1
|
Wang Z, Zhang S, Xu Q, Li Z, Gu X, Wood K, García Sakai V, Wan Q, Chu XQ. Experimental Evidence for the Role of Dynamics in pH-Dependent Enzymatic Activity. J Phys Chem B 2024; 128:5814-5822. [PMID: 38726956 DOI: 10.1021/acs.jpcb.4c00219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Enzymatic activity is heavily influenced by pH, but the rationale for the dynamical mechanism of pH-dependent enzymatic activity has not been fully understood. In this work, combined neutron scattering techniques, including quasielastic neutron scattering (QENS) and small angle neutron scattering (SANS), are used to study the structural and dynamic changes of a model enzyme, xylanase, under different pH and temperature environments. The QENS results reveal that xylanase at optimal pH exhibits faster relaxational dynamics and a lower energy barrier between conformational substates. The SANS results demonstrate that pH affects both xylanase's stability and monodispersity. Our findings indicate that enzymes have optimized stability and function under their optimal pH conditions, with both structure and dynamics being affected. The current study offers valuable insights into enzymatic functionality mechanisms, allowing for broad industrial applications.
Collapse
Affiliation(s)
- Zhixin Wang
- Graduate School of China Academy of Engineering Physics, Beijing 100193, China
| | - Shengkai Zhang
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, China
- Institute of Advanced Science Facilities, Shenzhen 518107, China
| | - Qin Xu
- College of Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhihong Li
- College of Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Xudong Gu
- Graduate School of China Academy of Engineering Physics, Beijing 100193, China
| | - Kathleen Wood
- Australian Nuclear Science and Technology Organization, Lucas Heights, NSW 2234, Australia
| | - Victoria García Sakai
- ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, United Kingdom
| | - Qun Wan
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizer, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Xiang-Qiang Chu
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, China
- Department of Physics, City University of Hong Kong, Hong Kong 999077, China
| |
Collapse
|
2
|
Chatterjee S, Salimi A, Lee JY. Histidine tautomerism-mediated transthyretin amyloidogenesis: A molecular insight. Arch Biochem Biophys 2023; 742:109618. [PMID: 37172673 DOI: 10.1016/j.abb.2023.109618] [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: 12/10/2022] [Revised: 04/26/2023] [Accepted: 05/01/2023] [Indexed: 05/15/2023]
Abstract
Characterization of the conformational alterations involved in monomer misfolding is essential for elucidating the molecular basis of the initial stage of protein accumulation. Here, we report the first structural analyses of transthyretin (TTR) (26-57) fragments with two histidine tautomeric states (δ; Nδ1H and ε; Nε2H) using replica-exchange molecular dynamics (REMD) simulations. Explaining the organizational properties and misfolding procedure is challenging because the δ and ε configurations can occur in the free neutral state. REMD revealed that β-sheet generation is favored for the δδ (16.8%) and εδ (6.7%) tautomeric isomers, showing frequent main-chain contacts between the stable regions near the head (N-terminus) and central (middle) part compared to the εε (4.8%) and δε (2.8%) isomers. The presence of smaller and wider local energy minima may be related to the structural stability and toxicity of δδ/εδ and εε/δε. Histidines31 and 56 were the parts of regular (such as β-strand) and nonregular (such as coil) secondary structures within the highly toxic TTR isomer. For TTR amyloidosis, focusing on hazardous isomeric forms with high sheet contents may be a potent treatment strategy. Overall, our findings support the tautomerism concept and aid in our comprehension of the basic tautomeric actions of neutral histidine throughout the misfolding process.
Collapse
Affiliation(s)
- Sompriya Chatterjee
- Department of Chemistry, Sungkyunkwan University, Suwon, 440-746, South Korea
| | - Abbas Salimi
- Department of Chemistry, Sungkyunkwan University, Suwon, 440-746, South Korea
| | - Jin Yong Lee
- Department of Chemistry, Sungkyunkwan University, Suwon, 440-746, South Korea.
| |
Collapse
|
3
|
Lee KH, Kuczera K. Effect of alanine versus serine at position 88 of human transthyretin mutants on the protein stability. Protein Eng Des Sel 2023; 36:6972274. [PMID: 36611015 DOI: 10.1093/protein/gzad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/22/2022] [Accepted: 12/05/2022] [Indexed: 01/09/2023] Open
Abstract
Human transthyretin (TTR) is a homo-tetrameric plasma protein associated with a high percentage of β-sheet forming amyloid fibrils. It accumulates in tissues or extracellular matrices to cause amyloid diseases. Free energy simulations with thermodynamic integration based on all-atom molecular dynamics simulations have been carried out to analyze the effects of the His88 → Ala and Ser mutations on the stability of human TTR. The calculated free energy change differences (ΔΔG) caused by the His88 → Ala and His88 → Ser mutations are -1.84 ± 0.86 and 7.56 ± 0.55 kcal/mol, respectively, which are in excellent agreement with prior reported experimental values. The simulation results show that the H88A mutant is more stable than the wild type, whereas the H88S mutant is less stable than the wild type. The free energy component analysis shows that the contribution to the free energy change difference (ΔΔG) for the His88 → Ala and His88 → Ser mutations mainly arise from electrostatic and van der Waals interactions, respectively. The electrostatic term stabilizes the H88A mutant more than the wild type, but the van der Waals interaction destabilizes the H88S mutant relative to the wild type. Individual residue contributions to the free energy change show neighboring residues exert stabilizing and destabilizing influence on the mutants. The implications of the simulation results for understanding the stabilizing and destabilizing effect and its contribution to protein stability are discussed.
Collapse
Affiliation(s)
- Kyung-Hoon Lee
- Department of Biology, Chowan University, One University Place, Murfreesboro, NC 27855, USA
| | - Krzysztof Kuczera
- Department of Chemistry and Department of Molecular Biosciences, University of Kansas, 1567 Irving Hill Road, Lawrence, KS 66045, USA
| |
Collapse
|
4
|
Xu Y, Sun Q, Chen W, Han Y, Gao Y, Ye J, Wang H, Gao L, Liu Y, Yang Y. The Taste-Masking Mechanism of Chitosan at the Molecular Level on Bitter Drugs of Alkaloids and Flavonoid Glycosides from Traditional Chinese Medicine. Molecules 2022; 27:7455. [PMID: 36364280 PMCID: PMC9658633 DOI: 10.3390/molecules27217455] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 10/25/2022] [Accepted: 10/31/2022] [Indexed: 09/16/2023] Open
Abstract
Taste masking of traditional Chinese medicines (TCMs) containing multiple bitter components remains an important challenge. In this study, berberine (BER) in alkaloids and phillyrin (PHI) in flavonoid glycosides, which are common bitter components in traditional Chinese medicines, were selected as model drugs. Chitosan (CS) was used to mask their unfriendly taste. Firstly, from the molecular level, we explained the taste-masking mechanism of CS on those two bitter components in detail. Based on those taste-masking mechanisms, the bitter taste of a mixture of BER and PHI was easily masked by CS in this work. The physicochemical characterization results showed the taste-masking compounds formed by CS with BER (named as BER/CS) and PHI (named as PHI/CS) were uneven in appearance. The drug binding efficiency of BER/CS and PHI/CS was 50.15 ± 2.63% and 67.10 ± 2.52%, respectively. The results of DSC, XRD, FTIR and molecular simulation further indicated that CS mainly masks the bitter taste by disturbing the binding site of bitter drugs and bitter receptors in the oral cavity via forming hydrogen bonds between its hydroxyl or amine groups and the nucleophilic groups of BER and PHI. The taste-masking evaluation results by the electronic tongue test confirmed the excellent taste-masking effects on alkaloids, flavonoid glycosides or a mixture of the two kinds of bitter components. The in vitro release as well as in vivo pharmacokinetic results suggested that the taste-masked compounds in this work could achieve rapid drug release in the gastric acid environment and did not influence the in vivo pharmacokinetic results of the drug. The taste-masking method in this work may have potential for the taste masking of traditional Chinese medicine compounds containing multiple bitter components.
Collapse
Affiliation(s)
- Yaqi Xu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Drug Delivery Technology and Novel Formulation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Qianwen Sun
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Drug Delivery Technology and Novel Formulation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Wei Chen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Drug Delivery Technology and Novel Formulation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Yanqi Han
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Drug Delivery Technology and Novel Formulation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Yue Gao
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Drug Delivery Technology and Novel Formulation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Jun Ye
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Drug Delivery Technology and Novel Formulation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Hongliang Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Drug Delivery Technology and Novel Formulation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Lili Gao
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Drug Delivery Technology and Novel Formulation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Yuling Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Drug Delivery Technology and Novel Formulation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Yanfang Yang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Drug Delivery Technology and Novel Formulation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| |
Collapse
|
5
|
Hartmann J, Zacharias M. Analysis of amyloidogenic transthyretin mutations using continuum solvent free energy calculations. Proteins 2022; 90:2080-2090. [PMID: 35841533 DOI: 10.1002/prot.26399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/26/2022] [Accepted: 07/08/2022] [Indexed: 12/28/2022]
Abstract
Many proteins can undergo pathological conformational changes that result in the formation of amyloidogenic fibril structures. Various neurodegenerative diseases are associated with such pathological fibril formation of specific proteins. Transthyretin (TTR) is a tetrameric globular transport protein in the blood plasma that can dissociate, unfold, and form long and stable fibrils. Many TTR mutations are known that promote (TTR) amyloidosis and cause severe diseases. TTR amyloidosis has been studied extensively using biochemical methods and structures of various mutations in the globular form have been characterized. Recently, also the structure of a TTR fibril has been determined. In an effort to better understand why some mutations increase or decrease the tendency of amyloid formation, we have applied a combined molecular dynamics and continuum solvent approach to calculate the energetic influence of residue changes in the globular versus fibril form. For 29 out of 36 tested TTR single residue mutations, the approach correctly predicts the increased or decreased tendency for amyloidosis allowing us also to elucidate the origins of the tendency. We find that indeed the destabilization of the globular monomer or changes in dimer and tetramer stability due to mutation has a dominant influence on the amyloidogenic tendency. The continuum solvent model predicts a significantly more favorable mean energy per residue of the fibril form compared to the globular form. This effect is only slightly modulated by single-point mutations preserving the energetic preference for fibril formation upon protein unfolding. It explains why no correlation between experimental amyloidosis and calculated change in fibril stability was observed.
