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Sequence heuristics to encode phase behaviour in intrinsically disordered protein polymers Proteins and synthetic polymers that undergo aqueous phase transitions mediate self assembly in nature and in man made material systems.
Yet little is known about how the phase behaviour of a protein is encoded in its amino acid sequence. Here, by synthesizing intrinsically disordered, repeat proteins to test motifs that we hypothesized would encode phase behaviour, mothers day jewellery australia we show that the proteins can be designed to exhibit tunable lower or upper critical solution temperature (LCST and UCST, respectively) transitions in physiological solutions. We also show that mutation of key residues at the repeat level abolishes phase behaviour or encodes an orthogonal transition. Furthermore, we provide heuristics to identify, at the proteome level, proteins that might exhibit phase behaviour and to design novel protein polymers consisting of biologically active peptide repeats that exhibit LCST or UCST transitions. These findings set the foundation for the prediction and encoding of phase behaviour at the sequence level. a, Abundance of individual P motifs among prototypical Pro and Gly rich IDPs relative to the total number of P motifs per protein. X is any amino acid except Pro or Gly, and n varies from 0 to 4. b, Overall abundance of individual P motifs relative to the total number of motifs (for n = 0 per protein among human, mouse and zebrafish proteins with Pro and Gly. The columns represent the average values and the error bars are the standard deviations. We excluded collagens and elastins and considered only proteins with more than 50 residues and at least 15 P motifs. The inset text shows the number of identified proteins per proteome and the corresponding average number of residues (that is, distance) that separate consecutive P motifs (n = 0 c, Abundance of individual P motifs among the top nine human proteins from b with the most P motifs. d, Abundance of all amino acids different from Pro and Gly among resilins and elastins from several species. Error bars are the standard deviations. The inset shows the corresponding distribution of hydropathy values to the Kyte scale: hydrophilic 0 hydrophobic56 each box delimits the 25th and 75th percentile and the inner line and square indicate the median and mean, respectively. Individual protein names and accession numbers for proteins in a are reported in Supplementary Table 1. Proteins in c are identified by their UniProt accession numbers. Figure 2: Protein polymers with repeating P motifs (n = 0 can be designed to exhibit LCST or UCST phase behaviour under physiologically relevant conditions. a, Temperature dependent turbidimetry for protein polymers with periodic Pro and Gly residues arranged as P units, where n = 0 (i), 1 (ii), and 2 (iii), and having pentapeptide, pandora charms sale australia hexapeptide and nonapeptide repeat units whose amino acid composition is reminiscent of elastins (Fig. 1d). b, Turbidimetry data on cooling for genetically encoded polymers with P units whose amino acid composition is reminiscent of resilins (Fig. 1d). Grey rectangles in a,b, indicate protein polymers that did not undergo a phase transition (that is, A350 = 0 over the studied temperature range). All turbidity measurements were performed in PBS (pH at a polypeptide concentration of 50 except for VPSALYGVG (+8 urea) and RGDSPYG (+1 urea). a, Protein polymers with repeating P motifs lack ordered secondary structures, as shown by their CD spectra (at 25 that are characteristic of IDPs. CD studies were conducted in water at a polypeptide concentration of 5 b, Turbidimetry data in PBS and on cooling for two protein polymers composed of Pro devoid motifs. c, Average hydropathy index for each amino acid motif studied in Fig. 2. This index corresponds to the average of the Kyte hydropathy indices56 of all residues in the motif. Each box delimits the 25th and 75th percentile and the inner square indicates the mean index. Solid circles with a coloured outline correspond to motifs in Fig. 2 that have a net charge and whose phase behaviour is revisited in d. d, Temperature dependent turbidimetry in PBS supplemented with salt or in acidified PBS for polymers in Fig. 2 that did not undergo a phase transition behaviour in PBS over the studied temperature range: VRPVG (+1 NaCl), VAPGVG (+0.5 NaCl), TVPGAG (+2 NaCl), APGVG (+2 NaCl), VPHSRNGG (+2 NaCl), VPSDDYGVG (PBS pH + 2 urea) and VPSDDYGQG (PBS pH a,b, Cloud points for a subset of LCST (a) and UCST pandor charms (b) protein polymers as a function of the number of repeats, as extracted from turbidimetry data at a polymer concentration of 50 in PBS (unless otherwise stated). c, UCST cloud points as in a,b a function of the average hydropathy index of the amino acid motif for protein polymers grouped by repeat length. To guide the eye, the size of the solid circles increases with the hydropathy index. d, UCST cloud points for (RGDAPYQG)28 as a function of the concentration of the polymer in PBS (Supplementary Fig. 8a shows the raw turbidimetry data). e, Turbidimetry data for representative UCST IDPPs on cooling and subsequent heating. f, The UCST behaviour of zwitterionic IDPPs is disrupted on losing charge neutrality under acidic conditions (PBS pH unless the acidified PBS is supplemented with salt (+0.5 NaCl). Turbidimetry data was acquired in PBS (pH at 50 unless otherwise stated. a, A fibronectin like polymer, which combines the repeat unit cell adhesion (GRGDSP) and the synergy (VPHSRN) motifs from fibronectin (inset in figure), exhibits a physiologically relevant UCST in PBS. b, The laminin derived, bioactive peptide DPGYIGSR is programmed into a UCST IDPP on polymerization, as shown by turbidimetry data in sterling silver pandora bracelet PBS. The repeat sequences are shown as red or grey amino acid letters.
Red corresponds to amino acids in the native peptide, whereas grey denotes residues introduced to modulate the UCST of the resulting polymers. c, Dynamic light scattering shows the temperature triggered decrease in hydrodynamic radius (Rh) of a block copolymer composed of a UCST and a LCST block. The error bars indicate the polydispersity or width of the Rh distribution.
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