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Pier Luigi Luisi - One of the best experts on this subject based on the ideXlab platform.
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investigation of de novo totally random biosequences part ii on the Folding Frequency in a totally random library of de novo proteins obtained by phage display
Chemistry & Biodiversity, 2006Co-Authors: Cristiano Chiarabelli, Jan Wim Vrijbloed, Davide De Lucrezia, Richard M Thomas, Pasquale Stano, Fabio Polticelli, Tiziana Ottone, Ester Papa, Pier Luigi LuisiAbstract:We present an investigation on theoretically possible protein structures which have not been selected by evolution and are, therefore, not present on our Earth ('Never Born Proteins' (NBP)). In particular, we attempt to assess whether and to what extent such polypeptides might be folded, thus acquiring a globular protein status. A library (ca. 10(9) clones) of totally random polypeptides, with a length of 50 amino acids, has been produced by phage display. The only structural bias in these sequences is a tripeptide substrate for thrombin: PRG, chosen according to the criteria described in the preceding Part I of this series. The presence of this substrate in an otherwise totally random sequence forms the basis for a qualitative experimental criterion which distinguishes unfolded from folded proteins, as folded proteins are more protected from protease digestion than unfolded ones. The investigation of 79 sequences, randomly selected from the initially large library, shows that over 20% of this population is thrombin-resistant, likely due to Folding. Analysis of the amino acid sequences of these clones shows no significant homology to extant proteins, which indicates that they are indeed totally de novo. A few of these sequences have been expressed, and here we describe the structural properties of two thrombin-resistant randomly selected ones. These two de novo proteins have been characterized by spectroscopic methods and, in particular, by circular dichroism. The data show a stable three-dimensional Folding, which is temperature-resistant and can be reversibly denatured by urea. The consequences of this finding within a library of 'Never Born Proteins' are discussed in terms of molecular evolution.
Cristiano Chiarabelli - One of the best experts on this subject based on the ideXlab platform.
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investigation of de novo totally random biosequences part ii on the Folding Frequency in a totally random library of de novo proteins obtained by phage display
Chemistry & Biodiversity, 2006Co-Authors: Cristiano Chiarabelli, Jan Wim Vrijbloed, Davide De Lucrezia, Richard M Thomas, Pasquale Stano, Fabio Polticelli, Tiziana Ottone, Ester Papa, Pier Luigi LuisiAbstract:We present an investigation on theoretically possible protein structures which have not been selected by evolution and are, therefore, not present on our Earth ('Never Born Proteins' (NBP)). In particular, we attempt to assess whether and to what extent such polypeptides might be folded, thus acquiring a globular protein status. A library (ca. 10(9) clones) of totally random polypeptides, with a length of 50 amino acids, has been produced by phage display. The only structural bias in these sequences is a tripeptide substrate for thrombin: PRG, chosen according to the criteria described in the preceding Part I of this series. The presence of this substrate in an otherwise totally random sequence forms the basis for a qualitative experimental criterion which distinguishes unfolded from folded proteins, as folded proteins are more protected from protease digestion than unfolded ones. The investigation of 79 sequences, randomly selected from the initially large library, shows that over 20% of this population is thrombin-resistant, likely due to Folding. Analysis of the amino acid sequences of these clones shows no significant homology to extant proteins, which indicates that they are indeed totally de novo. A few of these sequences have been expressed, and here we describe the structural properties of two thrombin-resistant randomly selected ones. These two de novo proteins have been characterized by spectroscopic methods and, in particular, by circular dichroism. The data show a stable three-dimensional Folding, which is temperature-resistant and can be reversibly denatured by urea. The consequences of this finding within a library of 'Never Born Proteins' are discussed in terms of molecular evolution.
Valette Rudy - One of the best experts on this subject based on the ideXlab platform.