Collapse
Affiliation(s)
- Julian Hartmann
- Physics Department and Center of Protein Assemblies, Technical University of Munich, Garching, Bavaria, Germany
| | - Martin Zacharias
- Physics Department and Center of Protein Assemblies, Technical University of Munich, Garching, Bavaria, Germany
| |
Collapse
|
6
|
Lee K, Kuczera K. Modulation of human transthyretin stability by the mutations at histidine 88 studied by free energy simulation. Proteins 2022; 90:1825-1836. [DOI: 10.1002/prot.26353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/03/2022] [Accepted: 04/20/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Kyung‐Hoon Lee
- Department of Biology Chowan University Murfreesboro North Carolina USA
| | - Krzysztof Kuczera
- Department of Chemistry and Department of Molecular Biosciences University of Kansas Lawrence Kansas USA
| |
Collapse
|
7
|
Molecular Mechanisms of Cardiac Amyloidosis. Int J Mol Sci 2021; 23:ijms23010025. [PMID: 35008444 PMCID: PMC8744761 DOI: 10.3390/ijms23010025] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/18/2021] [Accepted: 12/18/2021] [Indexed: 12/22/2022] Open
Abstract
Cardiac involvement has a profound effect on the prognosis of patients with systemic amyloidosis. Therapeutic methods for suppressing the production of causative proteins have been developed for ATTR amyloidosis and AL amyloidosis, which show cardiac involvement, and the prognosis has been improved. However, a method for removing deposited amyloid has not been established. Methods for reducing cytotoxicity caused by amyloid deposition and amyloid precursor protein to protect cardiovascular cells are also needed. In this review, we outline the molecular mechanisms and treatments of cardiac amyloidosis.
Collapse
|
8
|
Binding characteristics of hydroxylated polybrominated diphenyl ether with thyroid protein and its potential toxicity. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
|
9
|
Transthyretin Misfolding, A Fatal Structural Pathogenesis Mechanism. Int J Mol Sci 2021; 22:ijms22094429. [PMID: 33922648 PMCID: PMC8122960 DOI: 10.3390/ijms22094429] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/18/2021] [Accepted: 04/21/2021] [Indexed: 12/11/2022] Open
Abstract
Transthyretin (TTR) is an essential transporter of a thyroid hormone and a holo-retinol binding protein, found abundantly in human plasma and cerebrospinal fluid. In addition, this protein is infamous for its amyloidogenic propensity, causing various amyloidoses in humans, such as senile systemic amyloidosis, familial amyloid polyneuropathy, and familial amyloid cardiomyopathy. It has been known for over two decades that decreased stability of the native tetrameric conformation of TTR is the main cause of these diseases. Yet, mechanistic details on the amyloidogenic transformation of TTR were not clear until recent multidisciplinary investigations on various structural states of TTR. In this review, we discuss recent advancements in the structural understanding of TTR misfolding and amyloidosis processes. Special emphasis has been laid on the observations of novel structural features in various amyloidogenic species of TTR. In addition, proteolysis-induced fragmentation of TTR, a recently proposed mechanism facilitating TTR amyloidosis, has been discussed in light of its structural consequences and relevance to acknowledge the amyloidogenicity of TTR.
Collapse
|
10
|
Bezerra F, Saraiva MJ, Almeida MR. Modulation of the Mechanisms Driving Transthyretin Amyloidosis. Front Mol Neurosci 2020; 13:592644. [PMID: 33362465 PMCID: PMC7759661 DOI: 10.3389/fnmol.2020.592644] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/18/2020] [Indexed: 12/19/2022] Open
Abstract
Transthyretin (TTR) amyloidoses are systemic diseases associated with TTR aggregation and extracellular deposition in tissues as amyloid. The most frequent and severe forms of the disease are hereditary and associated with amino acid substitutions in the protein due to single point mutations in the TTR gene (ATTRv amyloidosis). However, the wild type TTR (TTR wt) has an intrinsic amyloidogenic potential that, in particular altered physiologic conditions and aging, leads to TTR aggregation in people over 80 years old being responsible for the non-hereditary ATTRwt amyloidosis. In normal physiologic conditions TTR wt occurs as a tetramer of identical subunits forming a central hydrophobic channel where small molecules can bind as is the case of the natural ligand thyroxine (T4). However, the TTR amyloidogenic variants present decreased stability, and in particular conditions, dissociate into partially misfolded monomers that aggregate and polymerize as amyloid fibrils. Therefore, therapeutic strategies for these amyloidoses may target different steps in the disease process such as decrease of variant TTR (TTRv) in plasma, stabilization of TTR, inhibition of TTR aggregation and polymerization or disruption of the preformed fibrils. While strategies aiming decrease of the mutated TTR involve mainly genetic approaches, either by liver transplant or the more recent technologies using specific oligonucleotides or silencing RNA, the other steps of the amyloidogenic cascade might be impaired by pharmacologic compounds, namely, TTR stabilizers, inhibitors of aggregation and amyloid disruptors. Modulation of different steps involved in the mechanism of ATTR amyloidosis and compounds proposed as pharmacologic agents to treat TTR amyloidosis will be reviewed and discussed.
Collapse
Affiliation(s)
- Filipa Bezerra
- Molecular Neurobiology Group, IBMC-Instituto de Biologia Molecular e Celular, i3S-Instituto de Investigação e Inovação em Saúde, Porto, Portugal.,Department of Molecular Biology, ICBAS-Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Maria João Saraiva
- Molecular Neurobiology Group, IBMC-Instituto de Biologia Molecular e Celular, i3S-Instituto de Investigação e Inovação em Saúde, Porto, Portugal.,Department of Molecular Biology, ICBAS-Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Maria Rosário Almeida
- Molecular Neurobiology Group, IBMC-Instituto de Biologia Molecular e Celular, i3S-Instituto de Investigação e Inovação em Saúde, Porto, Portugal.,Department of Molecular Biology, ICBAS-Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| |
Collapse
|
11
|
Kusaka K, Yokoyama T, Yamada T, Yano N, Tanaka I, Mizuguchi M. Neutron diffraction experiment with the Y116S variant of transthyretin using iBIX at J-PARC: application of a new integration method. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:1050-1056. [PMID: 33135676 DOI: 10.1107/s2059798320012498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 09/11/2020] [Indexed: 11/10/2022]
Abstract
Transthyretin (TTR) is one of more than 30 amyloidogenic proteins, and the amyloid fibrils found in patients afflicted with ATTR amyloidosis are composed of this protein. Wild-type TTR amyloids accumulate in the heart in senile systemic amyloidosis (SSA). ATTR amyloidosis occurs at a much younger age than SSA, and the affected individuals carry a TTR mutant. The naturally occurring amyloidogenic Y116S TTR variant forms more amyloid fibrils than wild-type TTR. Thus, the Y116S mutation reduces the stability of the TTR structure. A neutron diffraction experiment on Y116S TTR was performed to elucidate the mechanism of the changes in structural stability between Y116S variant and wild-type TTR through structural comparison. Large crystals of the Y116S variant were grown under optimal crystallization conditions, and a single 2.4 mm3 crystal was ultimately obtained. This crystal was subjected to time-of-flight (TOF) neutron diffraction using the IBARAKI biological crystal diffractometer (iBIX) at the Japan Proton Accelerator Research Complex, Tokai, Japan (J-PARC). A full data set for neutron structure analysis was obtained in 14 days at an operational accelerator power of 500 kW. A new integration method was developed and showed improved data statistics; the new method was applied to the reduction of the TOF diffraction data from the Y116S variant. Data reduction was completed and the integrated intensities of the Bragg reflections were obtained at 1.9 Å resolution for structure refinement. Moreover, X-ray diffraction data at 1.4 Å resolution were obtained for joint neutron-X-ray refinement.
