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Physics of Proteins: Intrinsically Disordered Proteins & Evolution

FOCUS · MAR-B71 · ID: 3112466

Presentations

  • How to Fold the Proteome (Mission Accomplished?)

    ORAL · Invited

    –

    Publication: Non-Refoldability is Pervasive Across the E. coli Proteome. PMID: 34308638<br>A Proteome-Wide Map of Chaperone-Assisted Protein Refolding in a Cytosol-like Milieu. PMID: 36417429<br>Intrinsically Disordered Regions Promote Protein Refoldability and Facilitate Retrieval from Biomolecular Condensates. 10.1101/2023.06.25.546465

    Presenters

    • Stephen Fried

      Johns Hopkins University

    Authors

    • Stephen Fried

      Johns Hopkins University

    View abstract →

  • Alpha helices are more evolutionarily robust to environmental perturbations than beta sheets: Bayesian theory for evolution

    ORAL

    –

    Publication: [1] Tobias Sikosek and Hue Sun Chan. Biophysics of protein<br>evolution and evolutionary protein biophysics. Journal<br>of The Royal Society Interface, 11(100):20140419, 2014.<br>[2] Yu Xia and Michael Levitt. Roles of mutation and re-<br>combination in the evolution of protein thermodynam-<br>ics. Proceedings of the National Academy of Sciences,<br>99(16):10382–10387, 2002.<br>[3] Jesse D Bloom, Zhongyi Lu, David Chen, Alpan Raval,<br>Ophelia S Venturelli, and Frances H Arnold. Evolution<br>favors protein mutational robustness in sufficiently large<br>populations. BMC biology, 5:1–21, 2007.<br>[4] Vijay Jayaraman, Saacnicteh Toledo-Pati˜no, Lianet<br>Noda-Garc´ıa, and Paola Laurino. Mechanisms of protein<br>evolution. Protein Science, 31:e4362, 2022.<br>[5] Jorge A Vila. Analysis of proteins in the light of muta-<br>tions. European Biophysics Journal, pages 1–11, 2024.<br>[6] Julia Hartling and Junhyong Kim. Mutational robust-<br>ness and geometrical form in protein structures. Journal<br>of Experimental Zoology Part B: Molecular and Develop-<br>mental Evolution, 310(3):216–226, 2008.<br>[7] Christian Schaefer, Avner Schlessinger, and Burkhard<br>Rost. Protein secondary structure appears to be robust<br>under in silico evolution while protein disorder appears<br>not to be. Bioinformatics, 26(5):625–631, 2010.<br>[8] Mary McLeod Rorick and Gunter P Wagner. Structural<br>robustness confers evolvability in proteins. In 2010 AAAI<br>Fall Symposium Series, 2010.<br>[9] Mary M Rorick and G¨unter P Wagner. Protein structural<br>modularity and robustness are associated with evolvabil-<br>ity. Genome biology and evolution, 3:456–475, 2011.<br>[10] Iain G Johnston, Kamaludin Dingle, Sam F Greenbury,<br>Chico Q Camargo, Jonathan PK Doye, Sebastian E Ah-<br>nert, and Ard A Louis. Symmetry and simplicity spon-<br>taneously emerge from the algorithmic nature of evolu-<br>tion. Proceedings of the National Academy of Sciences,<br>119(11):e2113883119, 2022.<br>[11] Qian-Yuan Tang, Tetsuhiro S Hatakeyama, and Kunihiko<br>Kaneko. Functional sensitivity and mutational robust-<br>ness of proteins. Physical Review Research, 2(3):033452,<br>2020.<br>[12] Qian-Yuan Tang and Kunihiko Kaneko. Dynamics-<br>evolution correspondence in protein structures. Physical<br>review letters, 127(9):098103, 2021.<br>[13] Ayaka Sakata and Kunihiko Kaneko. Dimensional re-<br>duction in evolving spin-glass model: correlation of<br>phenotypic responses to environmental and mutational<br>changes. Physical Review Letters, 124(21):218101, 2020.