Functional in vitro diversity of an intrinsically disordered plant protein during freeze–thawing is encoded by its structural plasticity

Intrinsically disordered late embryogenesis abundant (LEA) proteins play a central role in the tolerance of plants and other organisms to dehydration brought upon, for example, by freezing temperatures, high salt concentration, drought or desiccation, and many LEA proteins have been found to stabilize dehydration‐sensitive cellular structures. Their conformational ensembles are highly sensitive to the environment, allowing them to undergo conformational changes and adopt ordered secondary and quaternary structures and to participate in formation of membraneless organelles. In an interdisciplinary approach, we discovered how the functional diversity of the Arabidopsis thaliana LEA protein COR15A found in vitro is encoded in its structural repertoire, with the stabilization of membranes being achieved at the level of secondary structure and the stabilization of enzymes accomplished by the formation of oligomeric complexes. We provide molecular details on intra‐ and inter‐monomeric helix–helix interactions, demonstrate how oligomerization is driven by an α‐helical molecular recognition feature (α‐MoRF) and provide a rationale that the formation of noncanonical, loosely packed, right‐handed coiled‐coils might be a recurring theme for homo‐ and hetero‐oligomerization of LEA proteins.

[1]  Brett R. Janis,et al.  LEAfing through literature: Late embryogenesis abundant proteins coming of age - achievements and perspectives. , 2022, Journal of experimental botany.

[2]  S. Ovchinnikov,et al.  ColabFold: making protein folding accessible to all , 2022, Nature Methods.

[3]  Brett R. Janis,et al.  Functional and Conformational Plasticity of an Animal Group 1 LEA Protein , 2022, Biomolecules.

[4]  S. Graether,et al.  The Disordered Dehydrin and Its Role in Plant Protection: A Biochemical Perspective , 2022, Biomolecules.

[5]  D. Karcher,et al.  Subcellular Localization of Seed-Expressed LEA_4 Proteins Reveals Liquid-Liquid Phase Separation for LEA9 and for LEA48 Homo- and LEA42-LEA48 Heterodimers , 2021, Biomolecules.

[6]  D. Hassabis,et al.  AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models , 2021, Nucleic Acids Res..

[7]  J. Wang,et al.  Proteomic profiling of Arachis hypogaea in response to drought stress and overexpression of AhLEA2 improves drought tolerance. , 2021, Plant biology.

[8]  D. Bartels,et al.  Systems biology of resurrection plants , 2021, Cellular and Molecular Life Sciences.

[9]  Oriol Vinyals,et al.  Highly accurate protein structure prediction with AlphaFold , 2021, Nature.

[10]  Jianping Yang,et al.  Genome-wide identification and expression analysis of late embryogenesis abundant protein-encoding genes in rye (Secale cereale L.) , 2021, PloS one.

[11]  Hao Liu,et al.  Late embryogenesis abundant (LEA) gene family in Salvia miltiorrhiza: identification, expression analysis, and response to drought stress , 2021, Plant signaling & behavior.

[12]  M. R. Mozafari,et al.  Simple Equations Pertaining to the Particle Number and Surface Area of Metallic, Polymeric, Lipidic and Vesicular Nanocarriers , 2021, Scientia Pharmaceutica.

[13]  W. Yao,et al.  Genome-wide search and structural and functional analyses for late embryogenesis-abundant (LEA) gene family in poplar , 2021, BMC plant biology.

[14]  Tanushree Agarwal,et al.  Multiple copies of a novel amphipathic α-helix forming segment in Physcomitrella patens dehydrin play a key role in abiotic stress mitigation , 2021, The Journal of biological chemistry.

[15]  Xuncheng Liu,et al.  Characterization of LEA genes in Dendrobium officinale and one Gene in induction of callus. , 2020, Journal of plant physiology.

[16]  Alessandro Borgia,et al.  Polyelectrolyte interactions enable rapid association and dissociation in high-affinity disordered protein complexes , 2020, Nature Communications.

[17]  Brett R. Janis,et al.  Liquid-liquid phase separation promotes animal desiccation tolerance , 2020, Proceedings of the National Academy of Sciences.

[18]  Salla I. Virtanen,et al.  Heterogeneous dynamics in partially disordered proteins. , 2020, Physical chemistry chemical physics : PCCP.

[19]  J. Pomposo,et al.  Structure and Dynamics of Irreversible Single-Chain Nanoparticles in Dilute Solution. A Neutron Scattering Investigation , 2020 .

[20]  A. Skirycz,et al.  The Isolation of Stress Granules From Plant Material. , 2020, Current protocols in plant biology.

[21]  M. Hara,et al.  Cryoprotective activity of Arabidopsis KS-type dehydrin depends on the hydrophobic amino acids of two active segments. , 2020, Archives of biochemistry and biophysics.