Collapse
Affiliation(s)
- Katsuhiro Kusaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Takeshi Yokoyama
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama, Toyama 930-0194, Japan
| | - Taro Yamada
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Naomine Yano
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Ichiro Tanaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Mineyuki Mizuguchi
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama, Toyama 930-0194, Japan
| |
Collapse
|
12
|
Destabilisation of the structure of transthyretin is driven by Ca 2. Int J Biol Macromol 2020; 166:409-423. [PMID: 33129902 DOI: 10.1016/j.ijbiomac.2020.10.199] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/08/2020] [Accepted: 10/24/2020] [Indexed: 12/19/2022]
Abstract
Tetrameric transthyretin (TTR) transports thyroid hormones and retinol in plasma and cerebrospinal fluid and performs protective functions under stress conditions. Ageing and mutations result in TTR destabilisation and the formation of the amyloid deposits that dysregulate Ca2+ homeostasis. Our aim was to determine whether Ca2+ affects the structural stability of TTR. We show, using multiple techniques, that Ca2+ does not induce prevalent TTR dissociation and/or oligomerisation. However, in the presence of Ca2+, TTR exhibits altered conformational flexibility and different interactions with the solvent molecules. These structural changes lead to the formation of the sub-populations of non-native TTR conformers and to the destabilisation of the structure of TTR. Moreover, the sub-population of TTR molecules undergoes fragmentation that is augmented by Ca2+. We postulate that Ca2+ constitutes the structural and functional switch between the native and non-native forms of TTR, and therefore tip the balance towards age-dependent pathological calcification.
Collapse
|
13
|
Österlund N, Lundqvist M, Ilag LL, Gräslund A, Emanuelsson C. Amyloid-β oligomers are captured by the DNAJB6 chaperone: Direct detection of interactions that can prevent primary nucleation. J Biol Chem 2020; 295:8135-8144. [PMID: 32350108 PMCID: PMC7294096 DOI: 10.1074/jbc.ra120.013459] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/23/2020] [Indexed: 12/16/2022] Open
Abstract
A human molecular chaperone protein, DnaJ heat shock protein family (Hsp40) member B6 (DNAJB6), efficiently inhibits amyloid aggregation. This inhibition depends on a unique motif with conserved serine and threonine (S/T) residues that have a high capacity for hydrogen bonding. Global analysis of kinetics data has previously shown that DNAJB6 especially inhibits the primary nucleation pathways. These observations indicated that DNAJB6 achieves this remarkably effective and sub-stoichiometric inhibition by interacting not with the monomeric unfolded conformations of the amyloid-β symbol (Aβ) peptide but with aggregated species. However, these pre-nucleation oligomeric aggregates are transient and difficult to study experimentally. Here, we employed a native MS-based approach to directly detect oligomeric forms of Aβ formed in solution. We found that WT DNAJB6 considerably reduces the signals from the various forms of Aβ (1–40) oligomers, whereas a mutational DNAJB6 variant in which the S/T residues have been substituted with alanines does not. We also detected signals that appeared to represent DNAJB6 dimers and trimers to which varying amounts of Aβ are bound. These data provide direct experimental evidence that it is the oligomeric forms of Aβ that are captured by DNAJB6 in a manner which depends on the S/T residues. We conclude that, in agreement with the previously observed decrease in primary nucleation rate, strong binding of Aβ oligomers to DNAJB6 inhibits the formation of amyloid nuclei.
Collapse
Affiliation(s)
- Nicklas Österlund
- Department of Biochemistry and Biophysics, Stockholm University, Sweden
| | - Martin Lundqvist
- Department of Biochemistry and Structural Biology, Lund University, Sweden
| | - Leopold L Ilag
- Department of Materials and Environmental Chemistry, Stockholm University, Sweden
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Stockholm University, Sweden
| | | |
Collapse
|
14
|
Abstract
The IBARAKI Biological Crystal Diffractometer (iBIX) has been available for use at MLF (Material and Life Science Facility) in J-PARC (Japan Proton Accelerator Research Complex) since 2008. The development in state-of-the-art detector systems could enable iBIX to become one of the highest-performance neutron single-crystal diffractometers in the world. Here, together with other various developments, such as data reduction software, crystal growth, and new techniques in measurement coupled analysis, we provided new hydrogen and water structural data of several proteins and macromolecules. Although the proton power at MLF has not yet reached its planned maximum (1MW), a more powerful neutron source will be soon needed for neutron protein crystallography. A future idea is also proposed and discussed in this article.
Collapse
|
15
|
Wijaya AW, Nguyen AI, Roe LT, Butterfoss GL, Spencer RK, Li NK, Zuckermann RN. Cooperative Intramolecular Hydrogen Bonding Strongly Enforces cis-Peptoid Folding. J Am Chem Soc 2019; 141:19436-19447. [DOI: 10.1021/jacs.9b10497] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Andrew W. Wijaya
- The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Andy I. Nguyen
- The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Leah T. Roe
- The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Glenn L. Butterfoss
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Ryan K. Spencer
- Department of Chemistry, Department of Chemical Engineering & Material Science, University of California, Irvine, California 92697, United States
| | - Nan K. Li
- The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Ronald N. Zuckermann
- The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| |
Collapse
|
16
|
Koirala M, Alexov E. Computational chemistry methods to investigate the effects caused by DNA variants linked with disease. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2019. [DOI: 10.1142/s0219633619300015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Computational chemistry offers variety of tools to study properties of biological macromolecules. These tools vary in terms of levels of details from quantum mechanical treatment to numerous macroscopic approaches. Here, we provide a review of computational chemistry algorithms and tools for modeling the effects of genetic variations and their association with diseases. Particular emphasis is given on modeling the effects of missense mutations on stability, conformational dynamics, binding, hydrogen bond network, salt bridges, and pH-dependent properties of the corresponding macromolecules. It is outlined that the disease may be caused by alteration of one or several of above-mentioned biophysical characteristics, and a successful prediction of pathogenicity requires detailed analysis of how the alterations affect the function of involved macromolecules. The review provides a short list of most commonly used algorithms to predict the molecular effects of mutations as well.
Collapse
Affiliation(s)
- Mahesh Koirala
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29630, USA
| | - Emil Alexov
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29630, USA
| |
Collapse
|
17
|
Park GY, Jamerlan A, Shim KH, An SSA. Diagnostic and Treatment Approaches Involving Transthyretin in Amyloidogenic Diseases. Int J Mol Sci 2019; 20:E2982. [PMID: 31216785 PMCID: PMC6628571 DOI: 10.3390/ijms20122982] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 06/10/2019] [Accepted: 06/13/2019] [Indexed: 02/07/2023] Open
Abstract
Transthyretin (TTR) is a thyroid hormone-binding protein which transports thyroxine from the bloodstream to the brain. The structural stability of TTR in tetrameric form is crucial for maintaining its original functions in blood or cerebrospinal fluid (CSF). The altered structure of TTR due to genetic mutations or its deposits due to aggregation could cause several deadly diseases such as cardiomyopathy and neuropathy in autonomic, motor, and sensory systems. The early diagnoses for hereditary amyloid TTR with cardiomyopathy (ATTR-CM) and wild-type amyloid TTR (ATTRwt) amyloidosis, which result from amyloid TTR (ATTR) deposition, are difficult to distinguish due to the close similarities of symptoms. Thus, many researchers investigated the role of ATTR as a biomarker, especially its potential for differential diagnosis due to its varying pathogenic involvement in hereditary ATTR-CM and ATTRwt amyloidosis. As a result, the detection of ATTR became valuable in the diagnosis and determination of the best course of treatment for ATTR amyloidoses. Assessing the extent of ATTR deposition and genetic analysis could help in determining disease progression, and thus survival rate could be improved following the determination of the appropriate course of treatment for the patient. Here, the perspectives of ATTR in various diseases were presented.
Collapse
Affiliation(s)
- Gil Yong Park
- Department of Bionano Technology, Gachon Medical Research Institute, Gachon University, Seongnam-si 13120, Korea.
| | - Angelo Jamerlan
- Department of Bionano Technology, Gachon Medical Research Institute, Gachon University, Seongnam-si 13120, Korea.
| | - Kyu Hwan Shim
- Department of Bionano Technology, Gachon Medical Research Institute, Gachon University, Seongnam-si 13120, Korea.
| | - Seong Soo A An
- Department of Bionano Technology, Gachon Medical Research Institute, Gachon University, Seongnam-si 13120, Korea.
| |
Collapse
|
18
|
Hellman U, Lång K, Ihse E, Jonasson J, Olsson M, Lundgren HE, Pilebro B, Westermark P, Wixner J, Anan I. Transthyretin Glu54Leu - an unknown mutation within the Swedish population associated with amyloid cardiomyopathy and a unique fibril type. Scandinavian Journal of Clinical and Laboratory Investigation 2019; 79:372-376. [PMID: 31169435 DOI: 10.1080/00365513.2019.1624977] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
For the first time, we report of a Swedish family of five individuals with a TTR Glu54Leu (p. Glu74Leu) mutation in the transthyretin gene. This mutation has been previously described a few times in the literature, but no phenotypic or clinical description has been done before. The most common mutation in the Swedish population is TTRVal30Met and is mostly found in the Northern part of Sweden. Interestingly, the TTRGlu54Leu mutation was found in the same endemic area. The main phenotype of the TTR Glu54Leu patients is severe cardiomyopathy, which resulted in heart transplantation for the index person. As previously seen for ATTR amyloidosis patients with mainly cardiomyopathy, the amyloid fibrils consisted of a mixture of full-length and fragmented TTR species. However, western blot analyses detected a previously unrecognized band, indicating that these patients may have a third, so far unrecognized, fibril composition type that is distinct from the usual type A band pattern.
