human lysozyme into amyloid fibrils is associated with a rare but fatal hereditary form of nonneuropathic systemic amyloidosis. The accumulation of large amounts of aggregated protein is thought to be initiated by the formation of transient intermediate species of disease-related lysozyme variants, essentially due to the loss of global cooperativity under physiologically relevant conditions. Interestingly, all five naturally occurring, amyloidogenic, single-point mutations are located in the β-domain of lysozyme, the region that is predominantly unfolded during the formation of the transient intermediate species. Given the lack of known naturally occurring, amyloidogenic, single-point mutations in the α-domain, we chose three specific mutations to address the effects that location may have on native-state dynamics, as studied by hydrogen-deuterium (HD) exchange experiments analyzed by NMR spectroscopy, and mass spectrometry. We compared the effect of a destabilizing α-domain mutation (I23A) with that of the well-characterized I59T β-domain variant. We also investigated the effect of a mutation that has minor effects on native-state stability at the domain interface (I56V) and compared it with that of a variant with similar stability within the C-helix (I89V). We show that when variants have similar reduced native-state stabilities, the location of the mutation (I23A versus I59T) is crucial to the native-state dynamics, with the α-domain mutation having a significantly lower ability to populate transient intermediate species under physiologically relevant conditions. Interestingly, the mutation at the interface (I56V) has a greater effect in facilitating the formation of transient intermediate species at elevated temperatures compared with the variants containing α-domain mutations, even though this mutation results in only minor changes to the native-state stability of lysozyme. These findings reveal that the location of specific mutations is an important factor in determining the native-state dynamical properties of human lysozyme in the context of its propensity to populate the aggregation-prone transient intermediate species associated with pathogenic amyloid formation.
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Affiliation(s)
- Minkoo Ahn
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Christine L Hagan
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | | | - Erwin De Genst
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Francisco N Newby
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London, United Kingdom
| | - Anne Dhulesia
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Mireille Dumoulin
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, InBios, Institute of Chemistry, University of Liege, Liege (Sart Tilman), Belgium
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
| | | | - Janet R Kumita
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.
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10
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Pain C, Dumont J, Dumoulin M. Camelid single-domain antibody fragments: Uses and prospects to investigate protein misfolding and aggregation, and to treat diseases associated with these phenomena. Biochimie 2015; 111:82-106. [DOI: 10.1016/j.biochi.2015.01.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 01/23/2015] [Indexed: 12/19/2022]
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11
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De Simone A, Aprile FA, Dhulesia A, Dobson CM, Vendruscolo M. Structure of a low-population intermediate state in the release of an enzyme product. eLife 2015; 4:e02777. [PMID: 25575179 PMCID: PMC4383205 DOI: 10.7554/elife.02777] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 12/16/2014] [Indexed: 11/18/2022] Open
Abstract
Enzymes can increase the rate of biomolecular reactions by several orders of magnitude. Although the steps of substrate capture and product release are essential in the enzymatic process, complete atomic-level descriptions of these steps are difficult to obtain because of the transient nature of the intermediate conformations, which makes them largely inaccessible to standard structure determination methods. We describe here the determination of the structure of a low-population intermediate in the product release process by human lysozyme through a combination of NMR spectroscopy and molecular dynamics simulations. We validate this structure by rationally designing two mutations, the first engineered to destabilise the intermediate and the second to stabilise it, thus slowing down or speeding up, respectively, product release. These results illustrate how product release by an enzyme can be facilitated by the presence of a metastable intermediate with transient weak interactions between the enzyme and product.
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Affiliation(s)
- Alfonso De Simone
- Department of Life
Sciences, Imperial College London,
London, United Kingdom
| | - Francesco A Aprile
- Department of
Chemistry, University of Cambridge,
Cambridge, United Kingdom
| | - Anne Dhulesia
- Department of
Chemistry, University of Cambridge,
Cambridge, United Kingdom
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12
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Hesketh AR, Castrillo JI, Sawyer T, Archer DB, Oliver SG. Investigating the physiological response of Pichia (Komagataella) pastoris GS115 to the heterologous expression of misfolded proteins using chemostat cultures. Appl Microbiol Biotechnol 2013; 97:9747-9762. [PMID: 24022610 PMCID: PMC3825213 DOI: 10.1007/s00253-013-5186-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 08/05/2013] [Accepted: 08/10/2013] [Indexed: 01/12/2023]
Abstract
Pichia pastoris is widely used as a host system for heterologous protein expression in both academia and industry. Production is typically accomplished by a fed-batch induction process that is known to have negative impacts on cell physiology that impose limits on both protein yields and quality. We have analysed recombinant protein production in chemostat cultures to understand the physiological responses associated with methanol-induced production of two human lysozyme variants with different degrees of misfolding by P. pastoris. Confounding variables associated with nutrient stress or growth-rate are minimised during steady-state growth in chemostats. Comparison of transcriptome-level data obtained during the non-inducing and inducing steady states identified changes in expression of only about 1 % of the genome during production of either an amyloidogenic human lysozyme variant prone to intracellular aggregation (I56T) or a misfolded but secretable variant (T70N), indicating near-complete acclimation to their production. A marked, but temporary, stress response involving both the unfolded protein response (UPR) and ER-associated degradation pathway was observed during the transient between steady states, particularly following induction of the T70N variant synthesis, and was accompanied by changes in expression of around 50 antisense transcripts. The results suggest that optimal heterologous protein production could best be achieved by a continuous process that minimises the number of methanol-induced transients experienced by the cultures. The processing of HAC1 mRNA required for the UPR was found to be constitutive in the culture conditions used, even in the absence of recombinant protein induction.
