Advances in Understanding Stimulus-Responsive Phase Behavior of Intrinsically Disordered Protein Polymers.

Abstract:

:Proteins and synthetic polymers can undergo phase transitions in response to changes to intensive solution parameters such as temperature, proton chemical potentials (pH), and hydrostatic pressure. For proteins and protein-based polymers, the information required for stimulus-responsive phase transitions is encoded in their amino acid sequence. Here, we review some of the key physical principles that govern the phase transitions of archetypal intrinsically disordered protein polymers (IDPPs). These are disordered proteins with repetitive amino acid sequences. Advances in recombinant technologies have enabled the design and synthesis of protein sequences of a variety of sequence complexities and lengths. We summarize insights that have been gleaned from the design and characterization of IDPPs that undergo thermo-responsive phase transitions and build on these insights to present a general framework for IDPPs with pH and pressure responsive phase behavior. In doing so, we connect the stimulus-responsive phase behavior of IDPPs with repetitive sequences to the coil-to-globule transitions that these sequences undergo at the single-chain level in response to changes in stimuli. The proposed framework and ongoing studies of stimulus-responsive phase behavior of designed IDPPs have direct implications in bioengineering, where designing sequences with bespoke material properties broadens the spectrum of applications, and in biology and medicine for understanding the sequence-specific driving forces for the formation of protein-based membraneless organelles as well as biological matrices that act as scaffolds for cells and mediators of cell-to-cell communication.

journal_name

J Mol Biol

authors

Ruff KM,Roberts S,Chilkoti A,Pappu RV

doi

10.1016/j.jmb.2018.06.031

subject

Has Abstract

pub_date

2018-11-02 00:00:00

pages

4619-4635

issue

23

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(18)30659-4

journal_volume

430

pub_type

杂志文章,评审
  • Release of Human TFIIB from Actively Transcribing Complexes Is Triggered upon Synthesis of 7- and 9-nt RNAs.

    abstract::RNA polymerase II (Pol II) and its general transcription factors assemble on the promoters of mRNA genes to form large macromolecular complexes that initiate transcription in a regulated manner. During early transcription, these complexes undergo dynamic rearrangement and disassembly as Pol II moves away from the star...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2020.05.005

    authors: Ly E,Powell AE,Goodrich JA,Kugel JF

    更新日期:2020-06-26 00:00:00

  • Identification of a unique Fe-S cluster binding site in a glycyl-radical type microcompartment shell protein.

    abstract::Recently, progress has been made toward understanding the functional diversity of bacterial microcompartment (MCP) systems, which serve as protein-based metabolic organelles in diverse microbes. New types of MCPs have been identified, including the glycyl-radical propanediol (Grp) MCP. Within these elaborate protein c...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2014.07.018

    authors: Thompson MC,Wheatley NM,Jorda J,Sawaya MR,Gidaniyan SD,Ahmed H,Yang Z,McCarty KN,Whitelegge JP,Yeates TO

    更新日期:2014-09-23 00:00:00

  • PKA-dependent binding of mRNA to the mitochondrial AKAP121 protein.

    abstract::Protein kinase A (PKA) anchoring proteins (AKAPs) tether PKA to various subcellular locations. AKAP121, which tethers PKAII to the outer mitochondrial membrane, includes a K homology (KH) RNA-binding motif. Purified AKAP121 KH domain binds the 3' untranslated regions (3'UTRs) of transcripts encoding the Fo-f subunit o...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(03)00173-6

    authors: Ginsberg MD,Feliciello A,Jones JK,Avvedimento EV,Gottesman ME

    更新日期:2003-04-04 00:00:00

  • Native Escherichia coli and murine dihydrofolate reductases contain late-folding non-native structures.

    abstract::We have examined the equilibrium and kinetic folding properties of two structurally homologous dihydrofolate reductases, Escherichia coli DHFR (EcDHFR) and murine DHFR (MuDHFR), as a function of temperature and ligand concentration. Conformational heterogeneity in native DHFR is well documented, and the results demons...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.2402

    authors: Clark AC,Frieden C

    更新日期:1999-01-29 00:00:00

  • Crystallization and preliminary X-ray diffraction analysis of a type I beta-glucosidase encoded by the bgIA gene of Bacillus polymyxa.

    abstract::The enzyme encoded by the bgIA gene of Bacillus polymyxa, a type I beta-glucosidase belonging to family I of glycosyl hydrolases, has been purified to homogeneity from an Escherichia coli culture which overexpressed the gene, and crystallized. The crystals, which diffract to 3.0 A resolution, belong to the orthorhombi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.1441

    authors: Sanz-Aparicio J,Romero A,Martinez-Ripoll M,Madarro A,Flors A,Polaina J

    更新日期:1994-07-15 00:00:00

  • Invertebrate myosin filament: subfilament arrangement in the wall of tubular filaments of insect flight muscles.