Collapse
Affiliation(s)
- Urban Hellman
- Department of Public Health and Clinical Medicine, Umeå University , Umeå , Sweden
| | - Kenneth Lång
- Department of Medicine, Piteå Hospital , Piteå , Sweden
| | - Elisabet Ihse
- Department of Immunology, Genetics and Pathology, Uppsala University , Uppsala , Sweden
| | - Jenni Jonasson
- Clinical Genetics, Laboratory Medicine, Department of Medical Bioscience/Medical and Clinical Genetics, Umeå University , Umeå , Sweden
| | - Malin Olsson
- Department of Public Health and Clinical Medicine, Umeå University , Umeå , Sweden.,Wallenberg Centre for Molecular Medicine, Umeå University , Umeå , Sweden
| | - Hans-Erik Lundgren
- Department of Public Health and Clinical Medicine, Umeå University , Umeå , Sweden
| | - Björn Pilebro
- Department of Public Health and Clinical Medicine, Umeå University , Umeå , Sweden
| | - Per Westermark
- Department of Immunology, Genetics and Pathology, Uppsala University , Uppsala , Sweden
| | - Jonas Wixner
- Department of Public Health and Clinical Medicine, Umeå University , Umeå , Sweden
| | - Intissar Anan
- Department of Public Health and Clinical Medicine, Umeå University , Umeå , Sweden.,Wallenberg Centre for Molecular Medicine, Umeå University , Umeå , Sweden
| |
Collapse
|
19
|
Affiliation(s)
- Takeshi Yokoyama
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0914, Japan
| | - Mineyuki Mizuguchi
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0914, Japan
- Graduate School of Innovative Life Science, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| |
Collapse
|
20
|
Yokoyama T, Hanawa Y, Obita T, Mizuguchi M. The effect of amino acid substitution at position 88 on the structure and stability of transthyretin. Amyloid 2019; 26:43-44. [PMID: 31343290 DOI: 10.1080/13506129.2019.1582507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Takeshi Yokoyama
- a Faculty of Pharmaceutical Sciences, University of Toyama , Toyama , Japan
| | - Yuma Hanawa
- a Faculty of Pharmaceutical Sciences, University of Toyama , Toyama , Japan
| | - Takayuki Obita
- a Faculty of Pharmaceutical Sciences, University of Toyama , Toyama , Japan
| | - Mineyuki Mizuguchi
- a Faculty of Pharmaceutical Sciences, University of Toyama , Toyama , Japan
| |
Collapse
|
21
|
Yano N, Yamada T, Hosoya T, Ohhara T, Tanaka I, Niimura N, Kusaka K. Status of the neutron time-of-flight single-crystal diffraction data-processing software STARGazer. Acta Crystallogr D Struct Biol 2018; 74:1041-1052. [PMID: 30387763 PMCID: PMC6213574 DOI: 10.1107/s2059798318012081] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 08/24/2018] [Indexed: 11/10/2022] Open
Abstract
The STARGazer data-processing software is used for neutron time-of-flight (TOF) single-crystal diffraction data collected using the IBARAKI Biological Crystal Diffractometer (iBIX) at the Japan Proton Accelerator Research Complex (J-PARC). This software creates hkl intensity data from three-dimensional (x, y, TOF) diffraction data. STARGazer is composed of a data-processing component and a data-visualization component. The former is used to calculate the hkl intensity data. The latter displays the three-dimensional diffraction data with searched or predicted peak positions and is used to determine and confirm integration regions. STARGazer has been developed to make it easier to use and to obtain more accurate intensity data. For example, a profile-fitting method for peak integration was developed and the data statistics were improved. STARGazer and its manual, containing installation and data-processing components, have been prepared and provided to iBIX users. This article describes the status of the STARGazer data-processing software and its data-processing algorithms.
Collapse
Affiliation(s)
- Naomine Yano
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Taro Yamada
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Takaaki Hosoya
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
- College of Engineering, Ibaraki University, 4-12-1 Nakanarusawa, Hitachi, Ibaraki 316-8511, Japan
| | - Takashi Ohhara
- Neutron Science Section, J-PARC Center, Japan Atomic Energy Agency, 2-4 Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan
| | - Ichiro Tanaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
- College of Engineering, Ibaraki University, 4-12-1 Nakanarusawa, Hitachi, Ibaraki 316-8511, Japan
| | - Nobuo Niimura
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Katsuhiro Kusaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| |
Collapse
|
22
|
Neutron macromolecular crystallography. Emerg Top Life Sci 2018; 2:39-55. [DOI: 10.1042/etls20170083] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/12/2017] [Accepted: 12/19/2017] [Indexed: 01/02/2023]
Abstract
Neutron diffraction techniques permit direct determination of the hydrogen (H) and deuterium (D) positions in crystal structures of biological macromolecules at resolutions of ∼1.5 and 2.5 Å, respectively. In addition, neutron diffraction data can be collected from a single crystal at room temperature without radiation damage issues. By locating the positions of H/D-atoms, protonation states and water molecule orientations can be determined, leading to a more complete understanding of many biological processes and drug-binding. In the last ca. 5 years, new beamlines have come online at reactor neutron sources, such as BIODIFF at Heinz Maier-Leibnitz Zentrum and IMAGINE at Oak Ridge National Laboratory (ORNL), and at spallation neutron sources, such as MaNDi at ORNL and iBIX at the Japan Proton Accelerator Research Complex. In addition, significant improvements have been made to existing beamlines, such as LADI-III at the Institut Laue-Langevin. The new and improved instrumentations are allowing sub-mm3 crystals to be regularly used for data collection and permitting the study of larger systems (unit-cell edges >100 Å). Owing to this increase in capacity and capability, many more studies have been performed and for a wider range of macromolecules, including enzymes, signalling proteins, transport proteins, sugar-binding proteins, fluorescent proteins, hormones and oligonucleotides; of the 126 structures deposited in the Protein Data Bank, more than half have been released since 2013 (65/126, 52%). Although the overall number is still relatively small, there are a growing number of examples for which neutron macromolecular crystallography has provided the answers to questions that otherwise remained elusive.
Collapse
|
23
|
Xu J, Wei Y, Yang W, Yang L, Yi Z. The mechanism and conformational changes of polybrominated diphenyl ethers to TTR by fluorescence spectroscopy, molecular simulation, and quantum chemistry. Analyst 2018; 143:4662-4673. [DOI: 10.1039/c8an00435h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Free energy contribution of amino acid LYS (B and D chains) and PDBEs was analyzed combining quantum chemistry and molecular modeling.
Collapse
Affiliation(s)
- Jie Xu
- Guangxi Colleges and Universities Key Laboratory of Food Safety and Detection; College of Chemistry and Bioengineering
- Guilin University of Technology
- Guilin 541004
- China
| | - Yuchen Wei
- Guangxi Colleges and Universities Key Laboratory of Food Safety and Detection; College of Chemistry and Bioengineering
- Guilin University of Technology
- Guilin 541004
- China
| | - Wu Yang
- Guangxi Colleges and Universities Key Laboratory of Food Safety and Detection; College of Chemistry and Bioengineering
- Guilin University of Technology
- Guilin 541004
- China
| | - Lulu Yang
- Guangxi Colleges and Universities Key Laboratory of Food Safety and Detection; College of Chemistry and Bioengineering
- Guilin University of Technology
- Guilin 541004
- China
| | - Zhongsheng Yi
- Guangxi Colleges and Universities Key Laboratory of Food Safety and Detection; College of Chemistry and Bioengineering
- Guilin University of Technology
- Guilin 541004
- China
| |
Collapse
|
24
|
Sun X, Dyson HJ, Wright PE. Fluorotryptophan Incorporation Modulates the Structure and Stability of Transthyretin in a Site-Specific Manner. Biochemistry 2017; 56:5570-5581. [PMID: 28920433 DOI: 10.1021/acs.biochem.7b00815] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Abnormal deposition of aggregated wild-type (WT) human transthyretin (TTR) and its pathogenic variants is responsible for cardiomyopathy and neuropathy related to TTR amyloidosis. The tryptophan (Trp) fluorescence measurements typically used to study structural changes of TTR do not yield site-specific information on the two Trp residues per TTR protomer. To obtain such information, tryptophan labeled with fluorine at the 5 and 6 positions (5FW and 6FW) was incorporated into TTR. Fluorescence of 5FW and 6FW-labeled WT-TTR (WT-5FW and WT-6FW) and a single-Trp mutant W41Y showed that the photophysics of incorporated fluoro-Trp is consistent with site-specific solvation of the indole ring of W41 and W79. 19F-NMR showed that solvent accessibility depends on both the location of the Trp and the position of the fluorine substituent in the indole ring. Unexpectedly, differences were observed in the rates of aggregation, with WT-6FW aggregating more rapidly than WT-5FW or WT-TTR. Real-time 19F-NMR urea unfolding experiments revealed that WT-5FW is kinetically more stable than WT-6FW, consistent with the aggregation assay. In addition, structural perturbations of residues distant from either Trp site are more extensive in WT-6FW. Notably, residues in the dimer interfaces are perturbed by 6FW at residue 79; pathogenic mutations in these regions are associated with reduced tetramer stability and amyloidogenesis. The differences in behavior that arise from the replacement of a fluorine at the 5-position of a tryptophan with one at the adjacent 6-position emphasize the delicate balance of stability in the TTR tetramer.
