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opencc-zeroDec 2012View details →

Data from: Reconstructing the phylogenetic history of long-term effective population size and life-history traits using patterns of amino acid replacement in mitochondrial genomes of mammals and birds

The nearly neutral theory, which proposes that most mutations are deleterious or close to neutral, predicts that the ratio of nonsynonymous over synonymous substitution rates (dN/dS), and potentially also the ratio of radical over conservative amino acid replacement rates (Kr/Kc), are negatively correlated with effective population size. Previous empirical tests, using life-history traits (LHT) such as body-size or generation-time as proxies for population size, have been consistent with these predictions. This suggests that large-scale phylogenetic reconstructions of dN/dS or Kr/Kc might reveal interesting macroevolutionary patterns in the variation in effective population size among lineages. In this work, we further develop an integrative probabilistic framework for phylogenetic covariance analysis introduced previously, so as to estimate the correlation patterns between dN/dS, Kr/Kc, and three LHT, in mitochondrial genomes of birds and mammals. Kr/Kc displays stronger and more stable correlations with LHT than does dN/dS, which we interpret as a greater robustness of Kr/Kc, compared with dN/dS, the latter being confounded by the high saturation of the synonymous substitution rate in mitochondrial genomes. The correlation of Kr/Kc with LHT was robust when controlling for the potentially confounding effects of nucleotide compositional variation between taxa. The positive correlation of the mitochondrial Kr/Kc with LHT is compatible with previous reports, and with a nearly neutral interpretation, although alternative explanations are also possible. The Kr/Kc model was finally used for reconstructing life-history evolution in birds and mammals. This analysis suggests a fairly large-bodied ancestor in both groups. In birds, life-history evolution seems to have occurred mainly through size reduction in Neoavian birds, whereas in placental mammals, body mass evolution shows disparate trends across subclades. Altogether, our work represents a further step toward a more comprehensive phylogenetic reconstruction of the evolution of life-history and of the population-genetics environment.

opencc-zeroFeb 2022View details →

Supporting Data for: Assessing the potential of amino acid δ13C and δ15N analysis in terrestrial and freshwater ecosystems

Understanding the structure and dynamics of food webs requires accurate estimates of energy flow among organisms. Bulk tissue carbon (δ13C) and nitrogen (δ15N) isotope analysis is often used to this end, however, the limitations of this technique can outweigh the benefits. The isotope analysis of individual amino acids is being increasingly employed to trace energy flow and estimate consumer trophic level. Central to this compound-specific approach are the concepts of essential amino acid (AAESS) δ13C fingerprinting and amino acid (AA) δ15N beta-values, both of which have been understudied and are poorly constrained in terrestrial and freshwater producers. We present AAESS δ13C data for 112 terrestrial and freshwater producers collected from two aridland habitats in the northern Chihuahuan Desert (New Mexico, USA) and AA δ15N data for a subset (n=28) of these samples. We characterized AAESS δ13C fingerprints by performing linear discriminant analysis on the δ13C values of isoleucine, leucine, lysine, phenylalanine, threonine, and valine for four producer groups – C3 plants, C4 plants, CAM plants, and filamentous green algae. We explored potential biochemical mechanisms underlying these AAESS δ13C fingerprints by calculating differences between the δ13C values of AAESS products and their AA precursors. This allowed us to estimate and compare isotopic discrimination for specific AAESS synthesis pathways across producer groups. We found near perfect separation of AAESS δ13C fingerprints among producer groups; all groups reclassified with >95% success within our multivariate framework. We also found varied isotopic discrimination for specific AAESS synthesis pathways among producer groups. Contrary to previous studies, we found no differences in beta-values between terrestrial C3 and C4 plants for any trophic-source AA pairing. Furthermore, we found that Lys δ15N values were less variable and more closely related to bulk tissue δ15N values than Phe δ15N values in terrestrial and freshwater producers. We conclude that AAESS δ13C fingerprints are a higher-resolution tracer for freshwater food webs where instream algae have overlapping bulk tissue δ13C values with terrestrial C3 plants. Additionally, betaGlx-Lys and betaPro-Lys are the best for AA δ15N-based consumer trophic level estimates in freshwater food webs containing both terrestrial and aquatic resources.

opencc-zeroMar 2022View details →

Data from: Creation of photocyclic vertebrate rhodopsin by single amino acid substitution

Opsins are universal photoreceptive proteins in animals and can be classified into three types based on their photoreaction properties. Upon light irradiation, vertebrate rhodopsin forms a metastable active state, which cannot revert back to the original dark state via either photoreaction or thermal reaction. By contrast, after photoreception, most opsins form a stable active state which can photo-convert back to the dark state. Moreover, we recently found a novel type of opsins whose activity is regulated by photocycling. However, the molecular mechanism underlying this diversification of opsins remains unknown. In this study, we showed that vertebrate rhodopsin acquired the photocyclic and photoreversible properties upon introduction of a single mutation at position 188. This revealed that the residue at position 188 contributes to the diversification of photoreaction properties of opsins by its regulation of the recovery from the active state to the original dark state.