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Affiliation(s)
- Andrew R. Hesketh
- Cambridge Systems Biology Centre, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge, CB2 1GA UK
- Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge, CB2 1GA UK
| | - Juan I. Castrillo
- Cambridge Systems Biology Centre, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge, CB2 1GA UK
- Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge, CB2 1GA UK
| | - Trevor Sawyer
- Cambridge Systems Biology Centre, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge, CB2 1GA UK
| | - David B. Archer
- School of Biology, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Stephen G. Oliver
- Cambridge Systems Biology Centre, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge, CB2 1GA UK
- Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge, CB2 1GA UK
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13
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De Genst E, Chan PH, Pardon E, Hsu STD, Kumita JR, Christodoulou J, Menzer L, Chirgadze DY, Robinson CV, Muyldermans S, Matagne A, Wyns L, Dobson CM, Dumoulin M. A nanobody binding to non-amyloidogenic regions of the protein human lysozyme enhances partial unfolding but inhibits amyloid fibril formation. J Phys Chem B 2013; 117:13245-13258. [PMID: 23919586 PMCID: PMC4612432 DOI: 10.1021/jp403425z] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We report the effects of the interaction of two camelid antibody fragments, generally called nanobodies, namely cAb-HuL5 and a stabilized and more aggregation-resistant variant cAb-HuL5G obtained by protein engineering, on the properties of two amyloidogenic variants of human lysozyme, I56T and D67H, whose deposition in vital organs including the liver, kidney, and spleen is associated with a familial non-neuropathic systemic amyloidosis. Both NMR spectroscopy and X-ray crystallographic studies reveal that cAb-HuL5 binds to the α-domain, one of the two lobes of the native lysozyme structure. The binding of cAb-HuL5/cAb-HuL5G strongly inhibits fibril formation by the amyloidogenic variants; it does not, however, suppress the locally transient cooperative unfolding transitions, characteristic of these variants, in which the β-domain and the C-helix unfold and which represents key early intermediate species in the formation of amyloid fibrils. Therefore, unlike two other nanobodies previously described, cAb-HuL5/cAb-HuL5G does not inhibit fibril formation via the restoration of the global cooperativity of the native structure of the lysozyme variants to that characteristic of the wild-type protein. Instead, it inhibits a subsequent step in the assembly of the fibrils, involving the unfolding and structural reorganization of the α-domain. These results show that nanobodies can protect against the formation of pathogenic aggregates at different stages in the structural transition of a protein from the soluble native state into amyloid fibrils, illustrating their value as structural probes to study the molecular mechanisms of amyloid fibril formation. Combined with their amenability to protein engineering techniques to improve their stability and solubility, these findings support the suggestion that nanobodies can potentially be developed as therapeutics to combat protein misfolding diseases.
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Affiliation(s)
- Erwin De Genst
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Pak-Ho Chan
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
- State Key Laboratory of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, P.R. China
| | - Els Pardon
- Department of Structural Biology, Vlaams Interuniversitair Instituut voor Biotechnologie VIB, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Laboratory of Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Shang-Te D. Hsu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu, 30013, Taiwan
- Institute of Biological Chemistry, Academia Sinica, No 128, Section 2, Academia Road, Taipei 11529, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, No 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Janet R. Kumita
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, Gower Street, London WC1E 6BT, U.K
| | - Linda Menzer
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, Institute of Chemistry, University of Liege, B-4000 Liege (Sart Tilman), Belgium
| | - Dimitri Y. Chirgadze
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Carol V. Robinson
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, U.K
| | - Serge Muyldermans
- Department of Structural Biology, Vlaams Interuniversitair Instituut voor Biotechnologie VIB, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Research Unit of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - André Matagne
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, Institute of Chemistry, University of Liege, B-4000 Liege (Sart Tilman), Belgium
| | - Lode Wyns
- Department of Structural Biology, Vlaams Interuniversitair Instituut voor Biotechnologie VIB, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Laboratory of Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Christopher M. Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Mireille Dumoulin
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, Institute of Chemistry, University of Liege, B-4000 Liege (Sart Tilman), Belgium
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14
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Gustot A, Raussens V, Dehousse M, Dumoulin M, Bryant CE, Ruysschaert JM, Lonez C. Activation of innate immunity by lysozyme fibrils is critically dependent on cross-β sheet structure. Cell Mol Life Sci 2013; 70:2999-3012. [PMID: 23334185 PMCID: PMC11113201 DOI: 10.1007/s00018-012-1245-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 11/25/2012] [Accepted: 12/12/2012] [Indexed: 12/24/2022]
Abstract
Inflammation occurs in many amyloidoses, but its underlying mechanisms remain enigmatic. Here we show that amyloid fibrils of human lysozyme, which are associated with severe systemic amyloidoses, induce the secretion of pro-inflammatory cytokines through activation of the NLRP3 (NLR, pyrin domain containing 3) inflammasome and the Toll-like receptor 2, two innate immune receptors that may be involved in immune responses associated to amyloidoses. More importantly, our data clearly suggest that the induction of inflammatory responses by amyloid fibrils is linked to their intrinsic structure, because the monomeric form and a non-fibrillar type of lysozyme aggregates are both unable to trigger cytokine secretion. These lysozyme species lack the so-called cross-β structure, a characteristic structural motif common to all amyloid fibrils irrespective of their origin. Since fibrils of other bacterial and endogenous proteins have been shown to trigger immunological responses, our observations suggest that the cross-β structural signature might be recognized as a generic danger signal by the immune system.