Collapse
Affiliation(s)
- Xun Sun
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| |
Collapse
|
25
|
Cao H, Sun Y, Wang L, Zhao C, Fu J, Zhang A. Understanding the microscopic binding mechanism of hydroxylated and sulfated polybrominated diphenyl ethers with transthyretin by molecular docking, molecular dynamics simulations and binding free energy calculations. MOLECULAR BIOSYSTEMS 2017; 13:736-749. [PMID: 28217795 DOI: 10.1039/c6mb00638h] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Polybrominated diphenyl ethers (PBDEs), one typical type of persistent environmental contaminant, have toxicological effects such as disrupting thyroid homeostasis in the human body. The high binding affinities of hydroxylated metabolites of PBDEs (OH-PBDEs) with transthyretin (TTR) were considered to be one major reason for their extraordinary capacity of passing through the blood-brain barrier via competitive thyroid hormone (T4) transport protein binding. Recent findings showed that sulfated PBDEs can be formed in human liver cytosol as phase-II metabolites. However, experimentally determined data for the TTR binding potential of the sulfated PBDEs are still not available. Therefore, molecular docking and molecular dynamics (MD) simulations were employed in the present study to probe the molecular basis of TTR interacting with hydroxylated and sulfated PBDEs at the atomic level. The docking scores of LeDock were used to construct the structure-based predictive model. The calculated results showed that the sulfated PBDEs have stronger affinity for TTR than the corresponding OH-PBDEs. Further analysis of structural characteristics based on MD simulations indicated that upon the binding of PBDE metabolites, the stability of TTR was enhanced and the dissociation rate of the tetrameric protein structure was potentially decreased. Subsequent binding free energy calculations implied that van der Waals interactions are the dominant forces for the binding of these metabolites of PBDEs at the T4 site of TTR. The residues Ser117/Ser117' and Lys15/Lys15' were identified, by both residue energy decomposition and computational alanine-scanning mutagenesis methods, as key residues which play an important role in determining the binding orientations of the -OSO3- group of sulfated PBDEs by formation of either hydrogen bonds or electrostatic interactions, respectively. In general, the combination of docking calculations with MD simulations provided a theoretically toxicological assessment for the metabolites of PBDEs, deep insight into the recognition mechanism of TTR for these compounds, and thus more comprehensive understanding of the thyroid-related toxic effects of PBDEs as well.
Collapse
Affiliation(s)
- Huiming Cao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China. and College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Yuzhen Sun
- Institute of Environment and Health, Jianghan University, Wuhan 430056, China
| | - Ling Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China. and College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Chunyan Zhao
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Jianjie Fu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China. and College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Aiqian Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China. and College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China and Institute of Environment and Health, Jianghan University, Wuhan 430056, China
| |
Collapse
|
26
|
Yokoyama T, Hanawa Y, Obita T, Mizuguchi M. Stability and crystal structures of His88 mutant human transthyretins. FEBS Lett 2017; 591:1862-1871. [PMID: 28563699 DOI: 10.1002/1873-3468.12704] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/18/2017] [Accepted: 05/26/2017] [Indexed: 11/08/2022]
Abstract
Destabilization of human transthyretin (TTR) has been implicated in its misfolding and aggregation. A previous study on the neutron crystal structure of TTR suggested that a large hydrogen bond network around H88 which includes water molecules is significantly involved in the stability of wild-type TTR (WT-TTR). Here, we demonstrate that the H88R mutant associated with amyloid cardiomyopathy is substantially destabilized compared with WT-TTR. In order to clarify the role of H88 and the hydrogen bond network in the stability of TTR, we determined the thermodynamic stability and the crystal structure of H88 mutants (H88A, H88F, H88Y, and H88S). Our results suggest that in some cases TTR is destabilized due to alterations in bound water molecules as well as structural changes in TTR itself.
Collapse
Affiliation(s)
| | - Yuma Hanawa
- Faculty of Pharmaceutical Sciences, University of Toyama, Japan
| | - Takayuki Obita
- Faculty of Pharmaceutical Sciences, University of Toyama, Japan
| | | |
Collapse
|
27
|
Yee AW, Moulin M, Breteau N, Haertlein M, Mitchell EP, Cooper JB, Boeri Erba E, Forsyth VT. Impact of Deuteration on the Assembly Kinetics of Transthyretin Monitored by Native Mass Spectrometry and Implications for Amyloidoses. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ai Woon Yee
- Life Sciences group, ILL 71 avenue des Martyrs 38042 Grenoble France
- Faculty of Natural SciencesKeele University Staffordshire ST5 5BG UK
| | - Martine Moulin
- Life Sciences group, ILL 71 avenue des Martyrs 38042 Grenoble France
- Faculty of Natural SciencesKeele University Staffordshire ST5 5BG UK
| | - Nina Breteau
- Life Sciences group, ILL 71 avenue des Martyrs 38042 Grenoble France
| | - Michael Haertlein
- Life Sciences group, ILL 71 avenue des Martyrs 38042 Grenoble France
| | - Edward P. Mitchell
- Faculty of Natural SciencesKeele University Staffordshire ST5 5BG UK
- ESRF 71 avenue des Martyrs 38042 Grenoble France
| | - Jonathan B. Cooper
- Laboratory of Protein Crystallography, Drug Discovery GroupWolfson Institute for Biomedical Research, UCL London WC1E 6BT UK
| | - Elisabetta Boeri Erba
- Univ. Grenoble Alpes, IBS 38044 Grenoble France
- CNRS, IBS 38044 Grenoble France
- CEA, IBS 38044 Grenoble France
| | - V. Trevor Forsyth
- Life Sciences group, ILL 71 avenue des Martyrs 38042 Grenoble France
- Faculty of Natural SciencesKeele University Staffordshire ST5 5BG UK
| |
Collapse
|
28
|
Yee AW, Moulin M, Breteau N, Haertlein M, Mitchell EP, Cooper JB, Boeri Erba E, Forsyth VT. Impact of Deuteration on the Assembly Kinetics of Transthyretin Monitored by Native Mass Spectrometry and Implications for Amyloidoses. Angew Chem Int Ed Engl 2016; 55:9292-6. [PMID: 27311939 PMCID: PMC5094506 DOI: 10.1002/anie.201602747] [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: 03/18/2016] [Indexed: 01/13/2023]
Abstract
It is well established that the formation of transthyretin (TTR) amyloid fibrils is linked to the destabilization and dissociation of its tetrameric structure into insoluble aggregates. Isotope labeling is used for the study of TTR by NMR, neutron diffraction, and mass spectrometry (MS). Here MS, thioflavin T fluorescence, and crystallographic data demonstrate that while the X-ray structures of unlabeled and deuterium-labeled TTR are essentially identical, subunit exchange kinetics and amyloid formation are accelerated for the deuterated protein. However, a slower subunit exchange is noted in deuterated solvent, reflecting the poorer solubility of non-polar protein side chains in such an environment. These observations are important for the interpretation of kinetic studies involving deuteration. The destabilizing effects of TTR deuteration are rather similar in character to those observed for aggressive mutations of TTR such as L55P (associated with familial amyloid polyneuropathy).
Collapse
Affiliation(s)
- Ai Woon Yee
- Life Sciences group, ILL, 71 avenue des Martyrs, 38042, Grenoble, France
- Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK
| | - Martine Moulin
- Life Sciences group, ILL, 71 avenue des Martyrs, 38042, Grenoble, France
- Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK
| | - Nina Breteau
- Life Sciences group, ILL, 71 avenue des Martyrs, 38042, Grenoble, France
| | - Michael Haertlein
- Life Sciences group, ILL, 71 avenue des Martyrs, 38042, Grenoble, France
| | - Edward P Mitchell
- Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK
- ESRF, 71 avenue des Martyrs, 38042, Grenoble, France
| | - Jonathan B Cooper
- Laboratory of Protein Crystallography, Drug Discovery Group, Wolfson Institute for Biomedical Research, UCL, London, WC1E 6BT, UK
| | - Elisabetta Boeri Erba
- Univ. Grenoble Alpes, IBS, 38044, Grenoble, France.
- CNRS, IBS, 38044, Grenoble, France.
- CEA, IBS, 38044, Grenoble, France.
| | - V Trevor Forsyth
- Life Sciences group, ILL, 71 avenue des Martyrs, 38042, Grenoble, France.
- Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK.
| |
Collapse
|
29
|
O'Dell WB, Bodenheimer AM, Meilleur F. Neutron protein crystallography: A complementary tool for locating hydrogens in proteins. Arch Biochem Biophys 2016; 602:48-60. [DOI: 10.1016/j.abb.2015.11.033] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/12/2015] [Accepted: 11/16/2015] [Indexed: 10/22/2022]
|
30
|
Zou L, Zhu J, Dong Y, Han W, Guo Y, Zhou H. Models for the binding channel of wild type and mutant transthyretin with glabridin. RSC Adv 2016. [DOI: 10.1039/c6ra19814g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Our results indicate that additional high-occupancy hydrogen bonds were observed at the binding interface between the two dimers in V30A TTR, while stabilisation hydrophobic interactions between residues in the mutant AB loop decreased.