[22]  D. G. Pinheiro,et al.  Late Embryogenesis Abundant Protein–Client Protein Interactions , 2020, Plants.

[23]  Anne Bremer,et al.  Similar Yet Different–Structural and Functional Diversity among Arabidopsis thaliana LEA_4 Proteins , 2020, International journal of molecular sciences.

[24]  M. Hara,et al.  F-segments of Arabidopsis dehydrins show cryoprotective activities for lactate dehydrogenase depending on the hydrophobic residues. , 2020, Phytochemistry.

[25]  Zhongjie Wang,et al.  Genome-wide identification and expression analyses of the LEA protein gene family in tea plant reveal their involvement in seed development and abiotic stress responses , 2019, Scientific Reports.

[26]  S. Graether,et al.  Binding of a Vitis riparia dehydrin to DNA. , 2019, Plant science : an international journal of experimental plant biology.

[27]  M. Xing,et al.  Genome-wide identification of and functional insights into the late embryogenesis abundant (LEA) gene family in bread wheat (Triticum aestivum) , 2019, Scientific Reports.

[28]  Anne Bremer,et al.  Conformational selection of the intrinsically disordered plant stress protein COR15A in response to solution osmolarity - an X-ray and light scattering study. , 2019, Physical chemistry chemical physics : PCCP.

[29]  G. Daughdrill,et al.  Conserved Glycines Control Disorder and Function in the Cold-Regulated Protein, COR15A , 2019, Biomolecules.

[30]  Mario Orsi,et al.  Physical properties of model biological lipid bilayers: insights from all-atom molecular dynamics simulations , 2019, Journal of Molecular Modeling.

[31]  P. Giavalisco,et al.  Molecular signatures associated with increased freezing tolerance due to low temperature memory in Arabidopsis. , 2018, Plant, cell & environment.

[32]  Helgi I. Ingólfsson,et al.  Folding and Lipid Composition Determine Membrane Interaction of the Disordered Protein COR15A. , 2018, Biophysical journal.

[33]  Bin Wu,et al.  The suite of small‐angle neutron scattering instruments at Oak Ridge National Laboratory , 2018 .

[34]  Christopher B. Stanley,et al.  Intrinsically Disordered Protein Exhibits Both Compaction and Expansion under Macromolecular Crowding. , 2018, Biophysical journal.

[35]  Catarina B. Fernandes,et al.  Extreme disorder in an ultrahigh-affinity protein complex , 2018, Nature.

[36]  S. Graether,et al.  In vivo evidence for homo- and heterodimeric interactions of Arabidopsis thaliana dehydrins AtCOR47, AtERD10, and AtRAB18 , 2017, Scientific Reports.

[37]  T. Darwish,et al.  Intrinsically Disordered Stress Protein COR15A Resides at the Membrane Surface during Dehydration. , 2017, Biophysical journal.

[38]  M. Hara,et al.  The role of hydrophobic amino acids of K-segments in the cryoprotection of lactate dehydrogenase by dehydrins. , 2017, Journal of plant physiology.

[39]  Anne Bremer,et al.  Folding of intrinsically disordered plant LEA proteins is driven by glycerol‐induced crowding and the presence of membranes , 2017, The FEBS journal.

[40]  J. Pomposo,et al.  Structure and dynamics of single-chain nano-particles in solution , 2016 .

[41]  Jans H. Alzate-Morales,et al.  Molecular dynamics simulations and CD spectroscopy reveal hydration-induced unfolding of the intrinsically disordered LEA proteins COR15A and COR15B from Arabidopsis thaliana. , 2016, Physical chemistry chemical physics : PCCP.

[42]  K. Berendzen,et al.  Techniques for the Analysis of Protein-Protein Interactions in Vivo1[OPEN] , 2016, Plant Physiology.

[43]  G. Saab-Rincón,et al.  The Unstructured N-terminal Region of Arabidopsis Group 4 Late Embryogenesis Abundant (LEA) Proteins Is Required for Folding and for Chaperone-like Activity under Water Deficit* , 2016, The Journal of Biological Chemistry.

[44]  G C P van Zundert,et al.  The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes. , 2016, Journal of molecular biology.

[45]  Berk Hess,et al.  GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers , 2015 .

[46]  Yang Zhang,et al.  The I-TASSER Suite: protein structure and function prediction , 2014, Nature Methods.

[47]  Anja Thalhammer,et al.  A mechanistic model of COR15 protein function in plant freezing tolerance: integration of structural and functional characteristics , 2014, Plant signaling & behavior.

[48]  Wouter G. Touw,et al.  A series of PDB-related databanks for everyday needs , 2014, Nucleic Acids Res..