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Affiliation(s)
- Adelin Gustot
- Laboratory of Structure and Function of Biological Membranes, Université Libre de Bruxelles (ULB), Brussels, Belgium.
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15
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Lee YH, Goto Y. Kinetic intermediates of amyloid fibrillation studied by hydrogen exchange methods with nuclear magnetic resonance. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:1307-23. [DOI: 10.1016/j.bbapap.2012.07.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 07/24/2012] [Accepted: 07/26/2012] [Indexed: 01/28/2023]
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16
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Ahn M, De Genst E, Kaminski Schierle GS, Erdelyi M, Kaminski CF, Dobson CM, Kumita JR. Analysis of the native structure, stability and aggregation of biotinylated human lysozyme. PLoS One 2012; 7:e50192. [PMID: 23166837 PMCID: PMC3500338 DOI: 10.1371/journal.pone.0050192] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 10/22/2012] [Indexed: 11/29/2022] Open
Abstract
Fibril formation by mutational variants of human lysozyme is associated with a fatal form of hereditary non-neuropathic systemic amyloidosis. Defining the mechanistic details of lysozyme aggregation is of crucial importance for understanding the origin and progression of this disease and related misfolding conditions. In this study, we show that a biotin moiety can be introduced site-specifically at Lys33 of human lysozyme. We demonstrate, using biophysical techniques, that the structure and stability of the native-state of the protein are not detectably altered by this modification, and that the ability to form amyloid fibrils is unchanged. By taking advantage of biotin-avidin interactions, we show that super-resolution fluorescence microscopy can generate detailed images of the mature fibrils. This methodology can readily enable the introduction of additional probes into the protein, thereby providing the means through which to understand, in detail, the nature of the aggregation process of lysozyme and its variants under a variety of conditions.
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Affiliation(s)
- Minkoo Ahn
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Erwin De Genst
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | | | - Miklos Erdelyi
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
- National Physics Laboratory, Teddington, United Kingdom
| | - Clemens F. Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | | | - Janet R. Kumita
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
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17
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Gavrin LK, Denny RA, Saiah E. Small Molecules That Target Protein Misfolding. J Med Chem 2012; 55:10823-43. [DOI: 10.1021/jm301182j] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Lori Krim Gavrin
- BioTherapeutics
Chemistry, Pfizer Worldwide Medicinal Chemistry, 200 CambridgePark Drive, Cambridge,
Massachusetts 02140, United States
| | - Rajiah Aldrin Denny
- BioTherapeutics
Chemistry, Pfizer Worldwide Medicinal Chemistry, 200 CambridgePark Drive, Cambridge,
Massachusetts 02140, United States
| | - Eddine Saiah
- BioTherapeutics
Chemistry, Pfizer Worldwide Medicinal Chemistry, 200 CambridgePark Drive, Cambridge,
Massachusetts 02140, United States
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18
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Kumita JR, Helmfors L, Williams J, Luheshi LM, Menzer L, Dumoulin M, Lomas DA, Crowther DC, Dobson CM, Brorsson AC. Disease-related amyloidogenic variants of human lysozyme trigger the unfolded protein response and disturb eye development in Drosophila melanogaster. FASEB J 2011; 26:192-202. [PMID: 21965601 PMCID: PMC3250245 DOI: 10.1096/fj.11-185983] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We have created a Drosophila model of lysozyme amyloidosis to investigate the in vivo behavior of disease-associated variants. To achieve this objective, wild-type (WT) protein and the amyloidogenic variants F57I and D67H were expressed in Drosophila melanogaster using the UAS-gal4 system and both the ubiquitous and retinal expression drivers Act5C-gal4 and gmr-gal4. The nontransgenic w(1118) Drosophila line was used as a control throughout. We utilized ELISA experiments to probe lysozyme protein levels, scanning electron microscopy for eye phenotype classification, and immunohistochemistry to detect the unfolded protein response (UPR) activation. We observed that expressing the destabilized F57I and D67H lysozymes triggers UPR activation, resulting in degradation of these variants, whereas the WT lysozyme is secreted into the fly hemolymph. Indeed, the level of WT was up to 17 times more abundant than the variant proteins. In addition, the F57I variant gave rise to a significant disruption of the eye development, and this correlated to pronounced UPR activation. These results support the concept that the onset of familial amyloid disease is linked to an inability of the UPR to degrade completely the amyloidogenic lysozymes prior to secretion, resulting in secretion of these destabilized variants, thereby leading to deposition and associated organ damage.
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Affiliation(s)
- Janet R Kumita
- Department of Chemistry, University of Cambridge, Cambridge, UK
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19
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Dhulesia A, Cremades N, Kumita JR, Hsu STD, Mossuto MF, Dumoulin M, Nietlispach D, Akke M, Salvatella X, Dobson CM. Local cooperativity in an amyloidogenic state of human lysozyme observed at atomic resolution. J Am Chem Soc 2010; 132:15580-8. [PMID: 20958028 PMCID: PMC2974344 DOI: 10.1021/ja103524m] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Indexed: 12/22/2022]
Abstract
The partial unfolding of human lysozyme underlies its conversion from the soluble state into amyloid fibrils observed in a fatal hereditary form of systemic amyloidosis. To understand the molecular origins of the disease, it is critical to characterize the structural and physicochemical properties of the amyloidogenic states of the protein. Here we provide a high-resolution view of the unfolding process at low pH for three different lysozyme variants, the wild-type protein and the mutants I56T and I59T, which show variable stabilities and propensities to aggregate in vitro. Using a range of biophysical techniques that includes differential scanning calorimetry and nuclear magnetic resonance spectroscopy, we demonstrate that thermal unfolding under amyloidogenic solution conditions involves a cooperative loss of native tertiary structure, followed by progressive unfolding of a compact, molten globule-like denatured state ensemble as the temperature is increased. The width of the temperature window over which the denatured ensemble progressively unfolds correlates with the relative amyloidogenicity and stability of these variants, and the region of lysozyme that unfolds first maps to that which forms the core of the amyloid fibrils formed under similar conditions. Together, these results present a coherent picture at atomic resolution of the initial events underlying amyloid formation by a globular protein.