    abstract::Transverse sections (100 to 140 nm thick) of the flight muscles of the fleshfly Phormia terrae-novae and the housefly Musca domestica were studied. The images of 56 tubular myosin filaments of the fleshfly and 62 filaments of the housefly were digitized and computer processed by rotational averaging. The rotational po...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(88)90637-7

    authors: Beinbrech G,Ashton FT,Pepe FA

    更新日期:1988-06-05 00:00:00

  • Transcription regulation in thermophilic bacteria: high resolution contact probing of Bacillus stearothermophilus and Thermotoga neapolitana arginine repressor-operator interactions.

    abstract::Arginine-mediated regulation is remarkably well conserved in very divergent bacteria, and shows a number of unusual features that distinguish arginine regulation from other transcriptional control mechanisms. The arginine repressor subunit consists of a basic N-terminal DNA-binding domain, which belongs to the winged ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.5236

    authors: Song H,Wang H,Gigot D,Dimova D,Sakanyan V,Glansdorff N,Charlier D

    更新日期:2002-01-18 00:00:00

  • Alternative native flap conformation revealed by 2.3 A resolution structure of SIV proteinase.

    abstract::A large conformational change is observed between HIV-1 proteinase in the ligand-free state and in complexes with transition-state inhibitors. Crystal structures of this enzyme have either the flaps open for the native or ligand-free enzyme or the flaps closed for peptidomimetic ligand-bound enzyme. We describe the st...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.1353

    authors: Wilderspin AF,Sugrue RJ

    更新日期:1994-05-27 00:00:00

  • Cleavage mediated by the catalytic domain of bacterial RNase P RNA.

    abstract::Like other RNA molecules, RNase P RNA (RPR) is composed of domains, and these have different functions. Here, we provide data demonstrating that the catalytic (C) domain of Escherichia coli (Eco) RPR when separated from the specificity (S) domain mediates cleavage using various model RNA hairpin loop substrates. Compa...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2012.05.020

    authors: Wu S,Kikovska E,Lindell M,Kirsebom LA

    更新日期:2012-09-14 00:00:00

  • MOMP from Campylobacter jejuni Is a Trimer of 18-Stranded β-Barrel Monomers with a Ca2+ Ion Bound at the Constriction Zone.

    abstract::The Gram-negative organism Campylobacter jejuni is the major cause of food poisoning. Unlike Escherichia coli, which has two major porins, OmpC and OmpF, C. jejuni has one, termed major outer membrane protein (MOMP) through which nutrients and antibiotics transit. We report the 2.1-Å crystal structure of C. jejuni MOM...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2016.09.021

    authors: Ferrara LGM,Wallat GD,Moynié L,Dhanasekar NN,Aliouane S,Acosta-Gutiérrez S,Pagès JM,Bolla JM,Winterhalter M,Ceccarelli M,Naismith JH

    更新日期:2016-11-06 00:00:00

  • The major human structural IgE epitope of the Brazil nut allergen Ber e 1: a chimaeric and protein microarray approach.

    abstract::A protein microarray system containing different dilutions of 77 related and non-related proteins was used to show that IgE from subjects allergic to Brazil nut specifically recognise the seed 2S albumin protein (Ber e 1). Further, correctly folded chimaeric 2S albumin proteins containing structural epitope replacemen...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.08.065

    authors: Alcocer MJ,Murtagh GJ,Wilson PB,Progias P,Lin J,Archer DB

    更新日期:2004-10-22 00:00:00

  • Common physical properties of DNA affecting target site selection of sleeping beauty and other Tc1/mariner transposable elements.

    abstract::Sleeping Beauty (SB) is the most active Tc1/mariner-type transposable element in vertebrates, and is therefore a valuable vector for transposon mutagenesis in vertebrate models and for human gene therapy. We have analyzed factors affecting target site selection of SB in mammalian cells, by generating transposition eve...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(02)00991-9

    authors: Vigdal TJ,Kaufman CD,Izsvák Z,Voytas DF,Ivics Z

    更新日期:2002-10-25 00:00:00

  • Chimeric HIV-1 and feline immunodeficiency virus reverse transcriptases: critical role of the p51 subunit in the structural integrity of heterodimeric lentiviral DNA polymerases.

