Ribosome: The structure-function relation and a new paradigm to the protein folding problem

Debasis Das, Dibyendu Samanta, Anindita Das, Jaydip Ghosh, Arpita Bhattacharya, Arunima Basu, Abhijit Chakrabarti, Chanchal Das Gupta

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

The rate of protein synthesis is about seven and fifteen amino acids per second, in the eukaryotic and the bacterial ribosome, respectively. Hence, a few minutes is required to synthesize a polypeptide of an average length. This is much longer than the time needed for the hydrophobic collapse (folding) to take place. So a polypeptide gets enough time to form its local secondary to tertiary structures cotranslationally and put such segments in proper order while in association with the ribosome, unless something prevents its entire length from folding. As reported earlier, ribosomes from prokaryotes, eukaryotes, and mitochondria act as molds for protein folding, and each mold has a set of recognition sites for all proteins. More specifically, the mold is the peptidyl transferase center (PTC), a part of the large RNA of the large ribosomal subunit. Specific amino acids from different random coil regions in a protein interact with specific nucleotides in the PTC, which brings the entire length of the protein into the small space of the PTC mold. The mold thus helps to stabilize the entropy-driven collapsed state of the polypeptide. The process also divides the protein into small segments; each segment is connected at two ends with two nucleotides and can fold in the ribosomal environment. The segments dissociate in such a sequence that the organization proceeds hierarchically from the core of the globular protein radially towards the outer surface. Then the protein dissociates from the ribosome in a "folding competent state" which does the final fine tuning in folding outside the ribosome. While the ribosomal contact and release are over in 1-2 minutes in vitro, the fine tuning takes about 5-10 minutes. Release from the ribosome needs no added energy factor from outside, like ATP.

Original languageEnglish (US)
Pages (from-to)109-116
Number of pages8
JournalIsrael Journal of Chemistry
Volume50
Issue number1
DOIs
StatePublished - Jun 18 2010
Externally publishedYes

Fingerprint

Protein folding
Peptidyl Transferases
Proteins
Peptides
Nucleotides
Tuning
Amino Acids
Mitochondria
Molds
Entropy
Adenosine Triphosphate
Association reactions
RNA

Keywords

  • protein folding
  • PTC
  • ribosome

ASJC Scopus subject areas

  • Chemistry(all)

Cite this

Das, D., Samanta, D., Das, A., Ghosh, J., Bhattacharya, A., Basu, A., ... Das Gupta, C. (2010). Ribosome: The structure-function relation and a new paradigm to the protein folding problem. Israel Journal of Chemistry, 50(1), 109-116. https://doi.org/10.1002/ijch.201000004

Ribosome : The structure-function relation and a new paradigm to the protein folding problem. / Das, Debasis; Samanta, Dibyendu; Das, Anindita; Ghosh, Jaydip; Bhattacharya, Arpita; Basu, Arunima; Chakrabarti, Abhijit; Das Gupta, Chanchal.

In: Israel Journal of Chemistry, Vol. 50, No. 1, 18.06.2010, p. 109-116.

Research output: Contribution to journalArticle

Das, D, Samanta, D, Das, A, Ghosh, J, Bhattacharya, A, Basu, A, Chakrabarti, A & Das Gupta, C 2010, 'Ribosome: The structure-function relation and a new paradigm to the protein folding problem', Israel Journal of Chemistry, vol. 50, no. 1, pp. 109-116. https://doi.org/10.1002/ijch.201000004
Das, Debasis ; Samanta, Dibyendu ; Das, Anindita ; Ghosh, Jaydip ; Bhattacharya, Arpita ; Basu, Arunima ; Chakrabarti, Abhijit ; Das Gupta, Chanchal. / Ribosome : The structure-function relation and a new paradigm to the protein folding problem. In: Israel Journal of Chemistry. 2010 ; Vol. 50, No. 1. pp. 109-116.
@article{91be3cea90f3464f8ab79f7f54cd95f3,
title = "Ribosome: The structure-function relation and a new paradigm to the protein folding problem",
abstract = "The rate of protein synthesis is about seven and fifteen amino acids per second, in the eukaryotic and the bacterial ribosome, respectively. Hence, a few minutes is required to synthesize a polypeptide of an average length. This is much longer than the time needed for the hydrophobic collapse (folding) to take place. So a polypeptide gets enough time to form its local secondary to tertiary structures cotranslationally and put such segments in proper order while in association with the ribosome, unless something prevents its entire length from folding. As reported earlier, ribosomes from prokaryotes, eukaryotes, and mitochondria act as molds for protein folding, and each mold has a set of recognition sites for all proteins. More specifically, the mold is the peptidyl transferase center (PTC), a part of the large RNA of the large ribosomal subunit. Specific amino acids from different random coil regions in a protein interact with specific nucleotides in the PTC, which brings the entire length of the protein into the small space of the PTC mold. The mold thus helps to stabilize the entropy-driven collapsed state of the polypeptide. The process also divides the protein into small segments; each segment is connected at two ends with two nucleotides and can fold in the ribosomal environment. The segments dissociate in such a sequence that the organization proceeds hierarchically from the core of the globular protein radially towards the outer surface. Then the protein dissociates from the ribosome in a {"}folding competent state{"} which does the final fine tuning in folding outside the ribosome. While the ribosomal contact and release are over in 1-2 minutes in vitro, the fine tuning takes about 5-10 minutes. Release from the ribosome needs no added energy factor from outside, like ATP.",
keywords = "protein folding, PTC, ribosome",
author = "Debasis Das and Dibyendu Samanta and Anindita Das and Jaydip Ghosh and Arpita Bhattacharya and Arunima Basu and Abhijit Chakrabarti and {Das Gupta}, Chanchal",
year = "2010",
month = "6",
day = "18",
doi = "10.1002/ijch.201000004",
language = "English (US)",
volume = "50",
pages = "109--116",
journal = "Israel Journal of Chemistry",
issn = "0021-2148",
publisher = "Wiley-VCH Verlag",
number = "1",