[49]  S. Graether,et al.  A dehydrin-dehydrin interaction: the case of SK3 from Opuntia streptacantha , 2014, Front. Plant Sci..

[50]  Anja Thalhammer,et al.  Disordered Cold Regulated15 Proteins Protect Chloroplast Membranes during Freezing through Binding and Folding, But Do Not Stabilize Chloroplast Enzymes in Vivo1[W][OPEN] , 2014, Plant Physiology.

[51]  L. Gierasch,et al.  Physicochemical Properties of Cells and Their Effects on Intrinsically Disordered Proteins (IDPs) , 2014, Chemical reviews.

[52]  S. Graether,et al.  The Importance of Size and Disorder in the Cryoprotective Effects of Dehydrins1[C][W] , 2013, Plant Physiology.

[53]  Rekha Kushwaha,et al.  Uses of Phage Display in Agriculture: Sequence Analysis and Comparative Modeling of Late Embryogenesis Abundant Client Proteins Suggest Protein-Nucleic Acid Binding Functionality , 2013, Comput. Math. Methods Medicine.

[54]  C. Garvey,et al.  Phospholipid Membrane Protection by Sugar Molecules during Dehydration—Insights into Molecular Mechanisms Using Scattering Techniques , 2013, International journal of molecular sciences.

[55]  Abhijit Karnik,et al.  SDM-Assist software to design site-directed mutagenesis primers introducing “silent” restriction sites , 2013, BMC Bioinformatics.

[56]  Michael D. McLean,et al.  Utility of the P19 suppressor of gene-silencing protein for production of therapeutic antibodies in Nicotiana expression hosts. , 2012, Plant biotechnology journal.

[57]  M. Blatt,et al.  A 2in1 cloning system enables ratiometric bimolecular fluorescence complementation (rBiFC). , 2012, BioTechniques.

[58]  B. Hammouda Small‐Angle Scattering From Branched Polymers , 2012 .

[59]  C. Jonak,et al.  Drought, salt, and temperature stress-induced metabolic rearrangements and regulatory networks. , 2012, Journal of experimental botany.

[60]  A. Stadler,et al.  Macromolecular dynamics in red blood cells investigated using neutron spectroscopy , 2011, Journal of The Royal Society Interface.

[61]  M. Toner,et al.  LEA proteins during water stress: not just for plants anymore. , 2011, Annual review of physiology.

[62]  Boualem Hammouda,et al.  A new Guinier-Porod model , 2010 .

[63]  B. Trout,et al.  Mechanisms of protein stabilization and prevention of protein aggregation by glycerol. , 2009, Biochemistry.

[64]  M. Hara,et al.  DNA binding of citrus dehydrin promoted by zinc ion. , 2009, Plant, cell & environment.

[65]  P. Tompa,et al.  Disordered plant LEA proteins as molecular chaperones , 2008, Plant signaling & behavior.

[66]  A. Covarrubias,et al.  The Enigmatic LEA Proteins and Other Hydrophilins1[W] , 2008, Plant Physiology.

[67]  D. van der Spoel,et al.  GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.

[68]  J. Holton,et al.  Structure of a designed, right‐handed coiled‐coil tetramer containing all biological amino acids , 2007, Protein science : a publication of the Protein Society.

[69]  M. Wise,et al.  The continuing conundrum of the LEA proteins , 2007, Naturwissenschaften.

[70]  N. Tuteja Abscisic Acid and Abiotic Stress Signaling , 2007, Plant signaling & behavior.

[71]  Jack Snoeyink,et al.  Nucleic Acids Research Advance Access published April 22, 2007 MolProbity: all-atom contacts and structure validation for proteins and nucleic acids , 2007 .

[72]  H. Itoh,et al.  Arabidopsis Cor15am Is a Chloroplast Stromal Protein That Has Cryoprotective Activity and Forms Oligomers1[W][OA] , 2007, Plant Physiology.

[73]  M. Parrinello,et al.  Canonical sampling through velocity rescaling. , 2007, The Journal of chemical physics.

[74]  Marc S. Cortese,et al.  Analysis of molecular recognition features (MoRFs). , 2006, Journal of molecular biology.

[75]  Rossana Henriques,et al.  Agrobacterium-mediated transformation of Arabidopsis thaliana using the floral dip method , 2006, Nature Protocols.

[76]  Jianhua Zhu,et al.  Methods and concepts in quantifying resistance to drought, salt and freezing, abiotic stresses that affect plant water status. , 2006, The Plant journal : for cell and molecular biology.

[77]  F. Studier,et al.  Protein production by auto-induction in high density shaking cultures. , 2005, Protein expression and purification.