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20
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Pouget E, Fay N, Dujardin E, Jamin N, Berthault P, Perrin L, Pandit A, Rose T, Valéry C, Thomas D, Paternostre M, Artzner F. Elucidation of the self-assembly pathway of lanreotide octapeptide into beta-sheet nanotubes: role of two stable intermediates. J Am Chem Soc 2010; 132:4230-41. [PMID: 20199027 DOI: 10.1021/ja9088023] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Nanofabrication by molecular self-assembly involves the design of molecules and self-assembly strategies so that shape and chemical complementarities drive the units to organize spontaneously into the desired structures. The power of self-assembly makes it the ubiquitous strategy of living organized matter and provides a powerful tool to chemists. However, a challenging issue in the self-assembly of complex supramolecular structures is to understand how kinetically efficient pathways emerge from the multitude of possible transition states and routes. Unfortunately, very few systems provide an intelligible structure and formation mechanism on which new models can be developed. Here, we elucidate the molecular and supramolecular self-assembly mechanism of synthetic octapeptide into nanotubes in equilibrium conditions. Their complex hierarchical self-assembly has recently been described at the mesoscopic level, and we show now that this system uniquely exhibits three assembly stages and three intermediates: (i) a peptide dimer is evidenced by both analytical centrifugation and NMR translational diffusion experiments; (ii) an open ribbon and (iii) an unstable helical ribbon are both visualized by transmission electron microscopy and characterized by small angle X-ray scattering. Interestingly, the structural features of two stable intermediates are related to the final nanotube organization as they set, respectively, the nanotube wall thickness and the final wall curvature radius. We propose that a specific self-assembly pathway is selected by the existence of such preorganized and stable intermediates so that a unique final molecular organization is kinetically favored. Our findings suggests that the rational design of oligopeptides can encode both molecular- and macro-scale morphological characteristics of their higher-order assemblies, thus opening the way to ultrahigh resolution peptide scaffold engineering.
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Affiliation(s)
- Emilie Pouget
- Institut de Physique de Rennes, UMR 6251 CNRS & Universite Rennes 1, 263 Avenue du general Leclerc, F-35042 Rennes Cedex, France
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21
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Hagan CL, Johnson RJ, Dhulesia A, Dumoulin M, Dumont J, De Genst E, Christodoulou J, Robinson CV, Dobson CM, Kumita JR. A non-natural variant of human lysozyme (I59T) mimics the in vitro behaviour of the I56T variant that is responsible for a form of familial amyloidosis. Protein Eng Des Sel 2010; 23:499-506. [PMID: 20382744 PMCID: PMC2920300 DOI: 10.1093/protein/gzq023] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Revised: 03/08/2010] [Accepted: 03/14/2010] [Indexed: 11/14/2022] Open
Abstract
We report here the detailed characterisation of a non-naturally occurring variant of human lysozyme, I59T, which possesses a destabilising point mutation at the interface of the alpha- and beta-domains. Although more stable in its native structure than the naturally occurring variants that give rise to a familial form of systemic amyloidosis, I59T possesses many attributes that are similar to these disease-associated species. In particular, under physiologically relevant conditions, I59T populates transiently an intermediate in which a region of the structure unfolds cooperatively; this loss of global cooperativity has been suggested to be a critical feature underlying the amyloidogenic nature of the disease-associated lysozyme variants. In the present study, we have utilised this variant to provide direct evidence for the generic nature of the conformational transition that precedes the ready formation of the fibrils responsible for lysozyme-associated amyloid disease. This non-natural variant can be expressed at higher levels than the natural amyloidogenic variants, enabling, for example, singly isotopically labelled protein to be generated much more easily for detailed structural studies by multidimensional NMR spectroscopy. Moreover, we demonstrate that the I59T variant can readily form fibrils in vitro, similar in nature to those of the amyloidogenic I56T variant, under significantly milder conditions than are needed for the wild-type protein.