opencc-by-sa-4.0Dec 2021View details →

Know your amino acids chart

Amino acid structures and classification

opencc-by-sa-4.0Aug 2024View details →

Amino acids to proteins – levels of structure

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opencc-by-4.0Sep 2024View details →

Co-surfactant roles of amino acids at oil-water interface: application in low-pH emulsions to regulate physical and oxidative stabilities

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opencc-by-4.0Sep 2024View details →

Data for Single-molecule Detection of Modified Amino Acid Regulating Transcriptional Activity

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opencc-zeroDec 2018View details →

Data from: Bursts of amino acid replacements in protein evolution

Evolution can occur both gradually and through alternating episodes of stasis and rapid changes. However, the prevalence and magnitude of fluctuations of the rate of evolution remains obscure. Detecting a rapid burst of changes requires a detailed record of past evolution, so that events that occurred within a short time interval can be identified. Here, we use the phylogenies of the Baikal Lake amphipods and of Catarrhini, which contain very short internal edges facilitating this task. We detect 6 radical bursts of evolution of individual proteins during such short time periods, each involving between 6 and 38 amino acid substitutions. These bursts were extremely unlikely to have occurred neutrally, and were apparently caused by positive selection. On average, in the course of a time interval required for one synonymous substitution per site, a protein undergoes a strong burst of rapid evolution with probability at least ~0.01.

opencc-zeroDec 2017View details →

Data from: Characterization of C-ring component assembly in flagellar motors from amino acid coevolution

Bacterial flagellar motility, an important virulence factor, is energized by a rotary motor localized within the flagellar basal body. The rotor module consists of a large framework (C-ring), composed of the FliG, FliM and FliN proteins. FliN and FliM contacts the FliG torque ring to control the direction of flagellar rotation. We report that structure-based models constrained only by residue coevolution can recover the binding interface of atomic X-ray dimer complexes with remarkable accuracy (ca. 1 Å RMSD). We propose a model for FliM-FliN heterodimerization, which agrees accurately with homologous interfaces as well as in-situ cross-linking experiments, and hence supports a proposed architecture for the lower portion of the C-ring. Furthermore, this approach allowed the identification of two discrete and interchangeable homodimerization interfaces between FliM middle domains that agree with experimental measurements and might be associated with C-ring directional switching dynamics triggered upon binding of CheY signal protein. Our findings provide structural details of complex formation at the C-ring that have been difficult to obtain with previous methodologies and clarify the architectural principle that underpins the ultra-sensitive allostery exhibited by this ring assembly that controls the clockwise (CW) or counterclockwise (CCW) rotation of flagella.

opencc-zeroDec 2016View details →

Data from: Sequence entropy of folding and the absolute rate of amino acid substitutions

Adequate representations of protein evolution should consider how the acceptance of mutations depends on the sequence context in which they arise. However, epistatic interactions among sites in a protein result in hererogeneities in the substitution rate, both temporal and spatial, that are beyond the capabilities of current models. Here we use parallels between amino acid substitutions and chemical reaction kinetics to develop an improved theory of protein evolution. We constructed a mechanistic framework for modelling amino acid substitution rates that uses the formalisms of statistical mechanics, with principles of population genetics underlying the analysis. Theoretical analyses and computer simulations of proteins under purifying selection for thermodynamic stability show that substitution rates and the stabilization of resident amino acids (the 'evolutionary Stokes shift') can be predicted from biophysics and the effect of sequence entropy alone. Furthermore, we demonstrate that substitutions predominantly occur when epistatic interactions result in near neutrality; substitution rates are determined by how often epistasis results in such nearly neutral conditions. This theory provides a general framework for modelling protein sequence change under purifying selection, potentially explains patterns of convergence and mutation rates in real proteins that are incompatible with previous models, and provides a better null model for the detection of adaptive changes.

opencc-zeroJun 2019View details →

Data from: Detecting adaptive convergent amino acid evolution

In evolutionary genomics, researchers have taken an interest in identifying substitutions that subtend convergent phenotypic adaptations. This is a difficult question that requires distinguishing foreground convergent substitutions that are involved in the convergent phenotype from background convergent substitutions. Those may be linked to other adaptations, may be neutral or may be the consequence of mutational biases. Furthermore, there is no generally accepted definition of convergent substitutions. Various methods that use different definitions have been proposed in the literature, resulting in different sets of candidate foreground convergent substitutions. In this article, we first describe the processes that can generate foreground convergent substitutions in coding sequences, separating adaptive from non-adaptive processes. Second, we review methods that have been proposed to detect foreground convergent substitutions in coding sequences and expose the assumptions that underlie them. Finally, we examine their power on simulations of convergent changes—including in the presence of a change in the efficacy of selection—and on empirical alignments.

