Mass & secondary structure propensity of amino acids explain their mutability and evolutionary replacements

Why is an amino acid replacement in a protein accepted during evolution? The answer given by bioinformatics relies on the frequency of change of each amino acid by another one and the propensity of each to remain unchanged. We propose that these replacement rules are recoverable from the secondary structural trends of amino acids. A distance measure between high-resolution Ramachandran distributions reveals that structurally similar residues coincide with those found in substitution matrices such as BLOSUM: Asn Asp, Phe Tyr, Lys Arg, Gln Glu, Ile Val, Met → Leu; with Ala, Cys, His, Gly, Ser, Pro, and Thr, as structurally idiosyncratic residues. We also found a high average correlation (\overline{R} R = 0.85) between thirty amino acid mutability scales and the mutational inertia (I X ), which measures the energetic cost weighted by the number of observations at the most probable amino acid conformation. These results indicate that amino acid substitutions follow two optimally-efficient principles: (a) amino acids interchangeability privileges their secondary structural similarity, and (b) the amino acid mutability depends directly on its biosynthetic energy cost, and inversely with its frequency. These two principles are the underlying rules governing the observed amino acid substitutions. © 2017 The Author(s)

Erratum: Publisher Correction: Mass & secondary structure propensity of amino acids explain their mutability and evolutionary replacements

Why is an amino acid replacement in a protein accepted during evolution? The answer given by bioinformatics relies on the frequency of change of each amino acid by another one and the propensity of each to remain unchanged. We propose that these replacement rules are recoverable from the secondary structural trends of amino acids. A distance measure between high-resolution Ramachandran distributions reveals that structurally similar residues coincide with those found in substitution matrices such as BLOSUM: Asn ↔ Asp, Phe ↔ Tyr, Lys ↔ Arg, Gln ↔ Glu, Ile ↔ Val, Met → Leu; with Ala, Cys, His, Gly, Ser, Pro, and Thr, as structurally idiosyncratic residues. We also found a high average correlation (R¯¯¯¯ = 0.85) between thirty amino acid mutability scales and the mutational inertia (I X ), which measures the energetic cost weighted by the number of observations at the most probable amino acid conformation. These results indicate that amino acid substitutions follow two optimally-efficient principles: (a) amino acids interchangeability privileges their secondary structural similarity, and (b) the amino acid mutability depends directly on its biosynthetic energy cost, and inversely with its frequency. These two principles are the underlying rules governing the observed amino acid substitutions

Mass and secondary structure propensity of amino acids explain their mutability and evolutionary replacements

"Why is an amino acid replacement in a protein accepted during evolution? The answer given by bioinformatics relies on the frequency of change of each amino acid by another one and the propensity of each to remain unchanged. We propose that these replacement rules are recoverable from the secondary structural trends of amino acids. A distance measure between high-resolution Ramachandran distributions reveals that structurally similar residues coincide with those found in substitution matrices such as BLOSUM: Asn Asp, Phe Tyr, Lys Arg, Gln Glu, Ile Val, Met ? Leu; with Ala, Cys, His, Gly, Ser, Pro, and Thr, as structurally idiosyncratic residues. We also found a high average correlation (\overline{R} R = 0.85) between thirty amino acid mutability scales and the mutational inertia (I X ), which measures the energetic cost weighted by the number of observations at the most probable amino acid conformation. These results indicate that amino acid substitutions follow two optimally-efficient principles: (a) amino acids interchangeability privileges their secondary structural similarity, and (b) the amino acid mutability depends directly on its biosynthetic energy cost, and inversely with its frequency. These two principles are the underlying rules governing the observed amino acid substitutions. © 2017 The Author(s).

Diet composition of batoids on the continental shelf off Nayarit and Sinaloa, Mexico

Since elasmobranchs are frequently apex predators in marine ecosystems, information on their diet is essential for understanding trophic relationships in these systems. Trophic similarity between six batoid species (Rhinoptera steindachneri, Rhinobatos glaucostigma, Dasyatis dipterura, Urotrygon aspidura, U. nana, and U. rogersi) was examined by analyzing the stomach contents of 140 individuals. Specimens were caught by the commercial shrimp fishery in the central Mexican Pacific. In total, 88.6% of the stomachs were completely to partially full, allowing the identification of 77 types of prey. The primary dietary components were crustaceans, followed by annelids and mollusks. Values of diet breadth for the six species indicated low diversity in prey items. Diet similarity suggested two trophic guilds: R. glaucostigma, U. nana, and U. aspidura belong to the cancritrophic guild (P < 0.05) and U. rogersi and D. dipterura to the annelidcrustacean guild. Rhinoptera steindachneri showed no evident pattern of association (feeding primarily on ophiuroids). In light of these results, we argue that a distribution of alimentary resources (niche partitioning) between the six species favors their coexistence

Semi-empirical quantum evaluation of peptide – MHC class II binding

Peptide presentation by the major histocompatibility complex (MHC) is a key process for triggering a specific immune response. Studying peptide-MHC (pMHC) binding from a structural-based approach has potential for reducing the costs of investigation into vaccine development. This study involved using two semi-empirical quantum chemistry methods (PM7 and FMO-DFTB) for computing the binding energies of peptides bonded to HLA-DR1 and HLA-DR2. We found that key stabilising water molecules involved in the peptide binding mechanism were required for finding high correlation with IC50 experimental values. Our proposal is computationally non-intensive, and is a reliable alternative for studying pMHC binding interactions