}

TY - JOUR

T1 - Ribosome

T2 - The structure-function relation and a new paradigm to the protein folding problem

AU - Das, Debasis

AU - Samanta, Dibyendu

AU - Das, Anindita

AU - Ghosh, Jaydip

AU - Bhattacharya, Arpita

AU - Basu, Arunima

AU - Chakrabarti, Abhijit

AU - Das Gupta, Chanchal

PY - 2010/6/18

Y1 - 2010/6/18

N2 - The rate of protein synthesis is about seven and fifteen amino acids per second, in the eukaryotic and the bacterial ribosome, respectively. Hence, a few minutes is required to synthesize a polypeptide of an average length. This is much longer than the time needed for the hydrophobic collapse (folding) to take place. So a polypeptide gets enough time to form its local secondary to tertiary structures cotranslationally and put such segments in proper order while in association with the ribosome, unless something prevents its entire length from folding. As reported earlier, ribosomes from prokaryotes, eukaryotes, and mitochondria act as molds for protein folding, and each mold has a set of recognition sites for all proteins. More specifically, the mold is the peptidyl transferase center (PTC), a part of the large RNA of the large ribosomal subunit. Specific amino acids from different random coil regions in a protein interact with specific nucleotides in the PTC, which brings the entire length of the protein into the small space of the PTC mold. The mold thus helps to stabilize the entropy-driven collapsed state of the polypeptide. The process also divides the protein into small segments; each segment is connected at two ends with two nucleotides and can fold in the ribosomal environment. The segments dissociate in such a sequence that the organization proceeds hierarchically from the core of the globular protein radially towards the outer surface. Then the protein dissociates from the ribosome in a "folding competent state" which does the final fine tuning in folding outside the ribosome. While the ribosomal contact and release are over in 1-2 minutes in vitro, the fine tuning takes about 5-10 minutes. Release from the ribosome needs no added energy factor from outside, like ATP.

AB - The rate of protein synthesis is about seven and fifteen amino acids per second, in the eukaryotic and the bacterial ribosome, respectively. Hence, a few minutes is required to synthesize a polypeptide of an average length. This is much longer than the time needed for the hydrophobic collapse (folding) to take place. So a polypeptide gets enough time to form its local secondary to tertiary structures cotranslationally and put such segments in proper order while in association with the ribosome, unless something prevents its entire length from folding. As reported earlier, ribosomes from prokaryotes, eukaryotes, and mitochondria act as molds for protein folding, and each mold has a set of recognition sites for all proteins. More specifically, the mold is the peptidyl transferase center (PTC), a part of the large RNA of the large ribosomal subunit. Specific amino acids from different random coil regions in a protein interact with specific nucleotides in the PTC, which brings the entire length of the protein into the small space of the PTC mold. The mold thus helps to stabilize the entropy-driven collapsed state of the polypeptide. The process also divides the protein into small segments; each segment is connected at two ends with two nucleotides and can fold in the ribosomal environment. The segments dissociate in such a sequence that the organization proceeds hierarchically from the core of the globular protein radially towards the outer surface. Then the protein dissociates from the ribosome in a "folding competent state" which does the final fine tuning in folding outside the ribosome. While the ribosomal contact and release are over in 1-2 minutes in vitro, the fine tuning takes about 5-10 minutes. Release from the ribosome needs no added energy factor from outside, like ATP.

KW - protein folding

KW - PTC

KW - ribosome

UR - http://www.scopus.com/inward/record.url?scp=78649503999&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=78649503999&partnerID=8YFLogxK

U2 - 10.1002/ijch.201000004

DO - 10.1002/ijch.201000004

M3 - Article

AN - SCOPUS:78649503999

VL - 50

SP - 109

EP - 116

JO - Israel Journal of Chemistry

JF - Israel Journal of Chemistry

SN - 0021-2148

IS - 1

ER -