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      RNA and protein 3D structure modeling: similarities and differences

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          Abstract

          In analogy to proteins, the function of RNA depends on its structure and dynamics, which are encoded in the linear sequence. While there are numerous methods for computational prediction of protein 3D structure from sequence, there have been very few such methods for RNA. This review discusses template-based and template-free approaches for macromolecular structure prediction, with special emphasis on comparison between the already tried-and-tested methods for protein structure modeling and the very recently developed “protein-like” modeling methods for RNA. We highlight analogies between many successful methods for modeling of these two types of biological macromolecules and argue that RNA 3D structure can be modeled using “protein-like” methodology. We also highlight the areas where the differences between RNA and proteins require the development of RNA-specific solutions.

          Figure

          Approaches for predicting RNA structure. Top: Template-free modeling. Bottom: Template-based modeling

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          Most cited references60

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          Principles that govern the folding of protein chains.

          C ANFINSEN (1973)
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            Architecture and Secondary Structure of an Entire HIV-1 RNA Genome

            Single-stranded RNA viruses encompass broad classes of infectious agents and cause the common cold, cancer, AIDS, and other serious health threats. Viral replication is regulated at many levels, including using conserved genomic RNA structures. Most potential regulatory elements within viral RNA genomes are uncharacterized. Here we report the structure of an entire HIV-1 genome at single nucleotide resolution using SHAPE, a high-throughput RNA analysis technology. The genome encodes protein structure at two levels. In addition to the correspondence between RNA and protein primary sequences, a correlation exists between high levels of RNA structure and sequences that encode inter-domain loops in HIV proteins. This correlation suggests RNA structure modulates ribosome elongation to promote native protein folding. Some simple genome elements previously shown to be important, including the ribosomal gag-pol frameshift stem-loop, are components of larger RNA motifs. We also identify organizational principles for unstructured RNA regions. Highly used splice acceptors lie in unstructured motifs and hypervariable regions are sequestered from flanking genome regions by stable insulator helices. These results emphasize that the HIV-1 genome and, potentially, many coding RNAs are punctuated by numerous previously unrecognized regulatory motifs and that extensive RNA structure may constitute an additional level of the genetic code.
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              Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions.

              We explore the ability of a simple simulated annealing procedure to assemble native-like structures from fragments of unrelated protein structures with similar local sequences using Bayesian scoring functions. Environment and residue pair specific contributions to the scoring functions appear as the first two terms in a series expansion for the residue probability distributions in the protein database; the decoupling of the distance and environment dependencies of the distributions resolves the major problems with current database-derived scoring functions noted by Thomas and Dill. The simulated annealing procedure rapidly and frequently generates native-like structures for small helical proteins and better than random structures for small beta sheet containing proteins. Most of the simulated structures have native-like solvent accessibility and secondary structure patterns, and thus ensembles of these structures provide a particularly challenging set of decoys for evaluating scoring functions. We investigate the effects of multiple sequence information and different types of conformational constraints on the overall performance of the method, and the ability of a variety of recently developed scoring functions to recognize the native-like conformations in the ensembles of simulated structures.
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                Author and article information

                Contributors
                +48-22-5970750 , +48-22-5970715 , iamb@genesilico.pl
                Journal
                J Mol Model
                Journal of Molecular Modeling
                Springer-Verlag (Berlin/Heidelberg )
                1610-2940
                0948-5023
                22 January 2011
                22 January 2011
                September 2011
                : 17
                : 9
                : 2325-2336
                Affiliations
                [1 ]Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
                [2 ]Laboratory of Structural Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznan, Poland
                Article
                951
                10.1007/s00894-010-0951-x
                3168752
                21258831
                4afeeeae-d65a-4515-a626-ddbf42204cca
                © The Author(s) 2011
                History
                : 1 October 2010
                : 29 December 2010
                Categories
                Original Paper
                Custom metadata
                © Springer-Verlag 2011

                Molecular biology
                assessment,structure,tertiary,prediction,rna
                Molecular biology
                assessment, structure, tertiary, prediction, rna

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