Michael T. Woodside, Ph.D. - Related publications

Affiliations: 
2001 University of California, Berkeley, Berkeley, CA 
 2013- Physics University of Alberta, Edmonton, Alberta, Canada 
Area:
Protein folding, misfolding and aggregation; RNA folding and function; misfolding diseases; single-molecule approaches to biology
Website:
https://apps.ualberta.ca/directory/person/mwoodsid
NOTE: We are testing a new system for identifying relevant work based on semantic analysis that identifies similarities between recently published papers and the current author's publications. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches.
50 most relevant papers in past 60 days:
Year Citation  Score
2021 Dingfelder F, Macocco I, Benke S, Nettels D, Faccioli P, Schuler B. Slow Escape from a Helical Misfolded State of the Pore-Forming Toxin Cytolysin A. Jacs Au. 1: 1217-1230. PMID 34467360 DOI: 10.1021/jacsau.1c00175   
2021 Michael E, Simonson T. How much can physics do for protein design? Current Opinion in Structural Biology. 72: 46-54. PMID 34461593 DOI: 10.1016/j.sbi.2021.07.011   
2021 Li J, Hou C, Ma X, Guo S, Zhang H, Shi L, Liao C, Zheng B, Ye L, Yang L, He X. Entropy-Enthalpy Compensations Fold Proteins in Precise Ways. International Journal of Molecular Sciences. 22. PMID 34502559 DOI: 10.3390/ijms22179653   
2021 Florio G, Pugno NM, Buehler MJ, Puglisi G. A coarse-grained mechanical model for folding and unfolding of tropoelastin with possible mutations. Acta Biomaterialia. PMID 34303013 DOI: 10.1016/j.actbio.2021.07.032   
2021 Rösner HI, Caldarini M, Potel G, Malmodin D, Vanoni MA, Aliverti A, Broglia RA, Kragelund BB, Tiana G. The denatured state of HIV-1 protease under native conditions. Proteins. PMID 34312913 DOI: 10.1002/prot.26189   
2021 Song KC, Molina AV, Chen R, Gagnon IA, Koh YH, Roux B, Sosnick TR. Folding and misfolding of potassium channel monomers during assembly and tetramerization. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34413192 DOI: 10.1073/pnas.2103674118   
2021 Cresti JR, Manfredonia AJ, Bragança CE, Boscia JA, Hurley CM, Cundiff MD, Kraut DA. Proteasomal conformation controls unfolding ability. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34161281 DOI: 10.1073/pnas.2101004118   
2021 Cresti JR, Manfredonia AJ, Bragança CE, Boscia JA, Hurley CM, Cundiff MD, Kraut DA. Proteasomal conformation controls unfolding ability. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34161281 DOI: 10.1073/pnas.2101004118   
2021 Dreydoppel M, Dorn B, Modig K, Akke M, Weininger U. Transition-State Compressibility and Activation Volume of Transient Protein Conformational Fluctuations. Jacs Au. 1: 833-842. PMID 34467336 DOI: 10.1021/jacsau.1c00062   
2021 Mishra S, Looger LL, Porter LL. A sequence-based method for predicting extant fold switchers that undergo α-helix ↔ β-strand transitions. Biopolymers. e23471. PMID 34498740 DOI: 10.1002/bip.23471   
2021 Santhouse JR, Rao SR, Horne WS. Analysis of folded structure and folding thermodynamics in heterogeneous-backbone proteomimetics. Methods in Enzymology. 656: 93-122. PMID 34325801 DOI: 10.1016/bs.mie.2021.04.009   
2021 Dass R, Corlianò E, Mulder FAA. The contribution of electrostatics to hydrogen exchange in the unfolded protein state. Biophysical Journal. PMID 34370996 DOI: 10.1016/j.bpj.2021.08.003   
