A normal mode analysis of 20 proteins in 'open' or 'closed' forms was performed using simple potential and protein models. The quality of the results was found to depend upon the form of the protein studied, normal modes obtained with the open form of a given protein comparing better with the conformational change than those obtained with the closed form. Moreover, when the motion of the protein is a highly collective one, then, in all cases considered, there is a single low-frequency normal mode whose direction compares well with the conformational change. When it is not, in most cases there is still a single low-frequency normal mode giving a good description of the pattern of the atomic displacements, as they are observed experimentally during the conformational change. Hence a lot of information on the nature of the conformational change of a protein is often found in a single low-frequency normal mode of its open form. Since this information can be obtained through the normal mode analysis of a model as simple as that used in the present study, it is likely that the property captured by such an analysis is for the most part a property of the shape of the protein itself. One of the points that has to be clarified now is whether or not amino acid sequences have been selected in order to allow proteins to follow a single normal mode direction, as least at the very beginning of their conformational change.

Normal mode analysis of proteins of various sizes, ranging from 46 (crambin) up to 858 residues (dimeric citrate synthase) were performed, by using standard approaches, as well as a recently proposed method that rests on the hypothesis that low‐frequency normal modes of proteins can be described as pure rigid‐body motions of blocks of consecutive amino‐acid residues. Such a hypothesis is strongly supported by our results, because we show that the latter method, named RTB, yields very accurate approximations for the low‐frequency normal modes of all proteins considered. Moreover, the quality of the normal modes thus obtained depends very little on the way the polypeptidic chain is split into blocks. Noteworthy, with six amino‐acids per block, the normal modes are almost as accurate as with a single amino‐acid per block. In this case, for a protein of n residues and N atoms, the RTB method requires the diagonalization of an n × n matrix, whereas standard procedures require the diagonalization of a 3N × 3N matrix. Being a fast method, our approach can be useful for normal mode analyses of large systems, paving the way for further developments and applications in contexts for which the normal modes are needed frequently, as for example during molecular dynamics calculations. Proteins 2000;41:1–7. © 2000 Wiley‐Liss, Inc.

Combining structural data for the ribosome from x-ray crystallography and cryo-electron microscopy with dynamic models based on elastic network normal mode analysis, an atomically detailed picture of functionally important structural rearrangements that occur during translocation is elucidated. The dynamic model provides a near-atomic description of the ratchet-like rearrangement of the 70S ribosome seen in cryo-electron microscopy, and permits the identification of bridging interactions that either facilitate the conformational switching or maintain structural integrity of the 50S͞30S interface. Motions of the tRNAs residing in the A and P sites also suggest the early stages of tRNA translocation as a result of this ratchet-like movement. Displacement of the L1 stalk, alternately closing and opening the intersubunit space near the E site, is observed in the dynamic model, in line with growing experimental evidence for the role of this structural component in facilitating the exiting of tRNA. Finally, a hinge-like transition in the 30S ribosomal subunit, similar to that observed in crystal structures of this complex, is also manifest as a dynamic mode of the ribosome. The coincidence of these dynamic transitions with the individual normal modes of the ribosome and the good correspondence between these motions and those observed in experiment suggest an underlying principle of nature to exploit the shape of molecular assemblies such as the ribosome to provide robustness to functionally important motions.dynamical transitions ͉ ratchet-like reorganization ͉ translocation ͉ molecular machines T he ribosome synthesizes proteins by translating the genetic information residing on the mRNA into a specific sequence of amino acids. Binding of elongation factor G and subsequent GTP hydrolysis promotes the translocation process (1). This process is accompanied by large conformational rearrangements of the ribosome (2, 3). In particular, a ratchet-like relative rotation of the two ribosomal subunits has been observed, and proposed as a key mechanical step in the translocation of the mRNA⅐tRNAs complex (4). Other motions, such as a large displacement of the L1 stalk region (5-7, 37), rearrangement of the L7͞L12 stalk (2), and domain movement in the 30S subunit (8), have also been observed and implicated as functionally relevant for protein synthesis (9).Cryo-electron microscopy (cryo-EM) and x-ray crystallography have provided glimpses of functionally important conformational changes occurring during protein synthesis in the ribosome (2-4, 9-11). However, these static structural models provide key information mostly about the endpoint states of such large-scale conformational transitions and do not directly probe the conformational transitions. Theoretical techniques (modeling and simulation) can be used to augment this information, to lend an understanding of the dynamics at a close-to-atomic level. Recent atomic-resolution structures of the ribosome (12-14) make simulation methods based on atomic or near-atomic theories po...