    abstract::The reverse transcriptase (RT) of HIV-1 and feline immunodeficiency virus (FIV) consist of two subunits of 51 kDa (p51) and 66 kDa (p66). In order to elucidate the role of p51 in the heterodimer, chimeric HIV-1/FIV RT heterodimers were constructed and characterized. The FIV RT p51/HIV-1 RT p66 chimera showed a 2.5-fol...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.1739

    authors: Amacker M,Hübscher U

    更新日期:1998-05-15 00:00:00

  • Intermicrobial Interactions as a Driver for Community Composition and Stratification of Oral Biofilms.

    abstract::The oral cavity is accessible to microorganisms, and biofilms are present throughout on hard and soft tissues. The shedding of epithelial cell layers is usually effective for controlling biofilm development on soft tissues. Innate immune mechanisms are not so effective against biofilms on tooth surfaces, and oral hygi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2015.09.022

    authors: Jakubovics NS

    更新日期:2015-11-20 00:00:00

  • p53 blocks RuvAB promoted branch migration and modulates resolution of Holliday junctions by RuvC.

    abstract::The Holliday junction is the central intermediate in homologous recombination. Branch migration of this four-stranded DNA structure is a key step in genetic recombination that affects the extent of genetic information exchanged between two parental DNA molecules. Here, we have constructed synthetic Holliday junctions ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.5408

    authors: Prabhu VP,Simons AM,Iwasaki H,Gai D,Simmons DT,Chen J

    更新日期:2002-03-08 00:00:00

  • Structural comparisons of some small spherical plant viruses.

    abstract::The structures of tomato bushy stunt virus, southern bean mosaic virus and satellite tobacco necrosis virus have been compared quantitatively. The organization of the shell domains of tomato bushy stunt virus and southern bean mosaic virus within the icosahedral envelope is identical. The wedge-shaped end of the subun...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(83)80276-9

    authors: Rossmann MG,Abad-Zapatero C,Murthy MR,Liljas L,Jones TA,Strandberg B

    更新日期:1983-04-25 00:00:00

  • High-resolution structure of the major periplasmic domain from the cell shape-determining filament MreC.

    abstract::Bacterial cell shape is dictated by the cell wall, a plastic structure that must adapt to growth and division whilst retaining its function as a selectively permeable barrier. The modulation of cell wall structure is achieved by a variety of enzymatic functions, all of which must be spatially regulated in a precise ma...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.07.022

    authors: Lovering AL,Strynadka NCJ

    更新日期:2007-09-28 00:00:00

  • A thymine-like base analogue forms wobble pairs with adenine in a Z-DNA duplex.

    abstract::The DNA hexamer d(CACGPG), in which dP is the ambivalent pyrimidine nucleoside analogue 2'-deoxy-beta-d-ribofuranosyl-(6H,8H-3, 4-dihydropyrimido[4,5-c][1,2]oxazin-7-one), crystallises as a left-handed Z-DNA duplex. X-ray analysis at 1.5 A shows that both P. A base-pairs are of the wobble type. This result appears inc...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.2080

    authors: Schuerman GS,Van Meervelt L,Loakes D,Brown DM,Kong Thoo Lin P,Moore MH,Salisbury SA

    更新日期:1998-10-09 00:00:00

  • Alanine scanning of MS2 coat protein reveals protein-phosphate contacts involved in thermodynamic hot spots.

    abstract::The co-crystal structure of the MS2 coat protein dimer with its RNA operator reveals eight amino acid side-chains contacting seven of the RNA phosphates. These eight amino acids and five nearby control positions were individually changed to an alanine residue and the binding affinities of the mutant proteins to the RN...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.11.046

    authors: Hobson D,Uhlenbeck OC

    更新日期:2006-02-24 00:00:00

  • Weak and strong states of kinesin and ncd.

    abstract::Kinesin superfamily molecular motors step along microtubules (MTs) via a cycle of conformational changes which is coupled to ATP turnover. To probe the coupling mechanism, we titrated the effects of various nucleotides on MT binding by two superfamily members; MT plus-end-directed kinesin and MT minus-end-directed non...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0147

    authors: Crevel IM,Lockhart A,Cross RA

    更新日期:1996-03-22 00:00:00

  • Amplification of distinct subfamilies of short interspersed elements during evolution of the Salmonidae.

    abstract::There are at least three different kinds of short interspersed repetitive elements in salmonid genomes. Of these, members of the HpaI family are found to be most widely distributed in salmonid species. The HpaI family is present with high copy numbers in all members of the subfamily Salmoninae, such as salmon, trout a...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.1540

    authors: Kido Y,Himberg M,Takasaki N,Okada N

    更新日期:1994-09-02 00:00:00

  • Structure of the vanadate-induced crystals of sarcoplasmic reticulum Ca2+-ATPase.