Collapse
Affiliation(s)
- Liyun Zou
- School of Life Sciences
- Jilin University
- Changchun 130012
- China
| | - Jingxuan Zhu
- School of Life Sciences
- Jilin University
- Changchun 130012
- China
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education
| | - Yang Dong
- School of Life Sciences
- Jilin University
- Changchun 130012
- China
| | - Weiwei Han
- School of Life Sciences
- Jilin University
- Changchun 130012
- China
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education
| | - Yingjie Guo
- School of Life Sciences
- Jilin University
- Changchun 130012
- China
| | - Hui Zhou
- School of Life Sciences
- Jilin University
- Changchun 130012
- China
| |
Collapse
|
31
|
Yokoyama T, Takaki S, Chosa K, Sato T, Suico MA, Teranishi Y, Shuto T, Mizuguchi M, Kai H. Structural stabilization of transthyretin by a new compound, 6-benzoyl-2-hydroxy-1H-benzo[de]isoquinoline-1,3(2H)-dione. J Pharmacol Sci 2015; 129:240-3. [PMID: 26639444 DOI: 10.1016/j.jphs.2015.09.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 09/14/2015] [Accepted: 09/16/2015] [Indexed: 10/22/2022] Open
Abstract
Familial amyloid polyneuropathy (FAP) is a genetic, adult-onset, neurodegenerative disorder caused by amyloid formation of transthyretin (TTR), a thyroxine-binding protein. Mutation in TTR causes a propensity of TTR tetramer to dissociate to monomer, which is the first step to amyloidosis. Thus, a drug that can stabilize the tetramer structure will have therapeutic benefit. Here, by virtual screening and biochemical assays, we identified small molecule 6-benzoyl-2-hydroxy-1H-benzo[de]isoquinoline-1,3(2H)-dione (L6) that can prevent the dissociation of TTR to monomer. X-ray crystallography reveals that L6 binds to the T4 binding pocket of TTR. These findings show that L6 is a candidate TTR stabilizer.
Collapse
Affiliation(s)
- Takeshi Yokoyama
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0914, Japan
| | - Shun Takaki
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan
| | - Keisuke Chosa
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan
| | - Takashi Sato
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan
| | - Mary Ann Suico
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan
| | - Yuriko Teranishi
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan
| | - Tsuyoshi Shuto
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan
| | - Mineyuki Mizuguchi
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0914, Japan.
| | - Hirofumi Kai
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan.
| |
Collapse
|
32
|
Banerjee A, Dasgupta S, Mukhopadhyay BP, Sekar K. The putative role of some conserved water molecules in the structure and function of human transthyretin. ACTA ACUST UNITED AC 2015; 71:2248-66. [DOI: 10.1107/s1399004715016004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 08/26/2015] [Indexed: 11/10/2022]
Abstract
Human transthyretin (hTTR) is a multifunctional protein that is involved in several neurodegenerative diseases. Besides the transportation of thyroxin and vitamin A, it is also involved in the proteolysis of apolipoprotein A1 and Aβ peptide. Extensive analyses of 32 high-resolution X-ray and neutron diffraction structures of hTTR followed by molecular-dynamics simulation studies using a set of 15 selected structures affirmed the presence of 44 conserved water molecules in its dimeric structure. They are found to play several important roles in the structure and function of the protein. Eight water molecules stabilize the dimeric structure through an extensive hydrogen-bonding network. The absence of some of these water molecules in highly acidic conditions (pH ≤ 4.0) severely affects the interfacial hydrogen-bond network, which may destabilize the native tetrameric structure, leading to its dissociation. Three pairs of conserved water molecules contribute to maintaining the geometry of the ligand-binding cavities. Some other water molecules control the orientation and dynamics of different structural elements of hTTR. This systematic study of the location, absence, networking and interactions of the conserved water molecules may shed some light on various structural and functional aspects of the protein. The present study may also provide some rational clues about the conserved water-mediated architecture and stability of hTTR.
Collapse
|
33
|
Yokoyama T, Mizuguchi M, Ostermann A, Kusaka K, Niimura N, Schrader TE, Tanaka I. Protonation State and Hydration of Bisphosphonate Bound to Farnesyl Pyrophosphate Synthase. J Med Chem 2015; 58:7549-56. [PMID: 26314394 DOI: 10.1021/acs.jmedchem.5b01147] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Farnesyl pyrophosphate synthase (FPPS) catalyzes the condensation of isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate to FPP and is known to be a molecular target of osteoporosis drugs, such as risedronate (RIS), which is a nitrogen-containing bisphosphonate. The protonation states and hydration structure of RIS bound to FPPS were determined by neutron protein crystallography, which allows direct visualization of hydrogens and deuteriums. The structure analysis revealed that the phosphate groups of RIS were fully deprotonated with the abnormally decreased pKa, and that the roles of E93 and D264 consisted of canceling the extra negative charges upon the binding of ligands. Collectively, our neutron structures provided insights into the physicochemical properties during the bisphosphonate binding event.
Collapse
Affiliation(s)
- Takeshi Yokoyama
- Faculty of Pharmaceutical Sciences, University of Toyama , 2630 Sugitani, Toyama 930-0914, Japan
| | - Mineyuki Mizuguchi
- Faculty of Pharmaceutical Sciences, University of Toyama , 2630 Sugitani, Toyama 930-0914, Japan
| | - Andreas Ostermann
- Heinz Maier-Leibnitz Zentrum (MLZ), Technische Universität München , Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Katsuhiro Kusaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University , 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Nobuo Niimura
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University , 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Tabias E Schrader
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich GmbH, Lichtenbergstr. 1, 85747 Garching, Germany
| | - Ichiro Tanaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University , 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan.,College of Engineering, Ibaraki University , Naka-Narusawa 4-12-1, Hitachi, Ibaraki 316-8511, Japan
| |
Collapse
|
34
|
Hellman U, Lundgren HE, Westermark P, Stafberg C, Nahi H, Tachlinski S, Guggi M, Flogegård M, Hamid M, Escher SA, Suhr OB. A genealogical and clinical study of the phenotypical variation within the Swedish transthyretin His88Arg (p. His108Arg) amyloidosis family. Eur J Med Genet 2015; 58:211-5. [PMID: 25721874 DOI: 10.1016/j.ejmg.2015.02.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 02/12/2015] [Indexed: 10/23/2022]
Abstract
UNLABELLED In 2005 we reported the first case of transthyretin His88Arg (p. His108Arg) amyloidosis, a mutation characterised by cardiomyopathy. Six additional gene carriers of whom five have clinical symptoms of disease have now been identified in Sweden, and we have been able to identify a possible founder and to characterise the Swedish phenotype of the transthyretin (TTR) His88Arg mutation. Genealogical studies of church records were used to identify the individuals with the disease and their families. Routine clinical investigations of neurological and heart manifestation of the disease were utilised. We found that genealogically all seven individuals were related and originated from the same region in Sweden. Amyloid deposits were demonstrated in biopsies and the TTR His88Arg mutation was identified in all patients. Patients had a late onset disease (≥ 50 years of age) and all exhibited a severe amyloid cardiomyopathy. A pronounced peripheral axonal neuropathy was with certainty demonstrated in one patient only, who also was operated for a magnetic resonance confirmed spinal stenosis, however, without any effect on his neurological symptoms. Five of the patients had carpal tunnel syndrome. The first reported case is now deceased from cardiac failure. One patient has had a sequential heart and liver transplantation. One gene carrier had no symptoms or findings of disease on latest evaluation at the age of 44. IN CONCLUSION the Swedish TTRHis88Arg patients all have a common Swedish founder. Cardiomyopathy with heart failure, as well as carpal tunnel syndrome and spinal stenosis were early signs of disease; but peripheral neuropathy was present in one patient before symptoms of cardiomyopathy so the phenotypical presentation of this mutation is variable.
Collapse
Affiliation(s)
- Urban Hellman
- Cardiology, Heart Centre and Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Hans-Erik Lundgren
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Per Westermark
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | | | - Hareth Nahi
- Department of Haematology, Karolinska University Hospital, Huddinge, Sweden
| | | | - Michael Guggi
- Department of Cardiology, Falu Lasarett, Falun, Sweden
| | - Max Flogegård
- Department of Medicine, Falu Lasarett, Falun, Sweden
| | - Mehmet Hamid
- Department of Cardiology, Mälarsjukhuset, Eskildtuna, Sweden
| | - Stefan A Escher
- Department of Clinical Science, Genetic & Molecular Epidemiology Unit, Lund University, Malmö, Sweden
| | - Ole B Suhr
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden.
| |
Collapse
|
35
|
Haupt M, Blakeley MP, Fisher SJ, Mason SA, Cooper JB, Mitchell EP, Forsyth VT. Binding site asymmetry in human transthyretin: insights from a joint neutron and X-ray crystallographic analysis using perdeuterated protein. IUCRJ 2014; 1:429-38. [PMID: 25485123 PMCID: PMC4224461 DOI: 10.1107/s2052252514021113] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 09/22/2014] [Indexed: 05/12/2023]
Abstract
Human transthyretin has an intrinsic tendency to form amyloid fibrils and is heavily implicated in senile systemic amyloidosis. Here, detailed neutron structural studies of perdeuterated transthyretin are described. The analyses, which fully exploit the enhanced visibility of isotopically replaced hydrogen atoms, yield new information on the stability of the protein and the possible mechanisms of amyloid formation. Residue Ser117 may play a pivotal role in that a single water molecule is closely associated with the γ-hydrogen atoms in one of the binding pockets, and could be important in determining which of the two sites is available to the substrate. The hydrogen-bond network at the monomer-monomer interface is more extensive than that at the dimer-dimer interface. Additionally, the edge strands of the primary dimer are seen to be favourable for continuation of the β-sheet and the formation of an extended cross-β structure through sequential dimer couplings. It is argued that the precursor to fibril formation is the dimeric form of the protein.
