Edge Strand Dissociation and Conformational Changes in Transthyretin under Amyloidogenic Conditions

Childers, Matthew C.; Daggett, Valerie

doi:10.1016/j.bpj.2020.08.043

Title: Edge Strand Dissociation and Conformational Changes in Transthyretin under Amyloidogenic Conditions

Journal Article · Sun Nov 01 00:00:00 EDT 2020 · Biophysical Journal

DOI:https://doi.org/10.1016/j.bpj.2020.08.043· OSTI ID:2279907

; Daggett, Valerie

View Journal Article

Cite

Export

Save

Sponsoring Organization:: USDOE

OSTI ID:: 2279907

Journal Information:: Biophysical Journal, Journal Name: Biophysical Journal Vol. 119 Journal Issue: 10; ISSN 0006-3495

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

References (69)

New Dynamic Rotamer Libraries: Data-Driven Analysis of Side-Chain Conformational Propensities Towse, Clare-Louise; Rysavy, Steven J.; Vulovic, Ivan M. Structure, Vol. 24, Issue 1 https://doi.org/10.1016/j.str.2015.10.017	journal	January 2016
Precise representation of volume properties of water at one atmosphere Kell, G. S. Journal of Chemical & Engineering Data, Vol. 12, Issue 1 https://doi.org/10.1021/je60032a018	journal	January 1967
Validating Molecular Dynamics Simulations against Experimental Observables in Light of Underlying Conformational Ensembles Childers, Matthew Carter; Daggett, Valerie The Journal of Physical Chemistry B, Vol. 122, Issue 26 https://doi.org/10.1021/acs.jpcb.8b02144	journal	June 2018
Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution Levitt, Michael; Hirshberg, Miriam; Sharon, Ruth Computer Physics Communications, Vol. 91, Issue 1-3 https://doi.org/10.1016/0010-4655(95)00049-L	journal	September 1995
Initial Conformational Changes of Human Transthyretin under Partially Denaturing Conditions Yang, Mingfeng; Lei, Ming; Bruschweiler, Rafael Biophysical Journal, Vol. 89, Issue 1 https://doi.org/10.1529/biophysj.105.059642	journal	July 2005
Cutoff Size Need Not Strongly Influence Molecular Dynamics Results for Solvated Polypeptides ^† Beck, David A. C.; Armen, Roger S.; Daggett, Valerie Biochemistry, Vol. 44, Issue 2 https://doi.org/10.1021/bi0486381	journal	January 2005
Calibration and Testing of a Water Model for Simulation of the Molecular Dynamics of Proteins and Nucleic Acids in Solution Levitt, Michael; Hirshberg, Miriam; Sharon, Ruth The Journal of Physical Chemistry B, Vol. 101, Issue 25 https://doi.org/10.1021/jp964020s	journal	June 1997
Pauling and Corey's -pleated sheet structure may define the prefibrillar amyloidogenic intermediate in amyloid disease Armen, R. S.; DeMarco, M. L.; Alonso, D. O. V. Proceedings of the National Academy of Sciences, Vol. 101, Issue 32 https://doi.org/10.1073/pnas.0401781101	journal	July 2004
Mapping the early steps in the pH-induced conformational conversion of the prion protein Alonso, Darwin O. V.; DeArmond, Stephen J.; Cohen, Fred E. Proceedings of the National Academy of Sciences, Vol. 98, Issue 6 https://doi.org/10.1073/pnas.061555898	journal	February 2001
An Engineered Transthyretin Monomer that Is Nonamyloidogenic, Unless It Is Partially Denatured ^† Jiang, Xin; Smith, Craig S.; Petrassi, H. Michael Biochemistry, Vol. 40, Issue 38 https://doi.org/10.1021/bi011194d	journal	September 2001
Transthyretin mutation Leu-55-Pro significantly alters tetramer stability and increases amyloidogenicity McCutchen, Sandra L.; Colon, Wilfredo; Kelly, Jeffery W. Biochemistry, Vol. 32, Issue 45 https://doi.org/10.1021/bi00096a024	journal	November 1993
Probing Solvent Accessibility of Transthyretin Amyloid by Solution NMR Spectroscopy Olofsson, Anders; Ippel, Johannes H.; Wijmenga, Sybren S. Journal of Biological Chemistry, Vol. 279, Issue 7 https://doi.org/10.1074/jbc.M310605200	journal	November 2003
