The self-organization of selfishness: Reinforcement Learning shows how selfish behavior can emerge from agent-environment interaction dynamics

When biological communities use signaling structures for complex coordination, 'free-riders' emerge. The free-riding agents do not contribute to the community resources (signals), but exploit them. Most models of such 'selfish' behavior consider free-riding as evolving through mutation and selection. Over generations, the mutation -- which is considered to create a stable trait -- spreads through the population. This can lead to a version of the 'Tragedy of the Commons', where the community's coordination resource gets fully depleted or deteriorated. In contrast to this evolutionary view, we present a reinforcement learning model, which shows that both signaling-based coordination and free-riding behavior can emerge within a generation, through learning based on energy minimisation. Further, we show that there can be two types of free-riding, and both of these are not stable traits, but dynamic 'coagulations' of agent-environment interactions. Our model thus shows how different kinds of selfish behavior can emerge through self-organization, and suggests that the idea of selfishness as a stable trait presumes a model based on mutations. We conclude with a discussion of some social and policy implications of our model.Comment: 9 pages, 16 figs, 1 table. Reinforcement Learning - Parametric Analysis, Social Behavio

Peptide delta-turn: Literature survey and recent progress

Among the various types of a-peptide folding motifs, delta-turn, which requires a central cis-amide disposition, has been one of the least extensively investigated. In particular, this main-chain reversal topology has been studied in-depth neither in linear/cyclic peptides nor in proteins. This Minireview article assembles and critically analyzes relevant data from a literature survey on the d-turn conformation in those compounds. Unpublished results from recent conformational energy calculations and a preliminary solution-state analysis on a small model peptide, currently ongoing in our laboratories, are also briefly outlined.Postprint (published version

Respiratory and enzymatic changes in the Colletotrichum leaf spot of turmeric

Turmeric leaves infected by Colletotrichum capsici exhibit a higher respiratory rate with augmentation of the terminal oxidative system. A similar effect is brought about by the treatment of the turmeric leaves with toxins isolated from culture filtrate and mycelium of the pathogen. Ascorbic acid oxidase and polyphenol oxidase activity register the maximum increase both under infection and toxin treatment

Effect of infection by Colletotrichum capsici and toxin treatment on the permeability changes of turmeric leaves

A toxin produced by Colletotrichum capsici, pathogen of turmeric leaf spot disease has been found to alter the cell permeability of turmeric leaf tissue even at very low concentrations. This led to leaching of large quantities of water soluble constituents. The possibility of the involvement of a toxin in the pathogenesis is discussed

Stereochemical Assessment of (phi,psi) Outliers in Protein Structures Using Bond Geometry-Specific Ramachandran Steric-Maps

Ramachandran validation of protein structures is commonly performed using developments, such as MolProbity. We suggest tailoring such analyses by position-wise, geometry-specific steric-maps, which show (phi,psi) regions with steric-clash at every residue position. These maps are different from the classical steric-map because they are highly sensitive to bond length and angle values that are used, in our steric-maps, as observed in the residue positions in super-high-resolution peptide and protein structures. (phi,psi) outliers observed in such structures seldom have steric-clash. Therefore, we propose that a (phi,psi) outlier is unacceptable if it is located within the steric-clash region of a bond geometry-specific steric-map for a residue position. These steric-maps also suggest position-specific accessible (phi,psi) space. The PARAMA web resource performs in-depth position-wise analysis of protein structures using bond geometry-specific steric-maps

Inter-subunit recognition and manifestation of segmental mobility in Escherichia coli RNA polymerase: a case study with ω-β' interaction

