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An embryonic cell divides again and again

"The structural basis of ribosome activity in peptide bond synthesis."In the second of these two papers, the detailed catalytic mechanism ofRNA-mediated peptidyl bond formation is finally elucidated.

It has been known for almost 40 years that the chemical activity givingrise to peptide bond formation during messenger RNA (mRNA)-directed proteinsynthesis can be attributed to the large ribosomal subunit.

Where there was one cell there are two, then four, then eight,..

Non-covalent interactions - Wikipedia

49. “Synthesis of Zigzag-Chain and Cyclic-Octanuclear Calcium Complexes and Hexanuclear Bulky Aryl-Phosphate Sodium Complexes with Ortho-Amide Groups: Structural Transformation Involving a Network of Inter- and Intramolecular Hydrogen Bonds”
Y. Yamada, T. Okamura, M. Doi, H. Yamamoto, N. Ueyama
J. Am. Chem. Soc. 124, 1052–1059 (2002).

42. “Stabilization of Carboxylate Anion with NH···O Hydrogen Bond: Facilitation of the Deprotonation of Carboxylic Acid by the Neighboring Amide NH Groups”
Y. Yamada, J. Takeda, Y. Nakayama, T. Okamura, M. Doi, H. Yamamoto, N. Ueyama
Bull. Chem. Soc. Jpn., 77, 321–329 (2004).

Amine Structure & Synthesis

40. “Stabilization of Calcium- and Terbium-Carboxylate Bonds by NH···O Hydrogen Bonds in Mononuclear Complex: A Functional Model of the Active Site of Calcium Binding Proteins”
Y. Yamada, Y. Nakayama, H. Adachi, T. Okamura, A. Nakamura, H. Yamamoto, N. Ueyama, D. Vyprachticky, Y. Okamoto
Inorg. Chem., 43, 4447–4455 (2004).

AB - Green fluorescent protein has revolutionized cell labeling and molecular tagging, yet the driving force and mechanism for its spontaneous fluorophore synthesis are not established. Here we discover mutations that substantially slow the rate but not the yield of this posttranslational modification, determine structures of the trapped precyclization intermediate and oxidized postcyclization states, and identify unanticipated features critical to chromophore maturation. The protein architecture contains a dramatic ≈80° bend in the central helix, which focuses distortions at G67 to promote ring formation from amino acids S65, Y66, and G67. Significantly, these distortions eliminate potential helical hydrogen bonds that would otherwise have to be broken at an energetic cost during peptide cyclization and force the G67 nitrogen and S65 carbonyl oxygen atoms within van der Waals contact in preparation for covalent bond formation. Further, we determine that under aerobic, but not anaerobic, conditions the Gly-Gly-Gly chromophore sequence cyclizes and incorporates an oxygen atom. These results lead directly to a conjugation-trapping mechanism, in which a thermodynamically unfavorable cyclization reaction is coupled to an electronic conjugation trapping step, to drive chromophore maturation. Moreover, we propose primarily electrostatic roles for the R96 and E222 side chains in chromophore formation and suggest that the T62 carbonyl oxygen is the base that initiates the dehydration reaction. Our molecular mechanism provides the basis for understanding and eventually controlling chromophore creation.

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The N-H bonds in amines are somewhat polar


DNA Structure: DNA Replication RNA Synthesis Protein

Green fluorescent protein has revolutionized cell labeling and molecular tagging, yet the driving force and mechanism for its spontaneous fluorophore synthesis are not established. Here we discover mutations that substantially slow the rate but not the yield of this posttranslational modification, determine structures of the trapped precyclization intermediate and oxidized postcyclization states, and identify unanticipated features critical to chromophore maturation. The protein architecture contains a dramatic ≈80° bend in the central helix, which focuses distortions at G67 to promote ring formation from amino acids S65, Y66, and G67. Significantly, these distortions eliminate potential helical hydrogen bonds that would otherwise have to be broken at an energetic cost during peptide cyclization and force the G67 nitrogen and S65 carbonyl oxygen atoms within van der Waals contact in preparation for covalent bond formation. Further, we determine that under aerobic, but not anaerobic, conditions the Gly-Gly-Gly chromophore sequence cyclizes and incorporates an oxygen atom. These results lead directly to a conjugation-trapping mechanism, in which a thermodynamically unfavorable cyclization reaction is coupled to an electronic conjugation trapping step, to drive chromophore maturation. Moreover, we propose primarily electrostatic roles for the R96 and E222 side chains in chromophore formation and suggest that the T62 carbonyl oxygen is the base that initiates the dehydration reaction. Our molecular mechanism provides the basis for understanding and eventually controlling chromophore creation.

DNA, or deoxyribonucleic acid, is the genetic material of a cell

N2 - Green fluorescent protein has revolutionized cell labeling and molecular tagging, yet the driving force and mechanism for its spontaneous fluorophore synthesis are not established. Here we discover mutations that substantially slow the rate but not the yield of this posttranslational modification, determine structures of the trapped precyclization intermediate and oxidized postcyclization states, and identify unanticipated features critical to chromophore maturation. The protein architecture contains a dramatic ≈80° bend in the central helix, which focuses distortions at G67 to promote ring formation from amino acids S65, Y66, and G67. Significantly, these distortions eliminate potential helical hydrogen bonds that would otherwise have to be broken at an energetic cost during peptide cyclization and force the G67 nitrogen and S65 carbonyl oxygen atoms within van der Waals contact in preparation for covalent bond formation. Further, we determine that under aerobic, but not anaerobic, conditions the Gly-Gly-Gly chromophore sequence cyclizes and incorporates an oxygen atom. These results lead directly to a conjugation-trapping mechanism, in which a thermodynamically unfavorable cyclization reaction is coupled to an electronic conjugation trapping step, to drive chromophore maturation. Moreover, we propose primarily electrostatic roles for the R96 and E222 side chains in chromophore formation and suggest that the T62 carbonyl oxygen is the base that initiates the dehydration reaction. Our molecular mechanism provides the basis for understanding and eventually controlling chromophore creation.

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