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Affiliation(s)
- Christine L. Hagan
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Russell J.K. Johnson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Anne Dhulesia
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Mireille Dumoulin
- Laboratory of Enzymology and Protein Folding, Centre of Protein Engineering, Institute of Chemistry B6c, University of Liège, B-4000 Liège, Belgium
| | - Janice Dumont
- Laboratory of Enzymology and Protein Folding, Centre of Protein Engineering, Institute of Chemistry B6c, University of Liège, B-4000 Liège, Belgium
| | - Erwin De Genst
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - John Christodoulou
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Present address: Research Department of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Carol V. Robinson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Present address: Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Christopher M. Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Janet R. Kumita
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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22
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Liu X, Zhao YP. Switch region for pathogenic structural change in conformational disease and its prediction. PLoS One 2010; 5:e8441. [PMID: 20111584 PMCID: PMC2801591 DOI: 10.1371/journal.pone.0008441] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Accepted: 11/27/2009] [Indexed: 11/19/2022] Open
Abstract
Many diseases are believed to be related to abnormal protein folding. In the first step of such pathogenic structural changes, misfolding occurs in regions important for the stability of the native structure. This destabilizes the normal protein conformation, while exposing the previously hidden aggregation-prone regions, leading to subsequent errors in the folding pathway. Sites involved in this first stage can be deemed switch regions of the protein, and can represent perfect binding targets for drugs to block the abnormal folding pathway and prevent pathogenic conformational changes. In this study, a prediction algorithm for the switch regions responsible for the start of pathogenic structural changes is introduced. With an accuracy of 94%, this algorithm can successfully find short segments covering sites significant in triggering conformational diseases (CDs) and is the first that can predict switch regions for various CDs. To illustrate its effectiveness in dealing with urgent public health problems, the reason of the increased pathogenicity of H5N1 influenza virus is analyzed; the mechanisms of the pandemic swine-origin 2009 A(H1N1) influenza virus in overcoming species barriers and in infecting large number of potential patients are also suggested. It is shown that the algorithm is a potential tool useful in the study of the pathology of CDs because: (1) it can identify the origin of pathogenic structural conversion with high sensitivity and specificity, and (2) it provides an ideal target for clinical treatment.
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Affiliation(s)
- Xin Liu
- The State Key Laboratory of Nonlinear Mechanics, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China
| | - Ya-Pu Zhao
- The State Key Laboratory of Nonlinear Mechanics, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China
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23
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Liu X, Zhao YP. Simulated pathogenic conformational switch regions matched well with the biochemical findings. J Biomed Inform 2009; 43:365-75. [PMID: 20026248 DOI: 10.1016/j.jbi.2009.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Revised: 12/11/2009] [Accepted: 12/14/2009] [Indexed: 10/20/2022]
Abstract
Pathogenic conformational conversion is a general causation of many disease, such as transmissible spongiform encephalopathy (TSE) caused by misfolding of prion, sickle cell anemia, and etc. In such structural changes, misfolding occurs in regions important for the stability of native structure firstly. This destabilizes the normal conformation and leads to subsequent errors in folding pathway. Sites involved in the first stage can be deemed switch regions of the protein, and are vital for conformational conversion. Namely it could be a switch of disease at residue level. Here we report an algorithm that can identify such sites computationally with an accuracy of 93%, by calculating the probability of the native structure of a short segment jumping to a mistake one. Knowledge of such switch sites could be used to target clinical therapy, study physiological and pathologic mechanism of protein, and etc.
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Affiliation(s)
- Xin Liu
- The State Key Laboratory of Nonlinear Mechanics, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China.
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24
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Abstract
The conversion of proteins from their soluble states into well-organized fibrillar aggregates is associated with a wide range of pathological conditions, including neurodegenerative diseases and systemic amyloidoses. In this review, we discuss the mechanism of aggregation of globular proteins under conditions in which they are initially folded. Although a conformational change of the native state is generally necessary to initiate aggregation, we show that a transition across the major energy barrier for unfolding is not essential and that aggregation may well be initiated from locally unfolded states that become accessible, for example, via thermal fluctuations occurring under physiological conditions. We review recent evidence on this topic and discuss its significance for understanding the onset and potential inhibition of protein aggregation in the context of diseases.
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Affiliation(s)
- Fabrizio Chiti
- Dipartimento di Scienze Biochimiche, Università degli Studi di Firenze, Viale Morgagni 50, I-50134 Firenze, Italy.
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25
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Chan PH, Pardon E, Menzer L, De Genst E, Kumita JR, Christodoulou J, Saerens D, Brans A, Bouillenne F, Archer DB, Robinson CV, Muyldermans S, Matagne A, Redfield C, Wyns L, Dobson CM, Dumoulin M. Engineering a camelid antibody fragment that binds to the active site of human lysozyme and inhibits its conversion into amyloid fibrils. Biochemistry 2008; 47:11041-54. [PMID: 18816062 DOI: 10.1021/bi8005797] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A single-domain fragment, cAb-HuL22, of a camelid heavy-chain antibody specific for the active site of human lysozyme has been generated, and its effects on the properties of the I56T and D67H amyloidogenic variants of human lysozyme, which are associated with a form of systemic amyloidosis, have been investigated by a wide range of biophysical techniques. Pulse-labeling hydrogen-deuterium exchange experiments monitored by mass spectrometry reveal that binding of the antibody fragment strongly inhibits the locally cooperative unfolding of the I56T and D67H variants and restores their global cooperativity to that characteristic of the wild-type protein. The antibody fragment was, however, not stable enough under the conditions used to explore its ability to perturb the aggregation behavior of the lysozyme amyloidogenic variants. We therefore engineered a more stable version of cAb-HuL22 by adding a disulfide bridge between the two beta-sheets in the hydrophobic core of the protein. The binding of this engineered antibody fragment to the amyloidogenic variants of lysozyme inhibited their aggregation into fibrils. These findings support the premise that the reduction in global cooperativity caused by the pathogenic mutations in the lysozyme gene is the determining feature underlying their amyloidogenicity. These observations indicate further that molecular targeting of enzyme active sites, and of protein binding sites in general, is an effective strategy for inhibiting or preventing the aberrant self-assembly process that is often a consequence of protein mutation and the origin of pathogenicity. Moreover, this work further demonstrates the unique properties of camelid single-domain antibody fragments as structural probes for studying the mechanism of aggregation and as potential inhibitors of fibril formation.