    abstract::The projected structure of the vanadate-induced crystalline aggregates of Ca2+-ATPase molecules in isolated sarcoplasmic reticulum membranes has been determined. The molecules form tubular crystals with an oblique surface lattice having cell dimensions a = 65.9 A, b = 114.4 A and gamma = 77.9 degrees. The space group ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(84)90372-3

    authors: Taylor K,Dux L,Martonosi A

    更新日期:1984-03-25 00:00:00

  • Binding of fibulin-1 to nidogen depends on its C-terminal globular domain and a specific array of calcium-binding epidermal growth factor-like (EG) modules.

    abstract::The calcium-binding basement membrane protein fibulin-1C was shown to bind nidogen in a calcium-dependent fashion. Fibulin-1C consists of small N (domain 1) and C-terminal (domain III) globular structures connected by a central rod (domain II) composed of nine epidermal growth factor (EG) modules, eight of which posse...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1244

    authors: Adam S,Göhring W,Wiedemann H,Chu ML,Timpl R,Kostka G

    更新日期:1997-09-19 00:00:00

  • The crystal structure of Escherichia coli class II fructose-1, 6-bisphosphate aldolase in complex with phosphoglycolohydroxamate reveals details of mechanism and specificity.

    abstract::The structure of a class II fructose-1,6-bisphosphate aldolase in complex with the substrate analogue and inhibitor phosphoglycolohydroxamate (PGH) has been determined using X-ray diffraction terms to a resolution of 2.0 A (1 A=0.1 nm). The crystals are trigonal, space group P3121 with a=b=78.24 A, c=289.69 A. The asy...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.2609

    authors: Hall DR,Leonard GA,Reed CD,Watt CI,Berry A,Hunter WN

    更新日期:1999-03-26 00:00:00

  • Protein oligomerization through domain swapping: role of inter-molecular interactions and protein concentration.

    abstract::Domain swapping has been shown to be an important mechanism controlling multiprotein assembly and has been suggested recently as a possible mechanism underlying protein aggregation. Understanding oligomerization via domain swapping is therefore of theoretical and practical importance. By using a symmetrized structure-...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.06.062

    authors: Yang S,Levine H,Onuchic JN

    更新日期:2005-09-09 00:00:00

  • Surface, subunit interfaces and interior of oligomeric proteins.

    abstract::The solvent-accessible surface area (As) of 23 oligomeric proteins is calculated using atomic co-ordinates from high-resolution and well-refined crystal structures. As is correlated with the protein molecular weight, and a power law predicts its value to within 5% on average. The accessible surface of the average olig...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(88)90606-7

    authors: Janin J,Miller S,Chothia C

    更新日期:1988-11-05 00:00:00

  • The entericidin locus of Escherichia coli and its implications for programmed bacterial cell death.

    abstract::Antidote/toxin gene pairs known as "addiction modules" can maintain plasmids in bacterial populations by means of post-segregational killing. However, several chromosome-encoded addiction modules may provide an entirely distinct function in the programmed cell death of moribund subpopulations under starvation conditio...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.1894

    authors: Bishop RE,Leskiw BK,Hodges RS,Kay CM,Weiner JH

    更新日期:1998-07-24 00:00:00

  • Replication stress-induced genome instability: the dark side of replication maintenance by homologous recombination.

    abstract::Homologous recombination (HR) is an evolutionary-conserved mechanism involved in a subtle balance between genome stability and diversity. HR is a faithful DNA repair pathway and has been largely characterized in the context of double-strand break (DSB) repair. Recently, multiple functions for the HR machinery have bee...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2013.04.023

    authors: Carr AM,Lambert S

    更新日期:2013-11-29 00:00:00

  • A simple method to generate non-trivial alternate alignments of protein sequences.

    abstract::A major problem in sequence alignments based on the standard dynamic programming method is that the optimal path does not necessarily yield the best equivalencing of residues assessed by structural or functional criteria. An algorithm is presented that finds suboptimal alignments of protein sequences by a simple modif...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(91)90667-u

    authors: Saqi MA,Sternberg MJ

    更新日期:1991-06-20 00:00:00

  • Local interactions dominate folding in a simple protein model.

    abstract::Recent computational studies of simple models of protein folding have concluded that a pronounced energy minimum (i.e. large gap in energy between low-energy states of the model) is a necessary and sufficient condition to ensure folding of a sequence to its lowest-energy conformation. Here, we show that this conclusio...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0375

    authors: Unger R,Moult J

    更新日期:1996-06-28 00:00:00