Self‐Replicating Amphiphilic β‐Sheet Peptides

Rubinov, Boris; Wagner, Nathaniel; Rapaport, Hanna; Ashkenasy, Gonen

doi:10.1002/anie.200902790

Cited by 145 publications

(85 citation statements)

References 50 publications

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“…The addition of 22A product (12.5 μM) to the reaction buffer did not significantly affect the NCL rate, suggesting that E-N ligation did not occur autocatalytically unlike the self-replicating peptide systems governed by the autocatalytic templatebased NCL reactions. 14,24,25 In contrast, the NCL reaction with POPC vesicles proceeded faster than that without the vesicles (Figure 2a and Figure S5). We also observed pronounced enhancements in NCL reaction in the presence of 22A-POPC (1:4) nanodiscs in a concentration-dependent manner (Figure 2b).…”

Section: ■ Results and Discussionmentioning

confidence: 94%

Self-Reproduction of Nanoparticles through Synergistic Self-Assembly

Ikeda

Nakano

2014

Langmuir

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We describe a self-reproduction mechanism of nanometer-sized particles (i.e., nanodiscs) through chemical ligation of the precursors and self-assembly of the building blocks. The ligation reaction was accelerated on lipid bilayer surfaces, and the products spontaneously assembled into nanodiscs with lipid molecules. With the increase in the number of nanodiscs, a rapid proliferation of the nanodiscs occurred through the spatial rearrangements of the molecules between the pre-existing nanodiscs and the unreacted materials, rather than template- or complex-enhanced ligation of the precursors. The subsequent process of surface-enhanced ligation of integrated precursors matured the nanoparticles into identical copies of the pre-existing assembly. Our study showed that the synergistic self-assembly mechanism probably underlie the self-replication principles for heterogeneous multimolecular systems.

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Section: ■ Results and Discussionmentioning

confidence: 94%

Self-Reproduction of Nanoparticles through Synergistic Self-Assembly

Ikeda

Nakano

2014

Langmuir

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“…(2.1a) and (2.1b)) [57]. In this description, like in the mechanism shown in Figure 2.1a, the dimers T j T k are the only catalytically active species, while there are given propensities for association of monomers to form the dimers and trimers.…”

Section: Uniform Design Principles Of All Two-input Gatesmentioning

confidence: 84%

Peptide‐Based Computation: Switches, Gates, and Simple Arithmetic

Dadon

Samiappan

Wagner

et al. 2012

Biomolecular Information Processing

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IntroductionBoolean algebra deals with the ''0'' and ''1'' values, utilized as presentations of false and true statements, respectively. The Boolean logic thus provides simple and concise means to describe the output of chemical processes that depend on more than one factor. Historically, the study of chemical logic gates has started with the design of small organic molecules that perform the desired functions when triggered by simple entities such as protons, hydroxyls, or metal ions [1,2]. Since the first demonstration by de Silva, many different chemical logic systems were developed, including metal-organic complexes, peptides, and DNA. The response of these systems to additional chemical triggers, as well as to electrochemical and light triggers, has been demonstrated quite frequently [3][4][5][6][7]. Interestingly, many of the recently described logic operations, and also the more complex arithmetic units, were designed based on pursuing dynamic processes instead of simple binding to one operating molecule [8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24]. Beyond the basic demonstrations, scientists were able to exploit their new gates as smart devices that control various applications such as catalysis, sensing analytes, drug delivery, and even in vivo transcription. In a related line of research, modules of large biochemical systems have also been described to function as Boolean entities, in studies that used the ''top-down'' screening for such operations [25][26][27][28][29][30][31]. This chapter describes primarily our own research, in which we use synthetic networks made of small proteins as tools for performing chemical computations. We do so by practicing both the bottom-up approach, using individual molecules as gates, and the top-down approach, for which the entire molecular network is used to perform the desired functionality.Biology can serve as inspiration and can provide chemists with the design principles for engineering networks of interacting and replicating molecules. These can potentially be used as controllable tools for studying systems behavior. Toward this aim, different research groups have designed and characterized dynamic combinatorial libraries [32][33][34][35][36][37][38] and replication networks made of nucleic acids (DNA and RNA) [39][40][41][42], peptides [43][44][45][46], and small organic molecules [47][48][49][50].

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“…With respect to S-WLBU2, it has been shown [29, 30] that peptides with alternating hydrophobic and polar residues are able to self-assemble into stable β-sheet conformations. It is reasonable to expect that, as favorable peptide-PEO interactions which hold entrapped peptides in place give way at high surface densities to peptide-peptide associations, the peptides become more elutable as the population of coiled-coils increases.…”

Section: Resultsmentioning

confidence: 99%

Concentration effects on peptide elution from pendant PEO layers

Wu¹,

Ryder²,

McGuire³

et al. 2014

Colloids and Surfaces B: Biointerfaces

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In earlier work, we have provided direction for development of responsive drug delivery systems based on modulation of structure and amphiphilicity of bioactive peptides entrapped within pendant polyethylene oxide (PEO) brush layers. Amphiphilicity promotes retention of the peptides within the hydrophobic inner region of the PEO brush layer. In this work, we describe the effects of peptide surface density on the conformational changes caused by peptide-peptide interactions, and show that this phenomenon substantially affects the rate and extent of peptide elution from PEO brush layers. Three cationic peptides were used in this study: the arginine-rich amphiphilic peptide WLBU2, the chemically identical but scrambled peptide S-WLBU2, and the non-amphiphilic homopolymer poly-L-arginine (PLR). Circular dichroism (CD) was used to evaluate surface density effects on the structure of these peptides at uncoated (hydrophobic) and PEO-coated silica nanoparticles. UV spectroscopy and a quartz crystal microbalance with dissipation monitoring (QCM-D) were used to quantify changes in the extent of peptide elution caused by those conformational changes. For amphiphilic peptides at sufficiently high surface density, peptide-peptide interactions result in conformational changes which compromise their resistance to elution. In contrast, elution of a non-amphiphilic peptide is substantially independent of its surface density, presumably due to the absence of peptide-peptide interactions. The results presented here provide a strategy to control the rate and extent of release of bioactive peptides from PEO layers, based on modulation of their amphiphilicity and surface density.

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Self‐Replicating Amphiphilic β‐Sheet Peptides

Cited by 145 publications

References 50 publications

Self-Reproduction of Nanoparticles through Synergistic Self-Assembly

Self-Reproduction of Nanoparticles through Synergistic Self-Assembly

Peptide‐Based Computation: Switches, Gates, and Simple Arithmetic

Concentration effects on peptide elution from pendant PEO layers

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