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Affiliation(s)
- Pak-Ho Chan
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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26
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Valéry C, Pouget E, Pandit A, Verbavatz JM, Bordes L, Boisdé I, Cherif-Cheikh R, Artzner F, Paternostre M. Molecular origin of the self-assembly of lanreotide into nanotubes: a mutational approach. Biophys J 2008; 94:1782-95. [PMID: 17993497 PMCID: PMC2242760 DOI: 10.1529/biophysj.107.108175] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2007] [Accepted: 10/01/2007] [Indexed: 11/18/2022] Open
Abstract
Lanreotide, a synthetic, therapeutic octapeptide analog of somatostatin, self-assembles in water into perfectly hollow and monodisperse (24-nm wide) nanotubes. Lanreotide is a cyclic octapeptide that contains three aromatic residues. The molecular packing of the peptide in the walls of a nanotube has recently been characterized, indicating four hierarchical levels of organization. This is a fascinating example of spontaneous self-organization, very similar to the formation of the gas vesicle walls of Halobacterium halobium. However, this unique peptide self-assembly raises important questions about its molecular origin. We adopted a directed mutation approach to determine the molecular parameters driving the formation of such a remarkable peptide architecture. We have modified the conformation by opening the cycle and by changing the conformation of a Lys residue, and we have also mutated the aromatic side chains of the peptide. We show that three parameters are essential for the formation of lanreotide nanotubes: i), the specificity of two of the three aromatic side chains, ii), the spatial arrangement of the hydrophilic and hydrophobic residues, and iii), the aromatic side chain in the beta-turn of the molecule. When these molecular characteristics are modified, either the peptides lose their self-assembling capability or they form less-ordered architectures, such as amyloid fibers and curved lamellae. Thus we have determined key elements of the molecular origins of lanreotide nanotube formation.
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Affiliation(s)
- Céline Valéry
- Ipsen Pharma, 08980 Sant Feliu de Llobregat, Barcelona, Spain
| | - Emilie Pouget
- Unité mixte de Recherche du Centre National pour la Recherche Scientifique 6626, Université Rennes 1, F-35042 Rennes, France
| | - Anjali Pandit
- Institut de Bio Technologies de Saclay, Commisariat à l’Energie Atomique et Centre National pour la Recherche Scientifique, F-91191 Gif-sur-Yvette, France
| | - Jean-Marc Verbavatz
- Institut de Bio Technologies de Saclay, Commisariat à l’Energie Atomique et Centre National pour la Recherche Scientifique, F-91191 Gif-sur-Yvette, France
| | - Luc Bordes
- Institut de Bio Technologies de Saclay, Commisariat à l’Energie Atomique et Centre National pour la Recherche Scientifique, F-91191 Gif-sur-Yvette, France
| | - Isabelle Boisdé
- Institut de Bio Technologies de Saclay, Commisariat à l’Energie Atomique et Centre National pour la Recherche Scientifique, F-91191 Gif-sur-Yvette, France
| | | | - Franck Artzner
- Unité mixte de Recherche du Centre National pour la Recherche Scientifique 6626, Université Rennes 1, F-35042 Rennes, France
| | - Maité Paternostre
- Institut de Bio Technologies de Saclay, Commisariat à l’Energie Atomique et Centre National pour la Recherche Scientifique, F-91191 Gif-sur-Yvette, France
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27
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Jarymowycz VA, Stone MJ. Fast time scale dynamics of protein backbones: NMR relaxation methods, applications, and functional consequences. Chem Rev 2007; 106:1624-71. [PMID: 16683748 DOI: 10.1021/cr040421p] [Citation(s) in RCA: 312] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Virginia A Jarymowycz
- Department of Chemistry and Interdisciplinary Biochemistry Program, Indiana University, Bloomington, Indiana 47405-0001, USA
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28
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Kumita JR, Poon S, Caddy GL, Hagan CL, Dumoulin M, Yerbury JJ, Stewart EM, Robinson CV, Wilson MR, Dobson CM. The Extracellular Chaperone Clusterin Potently Inhibits Human Lysozyme Amyloid Formation by Interacting with Prefibrillar Species. J Mol Biol 2007; 369:157-67. [PMID: 17407782 DOI: 10.1016/j.jmb.2007.02.095] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2007] [Revised: 02/26/2007] [Accepted: 02/26/2007] [Indexed: 11/15/2022]
Abstract
We have studied the effects of the extracellular molecular chaperone, clusterin, on the in vitro aggregation of mutational variants of human lysozyme, including one associated with familial amyloid disease. The aggregation of the amyloidogenic variant I56T is inhibited significantly at clusterin to lysozyme ratios as low as 1:80 (i.e. one clusterin molecule per 80 lysozyme molecules). Experiments indicate that under the conditions where inhibition of aggregation occurs, clusterin does not bind detectably to the native or fibrillar states of lysozyme, or to the monomeric transient intermediate known to be a key species in the aggregation reaction. Rather, it seems to interact with oligomeric species that are present at low concentrations during the lag (nucleation) phase of the aggregation reaction. This behavior suggests that clusterin, and perhaps other extracellular chaperones, could have a key role in curtailing the potentially pathogenic effects of the misfolding and aggregation of proteins that, like lysozyme, are secreted into the extracellular environment.