Collapse
Affiliation(s)
- Melina Haupt
- Facility of Natural Sciences, Institute of Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, United Kingdom
- Institut Laue-Langevin, 71, avenue des Martyrs, Grenoble, CS 20156, France
- Partnership for Structural Biology, 71, avenue des Martyrs, Grenoble, CS 20156, France
| | - Matthew P. Blakeley
- Institut Laue-Langevin, 71, avenue des Martyrs, Grenoble, CS 20156, France
- Partnership for Structural Biology, 71, avenue des Martyrs, Grenoble, CS 20156, France
| | - Stuart J. Fisher
- Department of Molecular Biology, University of Salzburg, Billrothstrasse 11, Salzburg, 5020, Austria
- Diamond Light Source, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Sax A. Mason
- Institut Laue-Langevin, 71, avenue des Martyrs, Grenoble, CS 20156, France
| | - Jon B. Cooper
- Division of Medicine (Royal Free Campus), University College London, Rowland Hill Street, London NW3 2PF, United Kingdom
| | - Edward P. Mitchell
- Facility of Natural Sciences, Institute of Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, United Kingdom
- Partnership for Structural Biology, 71, avenue des Martyrs, Grenoble, CS 20156, France
- Business Development Office, European Synchrotron Radiation Facility, Grenoble, 38042, France
| | - V. Trevor Forsyth
- Facility of Natural Sciences, Institute of Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, United Kingdom
- Institut Laue-Langevin, 71, avenue des Martyrs, Grenoble, CS 20156, France
- Partnership for Structural Biology, 71, avenue des Martyrs, Grenoble, CS 20156, France
| |
Collapse
|
36
|
Geneste A, André C, Magy-Bertrand N, Lethier L, Tijani G, Guillaume YC. Thermodynamic study of transthyretin association (wild-type and senile forms) with heparan sulfate proteoglycan: pH effect and implication of the reactive histidine residue. Biomed Chromatogr 2014; 29:514-22. [DOI: 10.1002/bmc.3306] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 06/02/2014] [Accepted: 07/10/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Ambre Geneste
- Université de Franche-Comté, UFR SMP, EA 4662: Nanomedecine, Imagery Therapeupic Lab’, Laboratoire de Chimie Analytique Bioanalytique et Physique; 25030 Besançon cedex France
| | - Claire André
- Université de Franche-Comté, UFR SMP, EA 4662: Nanomedecine, Imagery Therapeupic Lab’, Laboratoire de Chimie Analytique Bioanalytique et Physique; 25030 Besançon cedex France
| | - Nadine Magy-Bertrand
- Université de Franche-Comté, UFR SMP, EA 4662: Nanomedecine, Imagery Therapeupic Lab’, Laboratoire de Chimie Analytique Bioanalytique et Physique; 25030 Besançon cedex France
- Département de Médecine Interne; CHRU Besançon; 25030 Besançon cedex France
| | - Lydie Lethier
- Université de Franche-Comté, UFR SMP, EA 4662: Nanomedecine, Imagery Therapeupic Lab’, Laboratoire de Chimie Analytique Bioanalytique et Physique; 25030 Besançon cedex France
| | - Gharbi Tijani
- Université de Franche-Comté, UFR SMP, EA 4662: Nanomedecine, Imagery Therapeupic Lab’, Laboratoire de Chimie Analytique Bioanalytique et Physique; 25030 Besançon cedex France
| | - Yves Claude Guillaume
- Université de Franche-Comté, UFR SMP, EA 4662: Nanomedecine, Imagery Therapeupic Lab’, Laboratoire de Chimie Analytique Bioanalytique et Physique; 25030 Besançon cedex France
- Pôle Pharmacie; CHRU Besançon; 25030 Besançon cedex France
| |
Collapse
|
37
|
Yokoyama T, Ostermann A, Mizuguchi M, Niimura N, Schrader TE, Tanaka I. Crystallization and preliminary neutron diffraction experiment of human farnesyl pyrophosphate synthase complexed with risedronate. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2014; 70:470-2. [PMID: 24699741 DOI: 10.1107/s2053230x14004087] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 02/21/2014] [Indexed: 11/10/2022]
Abstract
Nitrogen-containing bisphosphonates (N-BPs), such as risedronate and zoledronate, are currently used as a clinical drug for bone-resorption diseases and are potent inhibitors of farnesyl pyrophosphate synthase (FPPS). X-ray crystallographic analyses of FPPS with N-BPs have revealed that N-BPs bind to FPPS with three magnesium ions and several water molecules. To understand the structural characteristics of N-BPs bound to FPPS, including H atoms and hydration by water, neutron diffraction studies were initiated using BIODIFF at the Heinz Maier-Leibnitz Zentrum (MLZ). FPPS-risedronate complex crystals of approximate dimensions 2.8 × 2.5 × 1.5 mm (∼3.5 mm(3)) were obtained by repeated macro-seeding. Monochromatic neutron diffraction data were collected to 2.4 Å resolution with 98.4% overall completeness. Here, the first successful neutron data collection from FPPS in complex with N-BPs is reported.
Collapse
Affiliation(s)
- Takeshi Yokoyama
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0914, Japan
| | - Andreas Ostermann
- Heinz Maier-Leibnitz Zentrum (MLZ), Technische Universität München, Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Mineyuki Mizuguchi
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0914, Japan
| | - Nobuo Niimura
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Tobias E Schrader
- Jülich Centre for Neutron Science (JCNS), Forschungszentrum Jülich GmbH Outstation at MLZ, Lichtenbergstrasse 1, 85747 Garching, Germany
| | - Ichiro Tanaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| |
Collapse
|
38
|
Yokoyama T, Kosaka Y, Mizuguchi M. Crystal Structures of Human Transthyretin Complexed with Glabridin. J Med Chem 2014; 57:1090-6. [DOI: 10.1021/jm401832j] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Takeshi Yokoyama
- Faculty of Pharmaceutical
Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0914, Japan
| | - Yuto Kosaka
- Faculty of Pharmaceutical
Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0914, Japan
| | - Mineyuki Mizuguchi
- Faculty of Pharmaceutical
Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0914, Japan
| |
Collapse
|
39
|
Yokoyama T, Mizuguchi M, Nabeshima Y, Kusaka K, Yamada T, Hosoya T, Ohhara T, Kurihara K, Tanaka I, Niimura N. Hydrogen-bond network and pH sensitivity in human transthyretin. JOURNAL OF SYNCHROTRON RADIATION 2013; 20:834-7. [PMID: 24121323 PMCID: PMC3795539 DOI: 10.1107/s090904951302075x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 07/25/2013] [Indexed: 05/20/2023]
Abstract
Transthyretin (TTR) is a tetrameric protein. TTR misfolding and aggregation are associated with human amyloid diseases. Dissociation of the TTR tetramer is believed to be the rate-limiting step in the amyloid fibril formation cascade. Low pH is known to promote dissociation into monomer and the formation of amyloid fibrils. In order to reveal the molecular mechanisms underlying pH sensitivity and structural stabilities of TTR, neutron diffraction studies were conducted using the IBARAKI Biological Crystal Diffractometer with the time-of-flight method. Crystals for the neutron diffraction experiments were grown up to 2.5 mm(3) for four months. The neutron crystal structure solved at 2.0 Å revealed the protonation states of His88 and the detailed hydrogen-bond network depending on the protonation states of His88. This hydrogen-bond network is involved in monomer-monomer and dimer-dimer interactions, suggesting that the double protonation of His88 by acidification breaks the hydrogen-bond network and causes the destabilization of the TTR tetramer. Structural comparison with the X-ray crystal structure at acidic pH identified the three amino acid residues responsible for the pH sensitivity of TTR. Our neutron model provides insights into the molecular stability related to amyloidosis.
Collapse
Affiliation(s)
- Takeshi Yokoyama
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0914, Japan
| | - Mineyuki Mizuguchi
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0914, Japan
| | - Yuko Nabeshima
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0914, Japan
| | - Katsuhiro Kusaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Taro Yamada
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Takaaki Hosoya
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
- College of Engineering, Ibaraki University, 4-12-1 Naka-Narusawa, Hitachi, Ibaraki 316-8511, Japan
| | - Takashi Ohhara
- Research Center for Neutron Science and Technology, Comprehensive Research Organization for Science and Society, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Kazuo Kurihara
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai, Ibaraki 319-1195, Japan
| | - Ichiro Tanaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
- College of Engineering, Ibaraki University, 4-12-1 Naka-Narusawa, Hitachi, Ibaraki 316-8511, Japan
| | - Nobuo Niimura
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| |
Collapse
|
40
|
Bryan T, González JM, Bacik JP, DeNunzio NJ, Unkefer CJ, Schrader TE, Ostermann A, Dunaway-Mariano D, Allen KN, Fisher SZ. Neutron diffraction studies towards deciphering the protonation state of catalytic residues in the bacterial KDN9P phosphatase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1015-9. [PMID: 23989152 PMCID: PMC3758152 DOI: 10.1107/s1744309113021386] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 07/31/2013] [Indexed: 11/11/2022]
Abstract
The enzyme 2-keto-3-deoxy-9-O-phosphonononic acid phosphatase (KDN9P phosphatase) functions in the pathway for the production of 2-keto-3-deoxy-D-glycero-D-galacto-nononic acid, a sialic acid that is important for the survival of commensal bacteria in the human intestine. The enzyme is a member of the haloalkanoate dehalogenase superfamily and represents a good model for the active-site protonation state of family members. Crystals of approximate dimensions 1.5 × 1.0 × 1.0 mm were obtained in space group P2(1)2(1)2, with unit-cell parameters a = 83.1, b = 108.9, c = 75.7 Å. A complete neutron data set was collected from a medium-sized H/D-exchanged crystal at BIODIFF at the Heinz Maier-Leibnitz Zentrum (MLZ), Garching, Germany in 18 d. Initial refinement to 2.3 Å resolution using only neutron data showed significant density for catalytically important residues.