Identification and Characterization of the Unfolding Transition State of Chymotrypsin Inhibitor 2 by Molecular Dynamics Simulations Li, Aijun; Daggett, Valerie Journal of Molecular Biology, Vol. 257, Issue 2 https://doi.org/10.1006/jmbi.1996.0172	journal	March 1996
The role of gelsolin domain 3 in familial amyloidosis (Finnish type) Zorgati, Habiba; Larsson, Mårten; Ren, Weitong Proceedings of the National Academy of Sciences, Vol. 116, Issue 28 https://doi.org/10.1073/pnas.1902189116	journal	June 2019
Structural and functional diversity among amyloid proteins: Agents of disease, building blocks of biology, and implications for molecular engineering Bleem, Alissa; Daggett, Valerie Biotechnology and Bioengineering, Vol. 114, Issue 1 https://doi.org/10.1002/bit.26059	journal	August 2016
Towards a complete description of the structural and dynamic properties of the denatured state of barnase and the role of residual structure in folding 1 1Edited by B. Honig Wong, Kam-Bo; Clarke, Jane; Bond, Chris J. Journal of Molecular Biology, Vol. 296, Issue 5 https://doi.org/10.1006/jmbi.2000.3523	journal	March 2000
Importance of Context in Protein Folding: Secondary Structural Propensities versus Tertiary Contact-Assisted Secondary Structure Formation Scott, Kathryn A.; Alonso, Darwin O. V.; Pan, Yongping Biochemistry, Vol. 45, Issue 13 https://doi.org/10.1021/bi0517281	journal	March 2006
Simulations of Human Lysozyme: Probing the Conformations Triggering Amyloidosis Moraitakis, George; Goodfellow, Julia M. Biophysical Journal, Vol. 84, Issue 4 https://doi.org/10.1016/S0006-3495(03)75021-8	journal	April 2003
Characterization of Two Distinct β ₂ -Microglobulin Unfolding Intermediates that May Lead to Amyloid Fibrils of Different Morphology ^† Armen, Roger S.; Daggett, Valerie Biochemistry, Vol. 44, Issue 49 https://doi.org/10.1021/bi050731h	journal	December 2005
Days to criterion as an indicator of toxicity associated with human Alzheimer amyloid‐β oligomers Gandy, Sam; Simon, Adam J.; Steele, John W. Annals of Neurology, Vol. 68, Issue 2 https://doi.org/10.1002/ana.22052	journal	August 2010
Transthyretin Aggregation under Partially Denaturing Conditions Is a Downhill Polymerization ^† Hurshman, Amy R.; White, Joleen T.; Powers, Evan T. Biochemistry, Vol. 43, Issue 23 https://doi.org/10.1021/bi049621l	journal	June 2004
Mechanistic basis for the recognition of a misfolded protein by the molecular chaperone Hsp90 Oroz, Javier; Kim, Jin Hae; Chang, Bliss J. Nature Structural & Molecular Biology, Vol. 24, Issue 4 https://doi.org/10.1038/nsmb.3380	journal	February 2017
Identification of a Common Binding Mode for Imaging Agents to Amyloid Fibrils from Molecular Dynamics Simulations Skeby, Katrine Kirkeby; Sørensen, Jesper; Schiøtt, Birgit Journal of the American Chemical Society, Vol. 135, Issue 40 https://doi.org/10.1021/ja405530p	journal	August 2013
Conformational Conversion during Amyloid Formation at Atomic Resolution Eichner, Timo; Kalverda, Arnout P.; Thompson, Gary S. Molecular Cell, Vol. 41, Issue 2 https://doi.org/10.1016/j.molcel.2010.11.028	journal	January 2011
Variation in amount of wild-type transthyretin in different fibril and tissue types in ATTR amyloidosis Ihse, Elisabet; Suhr, Ole B.; Hellman, Ulf Journal of Molecular Medicine, Vol. 89, Issue 2 https://doi.org/10.1007/s00109-010-0695-1	journal	November 2010
UCSF Chimera?A visualization system for exploratory research and analysis Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Journal of Computational Chemistry, Vol. 25, Issue 13 https://doi.org/10.1002/jcc.20084	journal	January 2004
Characterization of the transition state of protein unfolding by use of molecular dynamics: chymotrypsin inhibitor 2. Li, A.; Daggett, V. Proceedings of the National Academy of Sciences, Vol. 91, Issue 22 https://doi.org/10.1073/pnas.91.22.10430	journal	October 1994