2021 Voith von Voithenberg L, Barth A, Trauschke V, Demarco B, Tyagi S, Koehler C, Lemke EA, Lamb DC. Comparative analysis of the coordinated motion of Hsp70s from different organelles observed by single-molecule three-color FRET. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34389669 DOI: 10.1073/pnas.2025578118   
2021 Ghosh B, Sengupta N. The protein hydration layer in high glucose concentration: Dynamical responses in folded and intrinsically disordered dimeric states. Biochemical and Biophysical Research Communications. 577: 124-129. PMID 34509724 DOI: 10.1016/j.bbrc.2021.09.005   
2021 Boucher L, Somani S, Negron C, Ma W, Jacobs S, Chan W, Malia T, Obmolova G, Teplyakov A, Gilliland GL, Luo J. Surface Salt bridges Contribute to the Extreme Thermal Stability of an FN3-like domain from a thermophilic bacterium. Proteins. PMID 34405904 DOI: 10.1002/prot.26218   
2021 Shmool TA, Martin LK, Bui-Le L, Moya-Ramirez I, Kotidis P, Matthews RP, Venter GA, Kontoravdi C, Polizzi KM, Hallett JP. An experimental approach probing the conformational transitions and energy landscape of antibodies: a glimmer of hope for reviving lost therapeutic candidates using ionic liquid. Chemical Science. 12: 9528-9545. PMID 34349928 DOI: 10.1039/d1sc02520a   
2021 Okuno Y, Yoo J, Schwieters CD, Best RB, Chung HS, Clore GM. Atomic view of cosolute-induced protein denaturation probed by NMR solvent paramagnetic relaxation enhancement. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34404723 DOI: 10.1073/pnas.2112021118   
2021 Papp D, Szigyártó IC, Nordén B, Perczel A, Beke-Somfai T. Structural Water Stabilizes Protein Motifs in Liquid Protein Phase: The Folding Mechanism of Short β-Sheets Coupled to Phase Transition. International Journal of Molecular Sciences. 22. PMID 34445303 DOI: 10.3390/ijms22168595   
2021 Lento C, Wilson DJ. Subsecond Time-Resolved Mass Spectrometry in Dynamic Structural Biology. Chemical Reviews. PMID 34324314 DOI: 10.1021/acs.chemrev.1c00222   
2021 Neupane K, Zhao M, Lyons A, Munshi S, Ileperuma SM, Ritchie DB, Hoffer NQ, Narayan A, Woodside MT. Structural dynamics of single SARS-CoV-2 pseudoknot molecules reveal topologically distinct conformers. Nature Communications. 12: 4749. PMID 34362921 DOI: 10.1038/s41467-021-25085-6   
2021 Škrbić T, Hoang TX, Giacometti A, Maritan A, Banavar JR. Spontaneous dimensional reduction and ground state degeneracy in a simple chain model. Physical Review. E. 104: L012101. PMID 34412247 DOI: 10.1103/PhysRevE.104.L012101   
2021 Van Deuren V, Yang YS, de Guillen K, Dubois C, Royer CA, Roumestand C, Barthe P. Comparative Assessment of NMR Probes for the Experimental Description of Protein Folding Pathways with High-Pressure NMR. Biology. 10. PMID 34356511 DOI: 10.3390/biology10070656   
2021 Olgenblum GI, Wien F, Sapir L, Harries D. β-Hairpin Miniprotein Stabilization in Trehalose Glass Is Facilitated by an Emergent Compact Non-Native State. The Journal of Physical Chemistry Letters. 7659-7664. PMID 34351767 DOI: 10.1021/acs.jpclett.1c02379   
2021 Halder P, Mitra P. Human prion protein: exploring the thermodynamic stability and structural dynamics of its pathogenic mutants. Journal of Biomolecular Structure & Dynamics. 1-17. PMID 34338141 DOI: 10.1080/07391102.2021.1957715   