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Folding instabilities in non-Newtonian viscous sheets: shear thinning and shear thickening effects
2021Co-Authors: Pereira Anselmo, Valade Nicolas, Hachem Elie, Valette RudyAbstract:In this work, we extend the analyses devoted to Newtonian viscous fluids previously reported by Ribe [Physical Review E 68, 036305 (2003)], by investigating shear thickening (dilatant) and shear thinning (pseudoplastic) effects on the development of Folding instabilities in non-Newtonian viscous sheets of which viscosity is given by a power-law constitutive equation. Such instabilities are trigged by compression stresses acting on viscous sheets that leave a channel at a very small initial velocity, fall, and then hit a solid surface or a fluid substrate. Our study is conducted through a mixed approach combining direct numerical simulations, energy budget analyses, scaling laws, and experiments. The numerical results are based on an adaptive variational multi-scale method for multiphase flows, while Carpobol gel sheets are considered for the conducted experiments. Two Folding regimes are observed: (1) the viscous regime; and (2) the gravitational one. Interestingly, only the latter is affected by shear thinning/thickening manifestations within the material. In short, when gravity is balanced by viscous forces along the non-Newtonian viscous sheet, both the Folding amplitude and the Folding Frequency are given by a power-law function of the sheet slenderness, the Galileo number (the ratio of the gravitational stress to the viscous one), and the flow behaviour index. Highly shear thickening materials develop large amplitude (and low Frequency) instabilities, which, in contrast, tend to be suppressed by shear thinning effects, and eventually cease. Lastly, nonNewtonian effects on Folding onset/cessation are also carefully explored. As a result, non-Newtonian Folding onset and cessation criteria are presented
Jason D Mckinney - One of the best experts on this subject based on the ideXlab platform.
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a band limited intermodulation based band Folding Frequency translation link using a single modulator
International Topical Meeting on Microwave Photonics, 2018Co-Authors: Bryan M Haas, Jason D MckinneyAbstract:We present, characterize, and demonstrate a simple, and novel, continuous-time band-Folding microwave photonic link. Implemented with a single dual-drive Mach-Zehnder modulator (DDMZM) acting as 2 parallel phase modulators, the link effects an 8:1 bandwidth Folding to enable direct sampling and digitization of an entire band. Two microwave tones modulated on one arm along with their 3rd-order intermodulation (IMD) products serve as the spectral comb that exists only in the desired band, and the microwave spectrum of interest (SOI) is modulated onto the other arm. Parallel implementation adds, rather than multiplies, the tone and signal together, eliminating many cross-modulation products and spurs that would otherwise complicate and limit the foldable bandwidth. The link can operate with no optical filters if biased or with no bias if an optical bandpass filter is used.
Ester Papa - One of the best experts on this subject based on the ideXlab platform.
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investigation of de novo totally random biosequences part ii on the Folding Frequency in a totally random library of de novo proteins obtained by phage display
Chemistry & Biodiversity, 2006Co-Authors: Cristiano Chiarabelli, Jan Wim Vrijbloed, Davide De Lucrezia, Richard M Thomas, Pasquale Stano, Fabio Polticelli, Tiziana Ottone, Ester Papa, Pier Luigi LuisiAbstract:We present an investigation on theoretically possible protein structures which have not been selected by evolution and are, therefore, not present on our Earth ('Never Born Proteins' (NBP)). In particular, we attempt to assess whether and to what extent such polypeptides might be folded, thus acquiring a globular protein status. A library (ca. 10(9) clones) of totally random polypeptides, with a length of 50 amino acids, has been produced by phage display. The only structural bias in these sequences is a tripeptide substrate for thrombin: PRG, chosen according to the criteria described in the preceding Part I of this series. The presence of this substrate in an otherwise totally random sequence forms the basis for a qualitative experimental criterion which distinguishes unfolded from folded proteins, as folded proteins are more protected from protease digestion than unfolded ones. The investigation of 79 sequences, randomly selected from the initially large library, shows that over 20% of this population is thrombin-resistant, likely due to Folding. Analysis of the amino acid sequences of these clones shows no significant homology to extant proteins, which indicates that they are indeed totally de novo. A few of these sequences have been expressed, and here we describe the structural properties of two thrombin-resistant randomly selected ones. These two de novo proteins have been characterized by spectroscopic methods and, in particular, by circular dichroism. The data show a stable three-dimensional Folding, which is temperature-resistant and can be reversibly denatured by urea. The consequences of this finding within a library of 'Never Born Proteins' are discussed in terms of molecular evolution.