Molecular Dynamics Simulation of Amyloid β Dimer Formation Urbanc, B.; Cruz, L.; Ding, F. Biophysical Journal, Vol. 87, Issue 4 https://doi.org/10.1529/biophysj.104.040980	journal	October 2004
The amyloid state and its association with protein misfolding diseases Knowles, Tuomas P. J.; Vendruscolo, Michele; Dobson, Christopher M. Nature Reviews Molecular Cell Biology, Vol. 15, Issue 6 https://doi.org/10.1038/nrm3810	journal	May 2014
Inhibition of protein aggregation and amyloid formation by small molecules Doig, Andrew J.; Derreumaux, Philippe Current Opinion in Structural Biology, Vol. 30 https://doi.org/10.1016/j.sbi.2014.12.004	journal	February 2015
The Role of Molecular Simulations in the Development of Inhibitors of Amyloid β-Peptide Aggregation for the Treatment of Alzheimer’s Disease Lemkul, Justin A.; Bevan, David R. ACS Chemical Neuroscience, Vol. 3, Issue 11 https://doi.org/10.1021/cn300091a	journal	April 2012
Potentially amyloidogenic conformational intermediates populate the unfolding landscape of transthyretin: Insights from molecular dynamics simulations Rodrigues, J. Rui; Simões, Carlos J. V.; Silva, Cândida G. Protein Science, Vol. 19, Issue 2 https://doi.org/10.1002/pro.289	journal	January 2010
The dynameomics rotamer library: Amino acid side chain conformations and dynamics from comprehensive molecular dynamics simulations in water: The Dynameomics Rotamer Library Scouras, Alexander D.; Daggett, Valerie Protein Science, Vol. 20, Issue 2 https://doi.org/10.1002/pro.565	journal	January 2011
Multidimensional scaling by optimizing goodness of fit to a nonmetric hypothesis Kruskal, J. B. Psychometrika, Vol. 29, Issue 1 https://doi.org/10.1007/BF02289565	journal	March 1964
Methods for molecular dynamics simulations of protein folding/unfolding in solution Beck, D. Methods, Vol. 34, Issue 1 https://doi.org/10.1016/j.ymeth.2004.03.008	journal	September 2004
Tafamidis, a potent and selective transthyretin kinetic stabilizer that inhibits the amyloid cascade Bulawa, C. E.; Connelly, S.; DeVit, M. Proceedings of the National Academy of Sciences, Vol. 109, Issue 24 https://doi.org/10.1073/pnas.1121005109	journal	May 2012
The Acid-Mediated Denaturation Pathway of Transthyretin Yields a Conformational Intermediate That Can Self-Assemble into Amyloid ^† Lai, Zhihong; Colón, Wilfredo; Kelly, Jeffery W. Biochemistry, Vol. 35, Issue 20 https://doi.org/10.1021/bi952501g	journal	January 1996
Characterization of residual structure in the thermally denatured state of barnase by simulation and experiment: Description of the folding pathway Bond, C. J.; Wong, K. -B.; Clarke, J. Proceedings of the National Academy of Sciences, Vol. 94, Issue 25 https://doi.org/10.1073/pnas.94.25.13409	journal	December 1997
Molecular Insight into Human Lysozyme and Its Ability to Form Amyloid Fibrils in High Concentrations of Sodium Dodecyl Sulfate: A View from Molecular Dynamics Simulations Jafari, Majid; Mehrnejad, Faramarz PLOS ONE, Vol. 11, Issue 10 https://doi.org/10.1371/journal.pone.0165213	journal	October 2016
Assessing the effect of D59P mutation in the DE loop region in amyloid aggregation propensity of β2‐microglobulin: A molecular dynamics simulation study Narang, Simranjeet S.; Shuaib, Suniba; Goyal, Deepti Journal of Cellular Biochemistry, Vol. 119, Issue 1 https://doi.org/10.1002/jcb.26241	journal	July 2017
Mild cognitive impairment due to Alzheimer disease in the community Petersen, Ronald C.; Aisen, Paul; Boeve, Bradley F. Annals of Neurology, Vol. 74, Issue 2 https://doi.org/10.1002/ana.23931	journal	August 2013