2021 Serpa JJ, Popov KI, Petrotchenko EV, Dokholyan NV, Borchers CH. Structure of prion β-oligomers as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations. Proteomics. e2000298. PMID 34482645 DOI: 10.1002/pmic.202000298   
2021 Sun B, Lv J, Chen J, Liu Z, Zhou Y, Liu L, Jin Y, Wang F. Size-Selective VAILase Proteolysis Provides Dynamic Insights into Protein Structures. Analytical Chemistry. PMID 34291915 DOI: 10.1021/acs.analchem.1c02042   
2021 Sun B, Lv J, Chen J, Liu Z, Zhou Y, Liu L, Jin Y, Wang F. Size-Selective VAILase Proteolysis Provides Dynamic Insights into Protein Structures. Analytical Chemistry. PMID 34291915 DOI: 10.1021/acs.analchem.1c02042   
2021 Ye X, Mayne L, Englander SW. A conserved strategy for structure change and energy transduction in Hsp104 and other AAA+ protein motors. The Journal of Biological Chemistry. 101066. PMID 34384781 DOI: 10.1016/j.jbc.2021.101066   
2021 Agrawal S, Govind Kumar V, Gundampati RK, Moradi M, Kumar TKS. Characterization of the structural forces governing the reversibility of the thermal unfolding of the human acidic fibroblast growth factor. Scientific Reports. 11: 15579. PMID 34341408 DOI: 10.1038/s41598-021-95050-2   
2021 Sharma B, Dill KA. MELD-accelerated molecular dynamics help determine amyloid fibril structures. Communications Biology. 4: 942. PMID 34354239 DOI: 10.1038/s42003-021-02461-y   
2021 Walker B, Jing Z, Ren P. Molecular dynamics free energy simulations of ATP:Mg and ADP:Mg using the polarizable force field AMOEBA. Molecular Simulation. 47: 439-448. PMID 34421214 DOI: 10.1080/08927022.2020.1725003   
2021 Bergasa-Caceres F, Rabitz HA. Identification of Two Early Folding Stage Prion Non-Local Contacts Suggested to Serve as Key Steps in Directing the Final Fold to Be Either Native or Pathogenic. International Journal of Molecular Sciences. 22. PMID 34445324 DOI: 10.3390/ijms22168619   
2021 Dubrow A, Kim I, Topo E, Cho JH. Understanding the Binding Transition State After the Conformational Selection Step: The Second Half of the Molecular Recognition Process Between NS1 of the 1918 Influenza Virus and Host p85β. Frontiers in Molecular Biosciences. 8: 716477. PMID 34307465 DOI: 10.3389/fmolb.2021.716477   
2021 Dubrow A, Kim I, Topo E, Cho JH. Understanding the Binding Transition State After the Conformational Selection Step: The Second Half of the Molecular Recognition Process Between NS1 of the 1918 Influenza Virus and Host p85β. Frontiers in Molecular Biosciences. 8: 716477. PMID 34307465 DOI: 10.3389/fmolb.2021.716477   
2021 Mayerthaler F, Feldberg AL, Alfermann J, Sun X, Steinchen W, Yang H, Mootz HD. Intermediary conformations linked to the directionality of the aminoacylation pathway of nonribosomal peptide synthetases. Rsc Chemical Biology. 2: 843-854. PMID 34458813 DOI: 10.1039/d0cb00220h   
2021 Caldararu O, Ekberg V, Logan DT, Oksanen E, Ryde U. Exploring ligand dynamics in protein crystal structures with ensemble refinement. Acta Crystallographica. Section D, Structural Biology. 77: 1099-1115. PMID 34342282 DOI: 10.1107/S2059798321006513   
2021 Maity D, Pal D. Molecular Dynamics of Hemoglobin Reveals Structural Alterations and Explains the Interactions Driving Sickle Cell Fibrillation. The Journal of Physical Chemistry. B. PMID 34459602 DOI: 10.1021/acs.jpcb.1c01684   