[78]  Ilme Schlichting,et al.  The VASP tetramerization domain is a right-handed coiled coil based on a 15-residue repeat. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[79]  Ian W. Davis,et al.  Structure validation by Cα geometry: ϕ,ψ and Cβ deviation , 2003, Proteins.

[80]  S. N. Timasheff,et al.  Protein-solvent preferential interactions, protein hydration, and the modulation of biochemical reactions by solvent components , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[81]  D. Hincha,et al.  Specific effects of fructo- and gluco-oligosaccharides in the preservation of liposomes during drying. , 2002, Glycobiology.

[82]  F. Salamini,et al.  Desiccation tolerance in the resurrection plant Craterostigma plantagineum. A contribution to the study of drought tolerance at the molecular level. , 2001, Plant physiology.

[83]  R. Friesner,et al.  Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides† , 2001 .

[84]  R. Kammerer,et al.  Crystal structure of a naturally occurring parallel right-handed coiled coil tetramer , 2001, Nature Structural Biology.

[85]  P. Schuck,et al.  Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and lamm equation modeling. , 2000, Biophysical journal.

[86]  A. Haymet,et al.  Winter Flounder “Antifreeze” Proteins: Synthesis and Ice Growth Inhibition of Analogues that Probe the Relative Importance of Hydrophobic and Hydrogen‐Bonding Interactions. , 1999 .

[87]  A. Haymet,et al.  Winter Flounder "Antifreeze" Proteins: Synthesis and Ice Growth Inhibition of Analogs that Probe the Relative Importance of Hydrophobic and Hydrogen-Bonding Interactions , 1999 .

[88]  M. Buck,et al.  Trifluoroethanol and colleagues: cosolvents come of age. Recent studies with peptides and proteins , 1998, Quarterly Reviews of Biophysics.

[89]  D Walther,et al.  WebMol--a Java-based PDB viewer. , 1997, Trends in biochemical sciences.

[90]  A. Lupas,et al.  Predicting coiled-coil regions in proteins. , 1997, Current opinion in structural biology.

[91]  W. L. Jorgensen,et al.  Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .

[92]  S. J. Gilmour,et al.  Constitutive expression of the cold-regulated Arabidopsis thaliana COR15a gene affects both chloroplast and protoplast freezing tolerance. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[93]  T. Darden,et al.  A smooth particle mesh Ewald method , 1995 .

[94]  T. Blundell,et al.  Comparative protein modelling by satisfaction of spatial restraints. , 1993, Journal of molecular biology.

[95]  L. Dure A repeating 11-mer amino acid motif and plant desiccation. , 1993, The Plant journal : for cell and molecular biology.

[96]  P. Kollman,et al.  Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models , 1992 .

[97]  M. Thomashow,et al.  A cold-regulated Arabidopsis gene encodes a polypeptide having potent cryoprotective activity. , 1992, Biochemical and biophysical research communications.

[98]  B. Green,et al.  Biochemical and biophysical properties of thylakoid acyl lipids , 1991 .

[99]  W. L. Jorgensen,et al.  The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. , 1988, Journal of the American Chemical Society.

[100]  H. Schägger,et al.  Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa. , 1987, Analytical biochemistry.

[101]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[102]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[103]  M. Parrinello,et al.  Polymorphic transitions in single crystals: A new molecular dynamics method , 1981 .

[104]  Y H Chen,et al.  Determination of the secondary structures of proteins by circular dichroism and optical rotatory dispersion. , 1972, Biochemistry.

[105]  N. A. Holtzman,et al.  The molecular size of lactate dehydrogenase isozymes in mature tests. , 1968, Biochimica et biophysica acta.

[106]  OUP accepted manuscript , 2021, Nucleic Acids Research.

[107]  Anja Thalhammer,et al.  Measuring Freezing Tolerance of Leaves and Rosettes: Electrolyte Leakage and Chlorophyll Fluorescence Assays. , 2020, Methods in molecular biology.

[108]  Anja Thalhammer,et al.  Disordered COR15 proteins protect chloroplast membranes during freezing through binding and folding, but do not stabilize chloroplast enzymes in-vivo , 2014 .

[109]  C. Kaminski,et al.  Intrinsically disordered proteins as molecular shields. , 2012, Molecular bioSystems.

[110]  P. Tompa,et al.  Fuzzy complexes: a more stochastic view of protein function. , 2012, Advances in experimental medicine and biology.

[111]  D. Hincha,et al.  LEA Proteins: Versatility of Form and Function , 2010 .

[112]  R D Appel,et al.  Protein identification and analysis tools in the ExPASy server. , 1999, Methods in molecular biology.

[113]  S. Provencher CONTIN: A general purpose constrained regularization program for inverting noisy linear algebraic and integral equations , 1984 .