A comparative analysis of 23 structures of the amyloidogenic protein transthyretin Hörnberg, Andreas; Eneqvist, Therese; Olofsson, Anders Journal of Molecular Biology, Vol. 302, Issue 3 https://doi.org/10.1006/jmbi.2000.4078	journal	September 2000
Solid-State NMR Studies Reveal Native-like β-Sheet Structures in Transthyretin Amyloid Lim, Kwang Hun; Dasari, Anvesh K. R.; Hung, Ivan Biochemistry, Vol. 55, Issue 37 https://doi.org/10.1021/acs.biochem.6b00649	journal	September 2016
Stability and crystal structures of His88 mutant human transthyretins Yokoyama, Takeshi; Hanawa, Yuma; Obita, Takayuki FEBS Letters, Vol. 591, Issue 13 https://doi.org/10.1002/1873-3468.12704	journal	June 2017
Molecular dynamics of native protein Levitt, Michael; Huber, R. Journal of Molecular Biology, Vol. 168, Issue 3 https://doi.org/10.1016/S0022-2836(83)80306-4	journal	August 1983
α-Sheet secondary structure in amyloid β-peptide drives aggregation and toxicity in Alzheimer’s disease Shea, Dylan; Hsu, Cheng-Chieh; Bi, Timothy M. Proceedings of the National Academy of Sciences, Vol. 116, Issue 18 https://doi.org/10.1073/pnas.1820585116	journal	April 2019
Different disease-causing mutations in transthyretin trigger the same conformational conversion Steward, R. E.; Armen, R. S.; Daggett, V. Protein Engineering Design and Selection, Vol. 21, Issue 3 https://doi.org/10.1093/protein/gzm086	journal	January 2008
Drivers of α-Sheet Formation in Transthyretin under Amyloidogenic Conditions Childers, Matthew Carter; Daggett, Valerie Biochemistry, Vol. 58, Issue 44 https://doi.org/10.1021/acs.biochem.9b00769	journal	October 2019
Kinetic control of dimer structure formation in amyloid fibrillogenesis Hwang, Wonmuk; Zhang, Shuguang; Kamm, Roger D. Proceedings of the National Academy of Sciences, Vol. 101, Issue 35 https://doi.org/10.1073/pnas.0402634101	journal	August 2004
Molecular dynamics simulation of the unfolding of barnase: characterization of the major intermediate 1 1Edited by A. R. Fersht Li, Aijun; Daggett, Valerie Journal of Molecular Biology, Vol. 275, Issue 4 https://doi.org/10.1006/jmbi.1997.1484	journal	January 1998
Structural Changes Associated with Transthyretin Misfolding and Amyloid Formation Revealed by Solution and Solid-State NMR Lim, Kwang Hun; Dasari, Anvesh K. R.; Hung, Ivan Biochemistry, Vol. 55, Issue 13 https://doi.org/10.1021/acs.biochem.6b00164	journal	March 2016
The x-ray crystal structure refinements of normal human transthyretin and the amyloidogenic Val-30–>Met variant to 1.7-A resolution. Hamilton, J. A.; Steinrauf, L. K.; Braden, B. C. Journal of Biological Chemistry, Vol. 268, Issue 4 https://doi.org/10.1016/S0021-9258(18)53792-3	journal	February 1993
The Early Phase of β2m Aggregation: An Integrative Computational Study Framed on the D76N Mutant and the ΔN6 Variant J. S. Loureiro, Rui; Vila-Viçosa, Diogo; Machuqueiro, Miguel Biomolecules, Vol. 9, Issue 8 https://doi.org/10.3390/biom9080366	journal	August 2019
The β-Slip Eneqvist, Therese; Andersson, Karin; Olofsson, Anders Molecular Cell, Vol. 6, Issue 5 https://doi.org/10.1016/S1097-2765(00)00117-9	journal	November 2000
Peptide Plane Can Flip in Two Opposite Directions: Implication in Amyloid Formation of Transthyretin Yang, Mingfeng; Lei, Ming; Yordanov, Boyan The Journal of Physical Chemistry B, Vol. 110, Issue 12 https://doi.org/10.1021/jp0570420	journal	March 2006
NMR Measurements Reveal the Structural Basis of Transthyretin Destabilization by Pathogenic Mutations Leach, Benjamin I.; Zhang, Xin; Kelly, Jeffery W. Biochemistry, Vol. 57, Issue 30 https://doi.org/10.1021/acs.biochem.8b00642	journal	July 2018
Agitation of amyloid proteins to speed aggregation measured by ThT fluorescence: A call for standardization Batzli, Kiersten M.; Love, Brian J. Materials Science and Engineering: C, Vol. 48 https://doi.org/10.1016/j.msec.2014.09.015	journal	March 2015