<br>[14] Shintaro Nagata and Macoto Kikuchi. Emergence of co-<br>operative bistability and robustness of gene regulatory<br>networks. PLoS computational biology, 16(6):e1007969,<br>2020.<br>[15] Tadamune Kaneko and Macoto Kikuchi. Evolution en-<br>hances mutational robustness and suppresses the emer-<br>gence of a new phenotype: A new computational ap-<br>proach for studying evolution. PLOS Computational Bi-<br>ology, 18(1):e1009796, 2022.<br>[16] Kunihiko Kaneko. Evolution of robustness to noise<br>and mutation in gene expression dynamics. PLoS one,<br>2(5):e434, 2007.<br>[17] Stefano Ciliberti, Olivier C Martin, and Andreas Wag-<br>ner. Robustness can evolve gradually in complex regula-<br>tory gene networks with varying topology. PLoS compu-<br>tational biology, 3(2):e15, 2007.<br>[18] Kit Fun Lau and Ken A Dill. A lattice statistical mechan-<br>ics model of the conformational and sequence spaces of<br>proteins. Macromolecules, 22(10):3986–3997, 1989.<br>[19] Helen M Berman, John Westbrook, Zukang Feng, Gary<br>Gilliland, Talapady N Bhat, Helge Weissig, Ilya N<br>Shindyalov, and Philip E Bourne. The protein data bank.<br>Nucleic acids research, 28(1):235–242, 2000.<br>[20] Hu Chen, Xin Zhou, and Zhong-Can Ou-Yang.<br>Secondary-structure-favored hydrophobic-polar lattice<br>model of protein folding. Physical Review E,<br>64(4):041905, 2001.<br>[21] Marek Cieplak and Jayanth R Banavar. Energy land-<br>scape and dynamics of proteins: an exact analysis of a<br>simplified lattice model. Physical Review E—Statistical,<br>Nonlinear, and Soft Matter Physics, 88(4):040702, 2013.<br>[22] Guangjie Shi, Thomas W¨ust, and David P Landau. Char-<br>acterizing folding funnels with replica exchange wang-<br>landau simulation of lattice proteins. Physical Review E,<br>94(5):050402, 2016.<br>[23] Erik Van Dijk, Patrick Varilly, Tuomas PJ Knowles,<br>Daan Frenkel, and Sanne Abeln. Consistent treatment<br>of hydrophobicity in protein lattice models accounts for<br>cold denaturation. Physical review letters, 116(7):078101,<br>2016.<br>[24] Christian Holzgr¨afe, Anders Irb¨ack, and Carl Troein.<br>Mutation-induced fold switching among lattice proteins.<br>The Journal of chemical physics, 135(19), 2011.<br>[25] Guangjie Shi, Thomas Vogel, Thomas W¨ust, Ying Wai<br>Li, and David P Landau. Effect of single-site mutations<br>on hydrophobic-polar lattice proteins. Physical Review<br>E, 90(3):033307, 2014.<br>[26] Shi-Jie Chen and Ken A Dill. Rna folding energy land-<br>scapes. Proceedings of the National Academy of Sciences,<br>97(2):646–651, 2000.<br>[27] Tomoei Takahashi, George Chikenji, and Kei Tokita. Lat-<br>tice protein design using bayesian learning. Physical Re-<br>view E, 104:014404, 2021.<br>[28] Valentino Bianco, Giancarlo Franzese, Christoph Del-<br>lago, and Ivan Coluzza. Role of water in the selection of<br>stable proteins at ambient and extreme thermodynamic<br>conditions. Physical Review X, 7(2):021047, 2017.<br>[29] Themis Lazaridis and Martin Karplus. Effective energy<br>function for proteins in solution. Proteins: Structure,<br>Function, and Bioinformatics, 35(2):133–152, 1999.<br>[30] Tomoei Takahashi, George Chikenji, and Kei Tokita.<br>The cavity method to protein design problem. Jour-<br>nal of Statistical Mechanics: Theory and Experiment,<br>2022(10):103403, 2022.