Tractable molecular adaptation patterns in a designed complex peptide system

•Enzymatic exchange of mixtures dipeptides leads to buildup tetrapeptides•Mixtures 15 lead 225 tetrapeptides that can be tracked using LCMS•Self-organization drive selective peptide sequence buildup•Increased compositional complexity increases robustness The building blocks and design strategies life used create materials with advanced functionalities exceed those synthetic materials. Despite progress, it is still a mystery how the assembly self-organization 20 amino acids make up proteins ultimately give rise functional matter. Our approach learn about emergence in biological space by it. By selecting collections interacting form longer peptides recombination exchange, we track them individually collectively. provided insights chemical systems patterns self-organization. We envisage will translate concepts for sensors, catalysts, energy conversion are not restricted designs or conditions evolution, enabling repurposing “chemistry-of-life” processes green technology. Molecular adaptation, robustness, stochastic characteristic living systems, arising from ability distribute impact applied stress huge numbers covalent noncovalent interactions molecules. study such behavior difficult due intractability have sufficient display these features. Herein, biomolecular bottom through selection interaction 5 dipeptides, which reversible enzymatic produces 25 dynamically tetrapeptides. Analysis tetrapeptide abundance readily interpretable patterns. These reveal system this degree able respond stochastically, self-organize oligomerization response changes external conditions, exhibit its share an change over multitude interactions. molecular adaptation consequent homeostasis far too complex fully analyzed detail. Consequently, adaptive functions typically studied rationalized global correlation approaches, lack detailed connections.1Chuang H.Y. Hofree M. Ideker T. A decade biology.Annu. Rev. Cell Dev. 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Evolving nanomaterials enzyme-driven (eDPL).Faraday Discuss. 2009; 143: 293-303https://doi.org/10.1039/B902065ACrossref note here deliberately more flexible operate shallow landscapes; hence, only modest yields anticipated. Thus, propose system-wide driven enable systems-level stabilization. thermolysin acts bonds adjacent uncharged hydrophobic acids, (Z–X↓Z–X), thus retaining alternating pattern critical achieving analytical tractability (Figure 1A). analyze full complement (25–225 sequences) amplified, whereas noninteracting broken down organized according readout shows accommodates sharing To demonstrate composition adjusts ligand, first DPL composed G–X presence varying ATP. oligomers strong aggregation propensity; distribution dominated introduced ligand. all G–X–G–X species formed after 1 day could detected analysis LC-MS-targeted screening S1 S8–S10). followed during 8 days minimal further observed, suggesting minimum state reached. Distributions ESI (electrospray ionization) peak areas normalized against total area 1B; see “normalization heat maps” supplemental information). differential ionization does allow direct quantitative (vide infra). maps 1C), provide absence Upregulated (blue) cationic accommodate electrostatic binding, downregulated (yellow) neutral anionic would compete (oppose) binding. observation systematic increasing 1B–1G) positively charged (particularly incorporating G–R) amplified concentrations. As charge reduced ADP AMP 1D, 1G, S11–S13), becomes systematically less gave little variation distributions, comparing repeat experiments ATP, behavior, specific show variability, but trends depletion subsets similar physical (compare Figures 1B 1C 1E, 1F, S8–S10; Run 1, GRGR dominates, 2, four GR/GH provides charge). Such notable feature enables different set appreciably next 7 days. 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Showing extent higher compared 37°C respect extensive. up- down-regulation produced comparable; same conclusions drawn—thus demonstrating calibration focusing expression S18 S19). 60°C, dramatically favor 2A), influential increased S16–S19). favors K relate contribution valine residues. On investigation (in ATP), initial collection dominant (mostly charged) further, others staying constant decreasing steadily 2B, 2C, S20). contrast, remain largely unchanged time. spontaneous thermal hydrolysis. transient ATP/ADP 2–8 sustain continued evolution S21, S22, S33, vide effect visible while analyzing time-dependent versus 2D 2E). discontinuous, competing breakdown predominantly must involve involving new re-equilibration system. reorganization coassembly heterogeneous giving spatially localized pockets creating environments abundant condensation, involved in/or excluded stabilization undergo establish whether domains indeed forming mixtures, cryo-TEM. fibers 3C, 3E, S23)—a morphology typical short line expectation histidine containing tetrapeptides.16Zhang Fabrication novel biomaterials self-assembly.Nat. 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VKVH, other hand, particulate S29 S30). support our conclusion helps structures forms upon peptides. enhanced oligomers, hexapeptides compositions common lineage tetrapeptides, ratios 3A, S31, S32). presents challenge isomers having retention times, few key determined S31). Peptides assist complexing oligomerized, contributing thermodynamic degrade 3B). Subsequent independent experiment terms suppressed peptides; however, owing aforementioned many possible, noted process gradually hydrolyzes least 4 remaining along appears self-organized duration S33). alanine (A–X) glycine S34–S39). alanine-based adheres charge-based temporally, DPLs. prevalent S40). therefore “challenge.”18Conrad Conrad Adaptability: significance variability molecule ecosystem. First Edition. Springer, 1983Crossref Scholar,19Shinar G. Alon Feinberg Sensitivity networks.SIAM Appl. Math. 69: 977-998https://doi.org/10.1137/080719820Crossref (43) investigate if including (G–X A–X GAV–X systems) S41). adjusted solubilities (100 G–X, 50 A–X, V–X) prevent becoming polar residues reactions. S42–S48). dramatic aggregation-prone (V) dominating low 4), G-to-V gradient map 4B, 4E, 4F), ensemble-wide reduction hydrophobicity amplifications lightly 4E 4F). drastically, amplifying populations hydrolyzing 4C, 4G, 4H). At 37°C, mainly lower (A G), understood aggregation-reducing ATP12Patel removing driving force production V-containing 4G enhancement 4D, 4I, 4J), level, adapt temperatures, bind perhaps aggregate 4A). under like ensemble pointing toward much pressure deviation S48). understand leading rebalancing simpler V–X, analyzed. reorganization, smaller 5A). Over time, preferred disorder-prone (G-rich) evident 37°C; 5B subset 5C 5F), contrasts observations 5D 5G). cumulative involvement (including additional A–X) 5E 5H), charge-driven response, reaction, Temporal indicates (as spread out larger system’s indications being present rearrange changing yet response. demonstrated behaviors designed reactants distinguishing oppose proof-of-concept study, (K, H, S) introduce (G, collectively induce sequence-specific displays aspects adaptability subsequently enabled domain formation, environment. across phases robustness. tempting consider origin scenarios. defining property use degenerate information input navigate vast network generate output. hierarchy central dogma. work, capacity significant manner, hierarchy.