2021 Kamenik AS, Singh I, Lak P, Balius TE, Liedl KR, Shoichet BK. Energy penalties enhance flexible receptor docking in a model cavity. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34475217 DOI: 10.1073/pnas.2106195118   
2021 Pham HA, Truong DT, Li MS. Dependence of Work on the Pulling Speed in Mechanical Ligand Unbinding. The Journal of Physical Chemistry. B. PMID 34292743 DOI: 10.1021/acs.jpcb.1c01818   
2021 Pham HA, Truong DT, Li MS. Dependence of Work on the Pulling Speed in Mechanical Ligand Unbinding. The Journal of Physical Chemistry. B. PMID 34292743 DOI: 10.1021/acs.jpcb.1c01818   
2021 Ortega-Alarcon D, Claveria-Gimeno R, Vega S, Jorge-Torres OC, Esteller M, Abian O, Velazquez-Campoy A. Stabilization Effect of Intrinsically Disordered Regions on Multidomain Proteins: The Case of the Methyl-CpG Protein 2, MeCP2. Biomolecules. 11. PMID 34439881 DOI: 10.3390/biom11081216   
2021 Burnaman SH, Kneller DW, Wang YF, Kovalevsky A, Weber IT. Revertant mutation V48G alters conformational dynamics of highly drug resistant HIV protease PRS17. Journal of Molecular Graphics & Modelling. 108: 108005. PMID 34419931 DOI: 10.1016/j.jmgm.2021.108005   
2021 Parkman JA, Barksdale CA, Michaelis DJ. CAN: A new program to streamline preparation of molecular coordinate files for molecular dynamics simulations. Journal of Computational Chemistry. PMID 34411332 DOI: 10.1002/jcc.26729   
2021 Cao Y, Das P, Chenthamarakshan V, Chen PY, Melnyk I, Shen Y. Fold2Seq: A Joint Sequence(1D)-Fold(3D) Embedding-based Generative Model for Protein Design. Proceedings of Machine Learning Research. 139: 1261-1271. PMID 34423306   
2021 Liang S, Li Z, Zhan J, Zhou Y. De Novo protein design by an energy function based on series expansion in distance and orientation dependence. Bioinformatics (Oxford, England). PMID 34406339 DOI: 10.1093/bioinformatics/btab598   
2021 Rout J, Swain BC, Subadini S, Mishra PP, Sahoo H, Tripathy U. Spectroscopic and computational insight into the conformational dynamics of hemoglobin in the presence of vitamin B12. International Journal of Biological Macromolecules. PMID 34419543 DOI: 10.1016/j.ijbiomac.2021.08.096   
2021 Pimpão C, Wragg D, Bonsignore R, Aikman B, Pedersen PA, Leoni S, Soveral G, Casini A. Mechanisms of irreversible aquaporin-10 inhibition by organogold compounds studied by combined biophysical methods and atomistic simulations. Metallomics : Integrated Biometal Science. PMID 34468767 DOI: 10.1093/mtomcs/mfab053   
2021 Zeng J, Weng J, Zhang Y, Xia F, Cui Q, Xu X. Conformational Features of Ras: Key Hydrogen-Bonding Interactions of Gln61 in the Intermediate State during GTP Hydrolysis. The Journal of Physical Chemistry. B. PMID 34324329 DOI: 10.1021/acs.jpcb.1c04679   
2021 Motono C, Yanagida S, Sato M, Hirokawa T. MDContactCom: a tool to identify differences of protein molecular dynamics from two MD simulation trajectories in terms of interresidue contacts. Bioinformatics (Oxford, England). PMID 34289011 DOI: 10.1093/bioinformatics/btab538   
2021 Fernández-Quintero ML, Kroell KB, Bacher LM, Loeffler JR, Quoika PK, Georges G, Bujotzek A, Kettenberger H, Liedl KR. Germline-Dependent Antibody Paratope States and Pairing Specific V-V Interface Dynamics. Frontiers in Immunology. 12: 675655. PMID 34447370 DOI: 10.3389/fimmu.2021.675655