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Affiliation(s)
- Janet R Kumita
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
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29
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Hydrogen/deuterium exchange mass spectrometric analysis of conformational changes accompanying the assembly of the yeast prion Ure2p into protein fibrils. J Mol Biol 2007; 369:1113-25. [PMID: 17482207 DOI: 10.1016/j.jmb.2007.04.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2007] [Revised: 04/02/2007] [Accepted: 04/04/2007] [Indexed: 11/24/2022]
Abstract
The Ure2 protein from baker's yeast (Saccharomyces cerevisiae) has prion properties. In vitro, at neutral pH, soluble Ure2p forms long, twisted fibrils. Two models have been proposed to account for Ure2p polymerization. The first postulates that a segment of 70 amino acid residues in the flexible N-terminal domain from different Ure2p molecules forms a parallel superpleated beta-structure running along the fibrils. The second hypothesizes that assembly of full-length Ure2p is driven by limited conformational rearrangements and non-native inter- and intramolecular interactions. The knowledge of the three-dimensional structure of the fibrillar form of Ure2p is critical for understanding the molecular events leading to the polymerization of soluble Ure2p into fibrils and hence for the design of inhibitors that might have therapeutic potential as yeast prions possessing domains rich in N and Q residues, similar to huntingtin. Solvent-accessibility studies using hydrogen/deuterium exchange monitored by mass spectrometry (HXMS) can provide insights into the structure of the fibrillar form of Ure2p and characterize at the molecular level the conformational rearrangements that occur upon assembly, in particular through the identification of protected regions and their localization in the overall structure of the protein. We have analyzed the changes in Ure2p structure associated with its assembly into fibrils using HXMS. The deuterium incorporation profile along the sequence allows the identification of the regions that exhibit the most important conformational change. Our data reveal that Ure2p undergoes minor structural changes upon assembly. While polypeptides [82-92] and [13-37] exhibit significant increased and decreased exposure to the solvent, respectively, no marked change was observed for the rest of the protein upon assembly. Our results afford new insights into the conformational rearrangements that lead to the assembly of Ure2p into fibrils and the propagation of the [URE3] element in yeast.
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30
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Mishra R, Sörgjerd K, Nyström S, Nordigården A, Yu YC, Hammarström P. Lysozyme Amyloidogenesis Is Accelerated by Specific Nicking and Fragmentation but Decelerated by Intact Protein Binding and Conversion. J Mol Biol 2007; 366:1029-44. [PMID: 17196616 DOI: 10.1016/j.jmb.2006.11.084] [Citation(s) in RCA: 166] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2006] [Revised: 11/29/2006] [Accepted: 11/29/2006] [Indexed: 01/03/2023]
Abstract
We have revisited the well-studied heat and acidic amyloid fibril formation pathway (pH 1.6, 65 degrees C) of hen egg-white lysozyme (HEWL) to map the barriers of the misfolding and amyloidogenesis pathways. A comprehensive kinetic mechanism is presented where all steps involving protein hydrolysis, fragmentation, assembly and conversion into amyloid fibrils are accounted for. Amyloid fibril formation of lysozyme has multiple kinetic barriers. First, HEWL unfolds within minutes, followed by irreversible steps of partial acid hydrolysis affording a large amount of nicked HEWL, the 49-101 amyloidogenic fragment and a variety of other species over 5-40 h. Fragmentation forming the 49-101 fragment is a requirement for efficient amyloid fibril formation, indicating that it forms the rate-determining nucleus. Nicked full-length HEWL is recruited efficiently into amyloid fibrils in the fibril growth phase or using mature fibrils as seeds, which abolished the lag phase completely. Mature amyloid fibrils of HEWL are composed mainly of nicked HEWL in the early equilibrium phase but go through a "fibril shaving" process, affording fibrils composed of the 49-101 fragment and 53-101 fragment during more extensive maturation (incubation for longer than ten days). Seeding of the amyloid fibril formation process using sonicated mature amyloid fibrils accelerates the fibril formation process efficiently; however, addition of intact full-length lysozyme at the end of the lag phase slows the rate of amyloidogenesis. The intact full-length protein, in contrast to nicked lysozyme, slows fibril formation due to its slow conversion into the amyloid fold, probably due to inclusion of the non-amyloidogenic 1-48/102-129 portion of HEWL in the fibrils, which can function as a "molecular bumper" stalling further growth.
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Affiliation(s)
- Rajesh Mishra
- IFM Department of Chemistry, Linköping University, SE-581 83 Linköping, Sweden
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31
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Bellotti V, Nuvolone M, Giorgetti S, Obici L, Palladini G, Russo P, Lavatelli F, Perfetti V, Merlini G. The workings of the amyloid diseases. Ann Med 2007; 39:200-7. [PMID: 17457717 DOI: 10.1080/07853890701206887] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
The amyloidoses constitute a large group of diseases caused by an alteration in the conformation and metabolism of several globular proteins which, under particular conditions, deposit in tissues as insoluble fibrillar aggregates. To date, at least 24 different proteins have been recognized as causative agents of amyloid diseases. Despite a high heterogeneity in amino acid sequence, three-dimensional structure, and biological function, all amyloidogenic proteins share a reduced folding stability, a strong propensity to acquire more than one conformation, and the capacity to form almost indistinguishable amyloid fibrils. In some cases, the generation of an aggregation-prone state can be triggered or enhanced by the occurrence of mutations, a proteolytic cleavage, or a seeding process. The interaction between the amyloidogenic precursor, some common components of amyloid deposits, and the extra-cellular environment also plays a role in fibrillogenesis and in particular in the organ tropism of amyloid deposition. The process of amyloid fibril formation exerts a cytotoxic effect, resulting in tissue damage and organ dysfunction. Prefibrillar aggregates are thought to have an active part in this process. Due to the pathogenic complexity of amyloid diseases, the integration of several therapeutic interventions involving different critical levels of the amyloidogenic cascade is envisaged.
