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232 results on '"peptide bond formation"'

1. Vacuum UV studies of protonated serine clusters.

Author

Licht, Ori, Nihamkin, Maria, Anaby, Mirit, Rousseau, Patrick, Giuliani, Alexandre, Milosavljević, Aleksandar R, Singh, Raj, Nguyen, Vy T T, Nahon, Laurent, and Toker, Yoni

Subjects
*LIGHT absorption, *CHEMICAL bonds, *MONOMERS, *PEPTIDE bonds
Abstract

In a recent work, we have shown that photon absorption can cause a chemical bond to be created between the two monomers within a protonated serine dimer, a process known as intra-cluster bond formation, despite this process not occurring following thermal excitation via low energy collision-induced dissociation (LE-CID). Here we show further evidence for non-statistical photon-induced dissociation (PID) of the protonated serine dimer. In addition we discuss LE-CID and PID studies of the protonated serine octamer, showing that in this case as well, PID leads to non-statistical fragmentation and to the formation of two bonds between three neighboring monomers. [ABSTRACT FROM AUTHOR]

Published
2023
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2. Ribosome

Author

Ballesta, Juan P. G., Gargaud, Muriel, editor, Irvine, William M., editor, Amils, Ricardo, editor, Claeys, Philippe, editor, Cleaves, Henderson James, editor, Gerin, Maryvonne, editor, Rouan, Daniel, editor, Spohn, Tilman, editor, Tirard, Stéphane, editor, and Viso, Michel, editor

Published
2023
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3. Peptide Bond Formation between Aminoacyl-Minihelices by a Scaffold Derived from the Peptidyl Transferase Center.

Author

Kawabata, Mai, Kawashima, Kentaro, Mutsuro-Aoki, Hiromi, Ando, Tadashi, Umehara, Takuya, and Tamura, Koji

Subjects
*PEPTIDE bonds, *TRANSFER RNA, *PEPTIDE synthesis
Abstract

The peptidyl transferase center (PTC) in the ribosome is composed of two symmetrically arranged tRNA-like units that contribute to peptide bond formation. We prepared units of the PTC components with putative tRNA-like structure and attempted to obtain peptide bond formation between aminoacyl-minihelices (primordial tRNAs, the structures composed of a coaxial stack of the acceptor stem on the T-stem of tRNA). One of the components of the PTC, P1c2UGGU (74-mer), formed a dimer and a peptide bond was formed between two aminoacyl-minihelices tethered by the dimeric P1c2UGGU. Peptide synthesis depended on both the existence of the dimeric P1c2UGGU and the sequence complementarity between the ACCA-3′ sequence of the minihelix. Thus, the tRNA-like structures derived from the PTC could have originated as a scaffold of aminoacyl-minihelices for peptide bond formation through an interaction of the CCA sequence of minihelices. Moreover, with the same origin, some would have evolved to constitute the present PTC of the ribosome, and others to function as present tRNAs. [ABSTRACT FROM AUTHOR]

Published
2022
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4. Peptide Bond Formation between Aminoacyl-Minihelices by a Scaffold Derived from the Peptidyl Transferase Center

Author

Mai Kawabata, Kentaro Kawashima, Hiromi Mutsuro-Aoki, Tadashi Ando, Takuya Umehara, and Koji Tamura

Subjects
tRNA, minihelix, peptide bond formation, ribosomal symmetrical region, proto-ribosome, Science
Abstract

The peptidyl transferase center (PTC) in the ribosome is composed of two symmetrically arranged tRNA-like units that contribute to peptide bond formation. We prepared units of the PTC components with putative tRNA-like structure and attempted to obtain peptide bond formation between aminoacyl-minihelices (primordial tRNAs, the structures composed of a coaxial stack of the acceptor stem on the T-stem of tRNA). One of the components of the PTC, P1c2UGGU (74-mer), formed a dimer and a peptide bond was formed between two aminoacyl-minihelices tethered by the dimeric P1c2UGGU. Peptide synthesis depended on both the existence of the dimeric P1c2UGGU and the sequence complementarity between the ACCA-3′ sequence of the minihelix. Thus, the tRNA-like structures derived from the PTC could have originated as a scaffold of aminoacyl-minihelices for peptide bond formation through an interaction of the CCA sequence of minihelices. Moreover, with the same origin, some would have evolved to constitute the present PTC of the ribosome, and others to function as present tRNAs.

Published
2022
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6. Natural Products from Photorhabdus and Other Entomopathogenic Bacteria

Author

Bozhüyük, Kenan A. J., Zhou, Qiuqin, Engel, Yvonne, Heinrich, Antje, Pérez, Alexander, Bode, Helge B., Compans, Richard W, Series editor, Honjo, Tasuku, Series editor, Oldstone, Michael B. A., Series editor, Vogt, Peter K., Series editor, Malissen, Bernard, Series editor, Aktories, Klaus, Series editor, Kawaoka, Yoshihiro, Series editor, Rappuoli, Rino, Series editor, Galan, Jorge E., Series editor, Ahmed, Rafi, Series editor, Palme, Klaus, Series editor, Casadevall, Arturo, Series editor, Garcia-Sastre, Adolfo, Series editor, and ffrench-Constant, Richard H., editor

Published
2017
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38. Uncatalyzed peptide bond formation between two double amino acid molecules in the gas phase.

Author

Czapla, Marcin and Freza, Sylwia

Subjects
*PEPTIDE bonds, *AMINO acids, *GASES, *DIPEPTIDES, *CATALYSIS
Abstract

The gas phase mechanism for peptide bond formation between two double amino acid (DAA) molecules ((NH2)2C(COOH)2) is investigated in the absence of any catalysts. Two different paths, concerted and stepwise, each leading to both cis and trans DAA-DAA dipeptide products (four mechanisms total) are examined on the basis of theoretical calculations carried out at the CCSD(T)/aug-cc-pVDZ//MP2/aug-cc-pVDZ level. The investigation indicates that the concerted mechanism leading to the trans configuration of the peptide bond in the DAA-DAA dipeptide product is thermodynamically favored by about 5 kcal mol−1 and requires slightly less energy than the remaining pathways considered. Moreover, the peptide bond formation process between two DAA molecules in the gas phase resembles the analogous reactions between two natural amino acids. [ABSTRACT FROM AUTHOR]

Published
2017
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