The Ribosome as a Conveying Thermal Ratchet Machine

Abstract

, and the other at the A. N. Bach Institute of Biochemistry, Academy of Sciences of the USSR. This biochemical group was one of the most creative in the country. It was world-renowned because of several important discoveries in the field of nucleic acid studies. In the thirties of the last century, it succeeded in settling the question of the universal occurrence of two known types of nucleic acids, ribonucleic acid (RNA) and deoxyribonucleic acid (DNA), in living matter. At that time, many biochemists believed that RNA is a characteristic component of plants and fungi, whereas DNA (designated as "thymonucleic acid" or "animal nucleic acid") belongs to the animal kingdom. The presence of DNA in plant cells raised doubts, as the positive cytochemical Feulgen reaction in plant cell nuclei was the only indirect evidence. Belozersky and colleagues were the first to isolate thymine and then DNA (thymonucleic acid) from higher plants (1, 2), thus proving the universal occurrence of DNA. The next series of studies was carried out on bacteria (3) and demonstrated that both RNA and DNA were present there, again confirming the idea of the universality of the occurrence of both types of nucleic acids in organisms of different phylogenetic kingdoms. At the same time, the studies on bacteria showed that these organisms were deserving of special attention because of the high content of nucleic acids in their cells. During the years from 1939 to 1947, the systematic studies of the content of nucleic acids in bacteria of various taxonomic families, of different ages, and under different physiological conditions were performed in both subgroups headed by Belozersky (4). The high level of nucleic acids in cells was postulated to be in direct relation to their biological activities, growth rate, and cell proliferation.I joined the group in 1954 as a graduate student, formally at the Institute of Biochemistry of the Academy of Sciences, but the place of my experimental work was in the well equipped new building of the Biological Faculty at the Moscow State University. By that time, the Journal of Biological Chemistry had published a series of papers by Chargaff and colleagues in which the first convincing results that the base composition of nucleic acids can vary in different organisms were presented (5-8). Crick and Watson had just published their famous papers on DNA structure and its implications for gene duplication and transcription into RNA (9, 10). The following questions had arisen. What is the range of variations of base compositions of DNA and RNA in different organisms? Does the total RNA just copy the total DNA of the cell, thus repeating its base composition, or do DNA-independent fractions of RNA exist? In 1956, I started work on testing the idea of the presumable correlation between the base compositions of RNA and DNA. The result was unexpected: the total DNA base composition manifested wide species variations, whereas the RNA composition was found to be surprisingly conserved (11). At the same time, statistical an...

Structural characterization of mRNA-tRNA translocation intermediates

“…These movements separate two distinct states during the first phase of translocation, termed macrostate I (MS I) and II (MS II) (4). The fact that the conformational changes of the ribosome and classical-hybrid transitions of tRNAs occur spontaneously in a pretrans-locational (PRE) ribosome (11)(12)(13)(14)(15)(16) has confirmed the view of the ribosome as a Brownian machine (17). In this view, the role of ribosomal factors is to modulate the free-energy landscape, promoting or controlling structural and kinetic routes underlying functional dynamics of translation (18,19).…”

Hypothesis: Emergence of Translation as a Result of RNA Helicase Evolution

“…The emergence of proteins allowed the helicase to further improve its efficiency by recruiting proteinaceous elongation factors, EF-Tu and EF-G, which additionally powered the existing molecular ratchet via GTP hydrolysis (Spirin 2002). I suggest that the helicase/ribosome has been working as a helicase until the specialised proteinaceous helicases replaced it, leaving protein synthesis as the only ribosomal function.…”

“…As observed from the above, in the absence of factors, the energy source for translocation comes from Brownian thermal motion, while unidirectionality is ensured by chemical modification of tRNAs during peptidyl transfer reaction (Noller 2006;Spirin 1985Spirin , 2009Woese 1970). This mode of translocation, known as 'molecular ratchet', can be imagined as 'directed diffusion' and is utilised by many other unrelated molecular machines of the modern cell, such as, for example, multi-subunit RNA polymerase (Abbondanzieri et al 2005).…”

The translation elongation cycle—capturing multiple states by cryo-electron microscopy

“…Alexander Spirin, who early on recognized the mechanistic challenge posed by this feat, spoke of the ribosome as a conveying machine [6], invoking the idea of conveyor belts used in industry and now at the cash registers of every grocery store, but the preferred term is mRNA-tRNA translocation or translocation for short. Indeed, the loss of reading frame, in most cases, would be a debacle leading to the formation of a product that is non-functioning at best and toxic for the cell at worst.…”