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Affiliation(s)
- Vittorio Bellotti
- Center for Amyloidosis, Department of Biochemistry, Biotechnology Research Laboratories, Foundation IRCCS Policlinico San Matteo, Pavia, Italy
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32
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Frare E, Mossuto MF, Polverino de Laureto P, Dumoulin M, Dobson CM, Fontana A. Identification of the core structure of lysozyme amyloid fibrils by proteolysis. J Mol Biol 2006; 361:551-61. [PMID: 16859705 DOI: 10.1016/j.jmb.2006.06.055] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2006] [Revised: 06/20/2006] [Accepted: 06/21/2006] [Indexed: 11/22/2022]
Abstract
Human lysozyme variants form amyloid fibrils in individuals suffering from a familial non-neuropathic systemic amyloidosis. In vitro, wild-type human and hen lysozyme, and the amyloidogenic mutants can be induced to form amyloid fibrils when incubated under appropriate conditions. In this study, fibrils of wild-type human lysozyme formed at low pH have been analyzed by a combination of limited proteolysis and Fourier-transform infrared (FTIR) spectroscopy, in order to map conformational features of the 130 residue chain of lysozyme when embedded in the amyloid aggregates. After digestion with pepsin at low pH, the lysozyme fibrils were found to be composed primarily of N and C-terminally truncated protein species encompassing residues 26-123 and 32-108, although a significant minority of molecules was found to be completely resistant to proteolysis under these conditions. FTIR spectra provide evidence that lysozyme fibrils contain extensive beta-sheet structure and a substantial element of non beta-sheet or random structure that is reduced significantly in the fibrils after digestion. The sequence 32-108 includes the beta-sheet and helix C of the native protein, previously found to be prone to unfold locally in human lysozyme and its pathogenic variants. Moreover, this core structure of the lysozyme fibrils encompasses the highly aggregation-prone region of the sequence recently identified in hen lysozyme. The present proteolytic data indicate that the region of the lysozyme molecule that unfolds and aggregates most readily corresponds to the most highly protease-resistant and thus highly structured region of the majority of mature amyloid fibrils. Overall, the data show that amyloid formation does not require the participation of the entire lysozyme chain. The majority of amyloid fibrils formed from lysozyme under the conditions used here contain a core structure involving some 50% of the polypeptide chain that is flanked by proteolytically accessible N and C-terminal regions.
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Affiliation(s)
- Erica Frare
- CRIBI Biotechnology Centre, University of Padua, Viale G. Colombo 3, 35121 Padua, Italy
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Kumita JR, Johnson RJK, Alcocer MJC, Dumoulin M, Holmqvist F, McCammon MG, Robinson CV, Archer DB, Dobson CM. Impact of the native-state stability of human lysozyme variants on protein secretion by Pichia pastoris. FEBS J 2006; 273:711-20. [PMID: 16441658 DOI: 10.1111/j.1742-4658.2005.05099.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We report the secreted expression by Pichia pastoris of two human lysozyme variants F57I and W64R, associated with systemic amyloid disease, and describe their characterization by biophysical methods. Both variants have a substantially decreased thermostability compared with wild-type human lysozyme, a finding that suggests an explanation for their increased propensity to form fibrillar aggregates and generate disease. The secreted yields of the F57I and W64R variants from P. pastoris are 200- and 30-fold lower, respectively, than that of wild-type human lysozyme. More comprehensive analysis of the secretion levels of 10 lysozyme variants shows that the low yields of these secreted proteins, under controlled conditions, can be directly correlated with a reduction in the thermostability of their native states. Analysis of mRNA levels in this selection of variants suggests that the lower levels of secretion are due to post-transcriptional processes, and that the reduction in secreted protein is a result of degradation of partially folded or misfolded protein via the yeast quality control system. Importantly, our results show that the human disease-associated mutations do not have levels of expression that are out of line with destabilizing mutations at other sites. These findings indicate that a complex interplay between reduced native-state stability, lower secretion levels, and protein aggregation propensity influences the types of mutation that give rise to familial forms of amyloid disease.
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Depristo MA, de Bakker PIW, Johnson RJK, Blundell TL. Crystallographic Refinement by Knowledge-Based Exploration of Complex Energy Landscapes. Structure 2005; 13:1311-9. [PMID: 16154088 DOI: 10.1016/j.str.2005.06.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2005] [Revised: 06/03/2005] [Accepted: 06/08/2005] [Indexed: 11/24/2022]
Abstract
Although X-ray crystallography remains the most versatile method to determine the three-dimensional atomic structure of proteins and much progress has been made in model building and refinement techniques, it remains a challenge to elucidate accurately the structure of proteins in medium-resolution crystals. This is largely due to the difficulty of exploring an immense conformational space to identify the set of conformers that collectively best fits the experimental diffraction pattern. We show here that combining knowledge-based conformational sampling in RAPPER with molecular dynamics/simulated annealing (MD/SA) vastly improves the quality and power of refinement compared to MD/SA alone. The utility of this approach is highlighted by the automated determination of a lysozyme mutant from a molecular replacement solution that is in congruence with a model prepared independently by crystallographers. Finally, we discuss the implications of this work on structure determination in particular and conformational sampling and energy minimization in general.
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Affiliation(s)
- Mark A Depristo
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom.
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