Omega (&#969; ), consisting of 91 amino acids, is the smallest of all the Escherichia coli RNA polymerase subunits and is organized into an N-terminal domain of 53 amino acids followed by an unstructured tail in the C-terminal region. Our earlier experiments have shown a chaperone-like function of &#969; in which it helps to maintain &#946;' in a correct conformation and recruit it to the &#945;<SUB>2</SUB>&#946; subassembly to form a functional core enzyme (&#945;<SUB>2</SUB>&#946; &#946;'&#969;). The X-ray structure analysis of Thermus aquaticus core RNA polymerase suggests that two regions of &#969; latch onto the N-terminal and C-terminal ends of the &#946;'-subunit. In the present study we have monitored the conformational changes in &#946;' as the denatured protein is refolded in the presence and absence of &#969; using tryptophan fluorescence emission of &#946;' as well as acrylamide quenching of Trp fluorescence. Results indicate that the presence of stoichiometric amounts of &#969; is helpful in &#946;' refolding. We have also monitored the behavior of the C-terminal tail of &#969; by engineering three cysteine residues at three different sites in &#969; and subsequently labeling them with a sulphydryl-specific fluorescent probe. Fluorescence anisotropy measurements of the labeled protein indicate that the C-terminal domain of &#969; is mobile in the free protein and gets restrained in the presence of &#946; '. Calculations on side-chain interactions show that out of the three mutated positions, two have near neighbourhood interactions only with side-chains in the &#946;' subunit whereas the end of the C-terminal of &#969;, although it is restrained in the presence of &#946;', has no interacting partner within a 4-&#197; radius

Conformational Choices for the Stereochemically Constrained gamma-Amino Acid Residue Gabapentin: Theoretical Studies and Correlation With Experimental Results

Gabapentin (1-aminomethylcyclohexaneacetic acid, Gpn) is an achiral, conformationally constrained gamma amino acid residue. A survey of available crystal structures of Gpn peptides reveals that the torsion angles about the C-gamma-C-beta (theta(1)) and C-beta-C-alpha(theta(2)) bonds are overwhelmingly limited to gauche, gauche (g(+)g(+)/g(-)g(-)) conformations. The Gpn residue forms C-7 and C-9 hydrogen bonds in which the donor and acceptor atoms come from the flanking peptide units. In combination with alpha amino acid residues alpha gamma and gamma alpha segments can adopt C-12 hydrogen bonded structures. The conformational choices available to the Gpn residue have been probed using energy calculations, adopting a grid search strategy. Ramachandran phi-psi maps have been constructed for fixed values of theta(1) and theta(2), corresponding to the gauche and trans conformations. The sterically allowed and energetically favorable regions of conformational space have been defined and experimental observations compared. C-7 and C-9 hydrogen bonded conformational families have been identified using a grid search approach in which theta(1) and theta(2) values are varied over a range of +/- 10 degrees about ideal values at 1 degrees intervals. The theoretical analysis together with experimental observations for 59 Gpn residues from 35 crystal structures permits definition of the limited range of conformational possibilities at this gamma amino acid residue.

Conformational choices for the stereochemically constrained γ-amino acid residue gabapentin: theoretical studies and correlation with experimental results

Gabapentin (1-aminomethylcyclohexaneacetic acid, Gpn) is an achiral, conformationally constrained γ amino acid residue. A survey of available crystal structures of Gpn peptides reveals that the torsion angles about the Cγ—Cβ(θ1) and Cβ—Cα(θ2) bonds are overwhelmingly limited to gauche,gauche (g+g+/g−g−) conformations. The Gpn residue forms C7 and C9 hydrogen bonds in which the donor and acceptor atoms come from the flanking peptide units. In combination with α amino acid residues αγand γαsegments can adopt C12 hydrogen bonded structures. The conformational choices available to the Gpn residue have been probed using energy calculations, adopting a grid search strategy. Ramachandran Φ-ψ maps have been constructed for fixed values of θ1 and θ2, corresponding to the gauche and trans conformations. The sterically allowed and energetically favorable regions of conformational space have been defined and experimental observations compared. C7 and C9 hydrogen bonded conformational families have been identified using a grid search approach in which θ1 and θ2 values are varied over a range of ±10° about ideal values at 1° intervals. The theoretical analysis together with experimental observations for 59 Gpn residues from 35 crystal structures permits definition of the limited range of conformational possibilities at this γ amino acid residue