<br>[31] Ivan Coluzza. Computational protein design: a review.<br>Journal of Physics: Condensed Matter, 29(14):143001,<br>2017.<br>[32] Simona Cocco, Christoph Feinauer, Matteo Figliuzzi,<br>R´emi Monasson, and Martin Weigt. Inverse statistical<br>physics of protein sequences: a key issues review. Re-<br>ports on Progress in Physics, 81(3):032601, 2018.<br>[33] Christian B Anfinsen. Principles that govern the folding<br>of protein chains. Science, 181(4096):223–230, 1973.<br>[34] Charles C Bigelow. On the average hydrophobicity of<br>proteins and the relation between it and protein struc-<br>12<br>ture. Journal of Theoretical Biology, 16(2):187–211, 1967.<br>[35] Yoshiyuki Kabashima and David Saad. Belief propa-<br>gation vs. tap for decoding corrupted messages. Euro-<br>physics Letters, 44(5):668, 1998.<br>[36] Hue Sun Chan and Ken A Dill. Compact polymers.<br>Macromolecules, 22(12):4559–4573, 1989.<br>[37] Khoi Tan Nguyen, St´ephanie V Le Clair, Shuji Ye, and<br>Zhan Chen. Orientation determination of protein helical<br>secondary structures using linear and nonlinear vibra-<br>tional spectroscopy. The journal of physical chemistry B,<br>113(36):12169–12180, 2009.<br>[38] Motoo Kimura et al. Evolutionary rate at the molecular<br>level. Nature, 217(5129):624–626, 1968.<br>[39] Gy¨orgy Abrus´an and Joseph A Marsh. Alpha helices<br>are more robust to mutations than beta strands. PLoS<br>computational biology, 12(12):e1005242, 2016.<br>[40] George Chikenji, Macoto Kikuchi, and Yukito Iba. Multi-<br>self-overlap ensemble for protein folding: ground state<br>search and thermodynamics. Physical Review Letters,<br>83(9):1886, 1999.<br>[41] Nobu C Shirai and Macoto Kikuchi. Multicanonical sim-<br>ulation of the domb-joyce model and the g¯o model: new<br>enumeration methods for self-avoiding walks. In Journal<br>of Physics: Conference Series, volume 454, page 012039.<br>IOP Publishing, 2013.<br>[42] Marc M´ezard and Giorgio Parisi. The bethe lattice<br>spin glass revisited. The European Physical Journal B-<br>Condensed Matter and Complex Systems, 20:217–233,<br>2001.<br>[43] Marc Mezard and Andrea Montanari. Information,<br>physics, and computation. Oxford University Press, 2009.<br>

    Presenters

    • Tomoei Takahashi

      The University of Tokyo

    Authors

    • Tomoei Takahashi

      The University of Tokyo

    • George Chikenji

      Nagoya University

    • Kei Tokita

      Nagoya University

    • Yoshiyuki Kabashima

      The University of Tokyo

    View abstract →

  • Understanding the Role of Excipients in the Stability of Biological Macromolecules

    ORAL

    –

    Publication: Planned Paper: Understanding the role of excipients in stability of biological molecules (in preparation)

    Presenters

    • Xianci Zeng

      University of Massachusetts Amherst

    Authors

    • Xianci Zeng

      University of Massachusetts Amherst

    • Idris Tohidian

      Michigan Technological University

    • Rohan Chaudhari

      Michigan Technological University

    • Jonathan Zajac

      University of Minnesota

    • Praveen Muralikrishnan

      University of Minnesota

    • Caryn L Heldt

      Michigan Technological University

    • Sapna Sarupria

      University of Minnesota

    • Sarah L Perry

      University of Massachusetts Amherst

    View abstract →