Anatomy of an Amyloidogenic Intermediate Armen, Roger S.; Alonso, Darwin O. V.; Daggett, Valerie Structure, Vol. 12, Issue 10 https://doi.org/10.1016/j.str.2004.08.005	journal	October 2004
Matplotlib: A 2D Graphics Environment Hunter, John D. Computing in Science & Engineering, Vol. 9, Issue 3 https://doi.org/10.1109/MCSE.2007.55	journal	January 2007
The Protein Data Bank Berman, H. M. Nucleic Acids Research, Vol. 28, Issue 1 https://doi.org/10.1093/nar/28.1.235	journal	January 2000
Staphylococcal protein A: Unfolding pathways, unfolded states, and differences between the B and E domains Alonso, Darwin O. V.; Daggett, Valerie Proceedings of the National Academy of Sciences, Vol. 97, Issue 1 https://doi.org/10.1073/pnas.97.1.133	journal	January 2000
Loss of a metal-binding site in gelsolin leads to familial amyloidosis–Finnish type Kazmirski, Steven L.; Isaacson, Rivka L.; An, Chahm Nature Structural Biology, Vol. 9, Issue 2 https://doi.org/10.1038/nsb745	journal	January 2002
H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations Anandakrishnan, R.; Aguilar, B.; Onufriev, A. V. Nucleic Acids Research, Vol. 40, Issue W1 https://doi.org/10.1093/nar/gks375	journal	May 2012
Localized Structural Fluctuations Promote Amyloidogenic Conformations in Transthyretin Lim, Kwang Hun; Dyson, H. Jane; Kelly, Jeffery W. Journal of Molecular Biology, Vol. 425, Issue 6 https://doi.org/10.1016/j.jmb.2013.01.008	journal	March 2013
Molecular dynamics simulation of β2-microglobulin in denaturing and stabilizing conditions Fogolari, Federico; Corazza, Alessandra; Varini, Nicola Proteins: Structure, Function, and Bioinformatics, Vol. 79, Issue 3 https://doi.org/10.1002/prot.22940	journal	December 2010
Amyloid nomenclature 2018: recommendations by the International Society of Amyloidosis (ISA) nomenclature committee Benson, Merrill D.; Buxbaum, Joel N.; Eisenberg, David S. Amyloid, Vol. 25, Issue 4 https://doi.org/10.1080/13506129.2018.1549825	journal	October 2018
Preventing Misfolding of the Prion Protein by Trimethylamine N -Oxide ^† Bennion, Brian J.; DeMarco, Mari L.; Daggett, Valerie Biochemistry, Vol. 43, Issue 41 https://doi.org/10.1021/bi0486379	journal	October 2004
The contribution of biophysical and structural studies of protein self-assembly to the design of therapeutic strategies for amyloid diseases Cremades, Nunilo; Dobson, Christopher M. Neurobiology of Disease, Vol. 109 https://doi.org/10.1016/j.nbd.2017.07.009	journal	January 2018
Soluble protein oligomers in neurodegeneration: lessons from the Alzheimer's amyloid β-peptide Haass, Christian; Selkoe, Dennis J. Nature Reviews Molecular Cell Biology, Vol. 8, Issue 2 https://doi.org/10.1038/nrm2101	journal	February 2007

Similar Records

Crystal structures of amyloidogenic segments of human transthyretin: Amyloid Structures of Transthyretin Segments

Journal Article · Wed Jun 13 00:00:00 EDT 2018 · Protein Science · OSTI ID:2279907

Saelices, Lorena; Sievers, Stuart A.; Sawaya, Michael R.; +1 more

Heating of proteins as a means of improving crystallization: a successful case study on a highly amyloidogenic triple mutant of human transthyretin

Journal Article · Wed Aug 01 00:00:00 EDT 2007 · Acta Crystallographica. Section F · OSTI ID:2279907

Karlsson, Anders

Structural Insight into pH-Induced Conformational Changes within the Native Human Transthyretin Tetramer

Journal Article · Thu Sep 18 00:00:00 EDT 2008 · J. Mol. Biol. · OSTI ID:2279907

Palaninathan, Satheesh K; Mohamedmohaideen, Nilofar N; Snee, William C; +2 more

Title: Edge Strand Dissociation and Conformational Changes in Transthyretin under Amyloidogenic Conditions

Citation Formats

References (69)

Similar Records

Related Subjects