Estudio del mecanismo responsable de la superconductividad en los óxidos de cobre superconductores de itrio y lantano

IP 1101-05-402-93ARTICULO(S) EN REVISTA: Calculo de correlaciones entre TCy laspropiedades electronicas y fononicas en los;nuevos superconductores / Jairo Giraldo, R. Baquero - En:Revista Colombiana de Fisica No. 27 (1995); p.;595-598 - Thermoelectric power of (Bi-Pb)SrCaCuO superconductingthin films / J.E Rodriguez, A. Mariño, Jairo;Giraldo, H. Rodriguez - En: Revista Colombiana de Fisica Vol.28, no.2 (1996); p. 197-200 - Electron-phonon;enhancement of thermopower in si doped superconducting bicompounds / Jairo Giraldo, J. E Rodriguez, A. Mariño;- En: Revista Colombiana de Fisica No. 28 (1996); p. 189-1-92Optical andstructural properties of Cd1-iZniTe;for high Zn concentrations / J.J Perez Bueno, M. E Rodriguez,L.Baños, O.Zelaya-Angel, Jairo Giraldo - En:;Revista Colombiana de Fisica vol. 29 No. 2 (1997); p. 207-210-Incrementoen la interaccion e-ph en;compuestos superconductores de BSCCO dopados con Si y Ag /J.ERodriguez,A . Mariño, J. Giraldo - En: Revista;Colombiana de Fisica vol. 29 No. 2 (1997); p. 231-234 - Estudioelectronico del C60 con un modelo de ruptura;de la simetria esferica a la icosaedrica / F. Alonso, J. JGiraldo - En: Revista Colombiana de Fisica vol. 30;No 1 (1998); p. 173-176 - Some tracks to a conventional approachin the cuprates / Jairo Giraldo - En: Revista;Colombiana de Fisica vol. 30 No 1 (1998); p.177-180 - Breve historia de lasuperconductividad de alta;temperatura critica / Jairo Giraldo Gallo - En: Momento Revistadel departamento de Fisica Universidad;Nacional de Colombia No. 9 (abril : 1995); p. 52-63 - Algunosproblemas conceptuales y metodologicos en la;superconductividad de alta temperatura critica / Jairo GiraldoGallo - En:Momentos Revista del departamento;de Fisica Universidad Nacional de Colombia No 9 (abril : 1995);p. 64-78 -Calculated bonding, structural, and;vibrational properties of YBa2Cu3-xCoxO7 / U. Yxklinten, JairoGiraldo, K.Holmlund - En: Physica C. No 234;(1994); p. 295-299 - CAPITULO(S) EN LIBRO: Tight-binding calculation of the van hove singularity shift from;the fermi level as a function of x for La2-xBaxCuO4 / Jairo Giraldo, R. Baquero. - p. 135-142. -- En:;Manifestation of the E-Ph interaction - proceedings of the2 nd(CINVESTAV) superconductivity symposium -;Mexico : 1994. : il. ; 29 cm. - ISBN 9810215452 - ARTICULO(S)ENREVISTA:Lattice properties of YBa2Cu3-xCoxO7;: pilot calculation using effective medium theory / JairoGiraldo, U. Yxklinten - En: journal of;superconductivity vol. 8 No 1 (1995); p. 1-2 - Electron-phononcontribution to thermopower in si-doped;superconducting bi compounds / Jairo Giraldo, J. E Rodriguez,A.Mariño -En: Physical Review B. VOL. 56 No 5;(1997 : aug. 1); p. 2383-2386 - Transport and structural properties of YBa2Cu3O7-g thin films and bulk samples;as a function of oxygen content - En: Friday morning vol.43 No1 (1998);p. 964 - EMT Applied to complex;systems: lattice properties of YBa2Cu3-xCoxO7 / Jairo Giraldo,Uno Yxklinten - En: American institute of;Physics (1996); p. 461-465. - Termopower and lattice parametersof YBa2Cu3O7-g thin films as a function of;oxygen content / Jairo Giraldo, A. Pulzara, P. Prieto, M.Chacon'- en: Revista Mexicana de Fisica No 44 sup.;(1998 : dic); p. 202-207 - Electron-phonon enhancement ofthermopower in silver-doped superconducting bi;compounds / J. E. Rodriguez, A. Mariño, Jairo Giraldo - En: Physica C. 282-287 (1997); p. 1253-1254 - An;aproximation to the optical absorption spectra of the ternarycompound ZnSexTe1-x / J. C Salcedo, Jairo;Giraldo, A. Camacho - En: Revista Mexicana de Fisica No. 44 sup.(1998 : dic.); p. 119-121. - Electronic and;vibrational properties of the C60 molecule / F. Alonso Marroquin, Jairo Giraldo, A.Calles, J. J Castro - En:;Revista Mexicana de Fisica No 44 sup. (1998 : dic); p. 18-21