Collapse
Affiliation(s)
- Tyrel Bryan
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Javier M. González
- BioScience Division B-11, Los Alamos National Laboratory, PO Box 1663, Los Alamos, NM 87545, USA
| | - John P. Bacik
- BioScience Division B-11, Los Alamos National Laboratory, PO Box 1663, Los Alamos, NM 87545, USA
| | - Nicholas J. DeNunzio
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA 02115, USA
| | - Clifford J. Unkefer
- BioScience Division B-11, Los Alamos National Laboratory, PO Box 1663, Los Alamos, NM 87545, USA
| | - Tobias E. Schrader
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich GmbH, Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Andreas Ostermann
- Heinz Maier-Leibnitz Zentrum (MLZ), Technische Universität München, Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Debra Dunaway-Mariano
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Karen N. Allen
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA 02115, USA
| | - S. Zoë Fisher
- BioScience Division B-11, Los Alamos National Laboratory, PO Box 1663, Los Alamos, NM 87545, USA
| |
Collapse
|
41
|
Stefl S, Nishi H, Petukh M, Panchenko AR, Alexov E. Molecular mechanisms of disease-causing missense mutations. J Mol Biol 2013; 425:3919-36. [PMID: 23871686 DOI: 10.1016/j.jmb.2013.07.014] [Citation(s) in RCA: 187] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 07/04/2013] [Accepted: 07/10/2013] [Indexed: 12/23/2022]
Abstract
Genetic variations resulting in a change of amino acid sequence can have a dramatic effect on stability, hydrogen bond network, conformational dynamics, activity and many other physiologically important properties of proteins. The substitutions of only one residue in a protein sequence, so-called missense mutations, can be related to many pathological conditions and may influence susceptibility to disease and drug treatment. The plausible effects of missense mutations range from affecting the macromolecular stability to perturbing macromolecular interactions and cellular localization. Here we review the individual cases and genome-wide studies that illustrate the association between missense mutations and diseases. In addition, we emphasize that the molecular mechanisms of effects of mutations should be revealed in order to understand the disease origin. Finally, we report the current state-of-the-art methodologies that predict the effects of mutations on protein stability, the hydrogen bond network, pH dependence, conformational dynamics and protein function.
Collapse
Affiliation(s)
- Shannon Stefl
- Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA
| | | | | | | | | |
Collapse
|
42
|
Ankner JF, Heller WT, Herwig KW, Meilleur F, Myles DAA. Neutron scattering techniques and applications in structural biology. ACTA ACUST UNITED AC 2013; Chapter 17:Unit17.16. [PMID: 23546619 DOI: 10.1002/0471140864.ps1716s72] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Neutron scattering is exquisitely sensitive to the position, concentration, and dynamics of hydrogen atoms in materials and is a powerful tool for the characterization of structure-function and interfacial relationships in biological systems. Modern neutron scattering facilities offer access to a sophisticated, nondestructive suite of instruments for biophysical characterization that provides spatial and dynamic information spanning from Ångstroms to microns and from picoseconds to microseconds, respectively. Applications in structural biology range from the atomic-resolution analysis of individual hydrogen atoms in enzymes through to meso- and macro-scale analysis of complex biological structures, membranes, and assemblies. The large difference in neutron scattering length between hydrogen and deuterium allows contrast variation experiments to be performed and enables H/D isotopic labeling to be used for selective and systematic analysis of the local structure, dynamics, and interactions of multi-component systems. This overview describes the available techniques and summarizes their practical application to the study of biomolecular systems.
Collapse
Affiliation(s)
- John F Ankner
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | | | | | | |
Collapse
|
43
|
Schönichen A, Webb BA, Jacobson MP, Barber DL. Considering protonation as a posttranslational modification regulating protein structure and function. Annu Rev Biophys 2013; 42:289-314. [PMID: 23451893 DOI: 10.1146/annurev-biophys-050511-102349] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Posttranslational modification is an evolutionarily conserved mechanism for regulating protein activity, binding affinity, and stability. Compared with established posttranslational modifications such as phosphorylation or ubiquitination, posttranslational modification by protons within physiological pH ranges is a less recognized mechanism for regulating protein function. By changing the charge of amino acid side chains, posttranslational modification by protons can drive dynamic changes in protein conformation and function. Addition and removal of a proton is rapid and reversible and, in contrast to most other posttranslational modifications, does not require an enzyme. Signaling specificity is achieved by only a minority of sites in proteins titrating within the physiological pH range. Here, we examine the structural mechanisms and functional consequences of proton posttranslational modification of pH-sensing proteins regulating different cellular processes.
Collapse
Affiliation(s)
- André Schönichen
- Department of Cell and Tissue Biology, University of California, San Francisco, USA
| | | | | | | |
Collapse
|
44
|
Sun Y, Gao H, Yang YW, Wang A, Wu G, Wang Y, Fan Y, Ma J. Layer-by-layer supramolecular assemblies based on linear and star-shaped poly(glycerol methacrylate)s for doxorubicin delivery. J Biomed Mater Res A 2012; 101:2164-73. [DOI: 10.1002/jbm.a.34519] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2012] [Revised: 09/17/2012] [Accepted: 09/18/2012] [Indexed: 12/29/2022]
|
45
|
Abstract
Carbon-oxygen (CH···O) hydrogen bonding represents an unusual category of molecular interactions first documented in biological structures over 4 decades ago. Although CH···O hydrogen bonding has remained generally underappreciated in the biochemical literature, studies over the last 15 years have begun to yield direct evidence of these interactions in biological systems. In this minireview, we provide a historical context of biological CH···O hydrogen bonding and summarize some major advancements from experimental studies over the past several years that have elucidated the importance, prevalence, and functions of these interactions. In particular, we examine the impact of CH···O bonds on protein and nucleic acid structure, molecular recognition, and enzyme catalysis and conclude by exploring overarching themes and unresolved questions regarding unconventional interactions in biomolecular structure.
Collapse
|
46
|
Nolasco MM, Vaz PM, Vaz PD, Ribeiro-Claro PJ. Exploring C–H···O hydrogen bonds in dihydrocoumarin from combined vibrational spectroscopy and DFT calculations. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.09.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
47
|
Direct observation of hydrogen atom dynamics and interactions by ultrahigh resolution neutron protein crystallography. Proc Natl Acad Sci U S A 2012; 109:15301-6. [PMID: 22949690 DOI: 10.1073/pnas.1208341109] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The 1.1 Å, ultrahigh resolution neutron structure of hydrogen/deuterium (H/D) exchanged crambin is reported. Two hundred ninety-nine out of 315, or 94.9%, of the hydrogen atom positions in the protein have been experimentally derived and resolved through nuclear density maps. A number of unconventional interactions are clearly defined, including a potential O─H…π interaction between a water molecule and the aromatic ring of residue Y44, as well as a number of potential C─H…O hydrogen bonds. Hydrogen bonding networks that are ambiguous in the 0.85 Å ultrahigh resolution X-ray structure can be resolved by accurate orientation of water molecules. Furthermore, the high resolution of the reported structure has allowed for the anisotropic description of 36 deuterium atoms in the protein. The visibility of hydrogen and deuterium atoms in the nuclear density maps is discussed in relation to the resolution of the neutron data.
Collapse
|
48
|
Mizuguchi M, Yokoyama T, Nabeshima Y, Kawano K, Tanaka I, Niimura N. Quaternary structure, aggregation and cytotoxicity of transthyretin. Amyloid 2012; 19 Suppl 1:5-7. [PMID: 22439750 DOI: 10.3109/13506129.2012.666510] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Transthyretin (TTR) with a Ser112-to-Ile mutation is known to cause amyloidosis with severe cardiomyopathy. We investigated the quaternary structure, aggregation and cytotoxicity of the S112I variant. This variant exists as a dimer at physiological pH, self-assembles into spherical aggregates and induces cell death in human neuroblastoma IMR-32 cells. In addition, we determined the neutron crystal structure of TTR at 2.0 Å resolution. The neutron structure revealed that the hydrogen-bond network involving His88 is important for the stabilization of the dimer-dimer and monomer-monomer interfaces.
Collapse
Affiliation(s)
- Mineyuki Mizuguchi
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama, Japan.
| | | | | | | | | | | |
Collapse
|