opencc-by-4.0Sep 2021View details →

294-fold mini all-α protein library encoded by 7,350 amino-acid sequences (project "flood of fold" )

This repository includes 3 compressed archive files for the “flood-of-fold” mini-protein library project.  <ol> <li>FloodOfFolds_294_backbone_models.tar.gz includes 294 mini all-α backbone models showing distinct topologies (folds). They are poly-VAL models. </li> <li>FloodOfFolds_7350_designs_MODEL.tar.gz includes 7,350 design protein models in the pdb format for the 294 mini-protein library. 25 amino-acid sequences were designed for each backbone model (25 x 294 = 7,350). </li> <li>FloodOfFolds_7350_designs_FASTA.tar.gz includes 7,350 fasta files derived from the pdb files in FloodOfFolds_7350_designs_MODEL.tar.gz.  </li> </ol> See also here for results of folding simulations: https://zenodo.org/record/5526849#.YWRhFBBBw1I Acknowledgement: K.S. and S.M. would like to deeply thank Koga laboratory at Institute for Molecular Science providing computational resources. Most of the computations for model building and folding simulations were performed using the facilities at the Research Center for Computational Science, Okazaki, Japan.

opencc-by-4.0Oct 2018View details →

Simulations of polyglutamic and polyaspartic oligopeptides of 32 amino acids in solution with counterions

Simulations of polyglutamic (GLU32) and polyaspartic (ASP32) oligopeptides of 32 amino acids in solution with only counterions (Na+ or K+). For each oligopeptide we have simulated the following variants: <ul> <li>amber99sb-ildn using ACE in the N-terminal and COO- in the C-terminal</li> <li>amber99sb-ildn-scaled using ACE in the N-terminal and COO- in the C-terminal</li> <li>charmm36m using ACE in the N-terminal and COO- in the C-terminal</li> <li>charmm36m-scaled using ACE in the N-terminal and COO- in the C-terminal</li> <li>charmm36m using NH2 in the N-terminal and COO- in the C-terminal</li> <li>charmm36m-scaled using NH2 in the N-terminal and COO- in the C-terminal</li> </ul> For each of these models we have used the following counterions: <ul> <li>Charmm36m - K+ or Na+ original charmm36 counterions</li> <li>Charmm36 (scaled version) - K_s or NA_s scaled counterions</li> <li>Amber99sb-ildn - K+ and Na+ original amber99sb-ildn counterions</li> <li>Amber99sb-ildn (scaled version) - K_s or NA_s scaled counterions</li> </ul> Scaled counterions can be found in  <a href="https://bitbucket.org/hseara/ions/">https://bitbucket.org/hseara/ions/</a> MD engine: gromacs 2018 or 2018.3 or 2018.4   Temperature: 300 K   Pressure: 1 bar Simulation time: 1000 ns Saving frequency: 100 ps

opencc-by-4.0Nov 2022View details →

Amino Acid Composition in each analyzed species

Amino Acid Composition in each analyzed species

opennotspecifiedJun 2020View details →

Fig. 1 in Mycosporine-like amino acids, brominated and sulphated phenols: Suitable chemotaxonomic markers for the reassessment of classification of Bostrychia calliptera (Ceramiales, Rhodophyta)

Fig. 1. The structures of compounds 1–6.

opennotspecifiedJun 2021View details →

Figure 4 in Analysis of amino acids, fatty acids and neurotoxins using gas chromatography-mass spectrometry in four scorpions species inhabiting New Valley Governorate, Egypt

Figure 4. GC-MS chromatogram of Buthacus leptochelys.

Effects of Amino Acid Supplementation on Liver Lipid Content and Protein Metabolism in Obese Children

ClinicalTrials.gov study NCT02337894. IPD Sharing: Not stated. Countries: 0. Publications: 3.

Exercise-induced Muscle Damage is Reduced in Resistance Trained Athletes by Branch Chain Amino Acids

ClinicalTrials.gov study NCT01529281. IPD Sharing: Not stated. Countries: 0. Publications: 1.

Amino Acid PET-based Response Assessment in IDH-mutant Gliomas (APPEAR)

ClinicalTrials.gov study NCT07159607. IPD Sharing: UNDECIDED. Countries: 2. Publications: 0.

Free Amino Acid-based Formula to Treat Children Cow's Milk Protein Allergy

ClinicalTrials.gov study NCT02536482. IPD Sharing: Not stated. Countries: 0. Publications: 1.