Dissection of the role of hydrogen bonds in RNA-protein recognition
نویسندگان
چکیده
Institute of Protein Research RAS, Pushchino, Moscow Region, 142290 Russia Engelhardt Institute of Molecular Biology RAS, Moscow, 32 Vavilov Street, 119991 Russia Running Title: ribosomal TL5-5S rRNA complex Address correspondence to: George M. Gongadze and Maria B. Garber, Institute of Protein Research RAS, Pushchino, Moscow Region, 142290 Russia, Tel. (0967) 73-27-70; Fax. (095) 632-78-71; § E-mail: [email protected]; [email protected]
منابع مشابه
Dissecting the protein–RNA interface: the role of protein surface shapes and RNA secondary structures in protein–RNA recognition
Protein-RNA interactions are essential for many biological processes. However, the structural mechanisms underlying these interactions are not fully understood. Here, we analyzed the protein surface shape (dented, intermediate or protruded) and the RNA base pairing properties (paired or unpaired nucleotides) at the interfaces of 91 protein-RNA complexes derived from the Protein Data Bank. Dente...
متن کاملTheoretical Study of Heteroatom Resonance-Assisted Hydrogen Bond: Effect of Substituent on π-delocalization
The concept of Resonance Assisted Hydrogen Bond (RAHB), which usually occurs in b diketons, has a remarkable role in chemistry. These molecules, which contain heteroatom particularly O and N, are species with biological interest in protein folding and DNA pairing. Therefore, the amplification of hydrogen bonds strength by substituents may be important in life scie...
متن کاملA zero one programming model for RNA structures with arclength ≥ 4
In this paper, we consider RNA structures with arc-length 4 . First, we represent these structures as matrix models and zero-one linearprogramming problems. Then, we obtain an optimal solution for this problemusing an implicit enumeration method. The optimal solution corresponds toan RNA structure with the maximum number of hydrogen bonds.
متن کاملAtomic resolution structures of rieske iron-sulfur protein: role of hydrogen bonds in tuning the redox potential of iron-sulfur clusters.
The Rieske [2Fe-2S] iron-sulfur protein of cytochrome bc(1) functions as the initial electron acceptor in the rate-limiting step of the catalytic reaction. Prior studies have established roles for a number of conserved residues that hydrogen bond to ligands of the [2Fe-2S] cluster. We have constructed site-specific variants at two of these residues, measured their thermodynamic and functional p...
متن کاملThe role of RNA conformation in RNA-protein recognition
Interactions between protein and RNA play a key role in many biological processes in the gene expression pathway. Those interactions are mediated through a variety of RNA-binding protein domains, among them the highly abundant RNA recognition motif (RRM). Here we studied protein-RNA complexes from different RNA binding domain families solved by NMR and x-ray crystallography. Characterizing the ...
متن کامل