Biochemistry and Molecular Biology
Penn State Science
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Andrey Krasilnikov

Andrey Krasilnikov

Main Content

  • Associate Professor of Biochemistry and Molecular Biology
106 Althouse Laboratory
University Park, PA 16802
Phone: (814) 865-5050

Research Interests

Structural biology of RNA and RNA-protein complexes

Graduate Programs


Research Summary

Structural studies of RNA and RNA-protein complexes

At first glance, the destiny of an RNA molecule might appear to be restrained by the simplicity of its components - limited to carrying genetic information and helping decode it. Indeed, RNA molecules are made of only four different types of building blocks: even after the addition of common modifications of the bases, the variety does not approach the diversity found in proteins. What can be built with only four different bases? Remarkably, RNA is a very versatile molecule capable of forming intricate networks of various intramolecular interactions. This property allows RNA to fold into complicated three-dimensional structures with features going far beyond simple single strands and double helices. The complexity and diversity of such RNA structures allow RNA to play various advanced roles, including substrate recognition and catalysis. RNA-based enzymes (ribozymes) and complexes of highly structured RNA and proteins play crucial roles in many biological processes including translation, splicing, tRNA and rRNA processing, and so on.

My laboratory is interested in learning the atomic-resolution details of the spatial organization of highly structured RNA molecules and complexes of such molecules with RNA-binding proteins. Using X-ray crystallography we can determine three-dimensional structures of molecules to the finest details; using a combination of crystallographic and biochemical studies we can answer a very broad variety of fundamental questions, ranging from the mechanisms of substrate recognition and catalysis to the structural and functional roles of individual parts of the molecule or complex. Currently we are involved in structural studies of several important RNA molecules and RNA-protein complexes, including Ribonuclease P, Ribonuclease MRP and some other fascinating and important molecules.

Crystal Structure-Krasilnikov

Figure: Crystal structure of the P3 domain of yeast RNase MRP in a complex with protein components Pop6 and Pop7.

Selected Publications

  • Perederina A, Berezin I, Krasilnikov AS (2018). In vitro reconstitution and analysis of eukaryotic RNase P RNPs. Nucleic Acids Research, in press.
  • Gopalan V, Jarrous N, Krasilnikov AS (2018). Change and necessity in the evolution of RNase P. RNA 24: 1-5.
  • Lemieux B, Laterreur N, Perederina A, Noel J-F, Dubois M-L, Krasilnikov AS, Wellinger RJ (2016). Active yeast telomerase shares subunits with ribonucleoproteins RNase P and RNase MRP. Cell 165: 1171-1181.
  • Fagerlund RD, Perederina A, Berezin I, Krasilnikov AS (2015). Footprinting analysis of interactions between the largest eukaryotic RNase P/MRP protein Pop1 and RNase P/MRP RNA components. RNA21: 1591-1605.
  • Krasilnikov AS (2014). Applying UV-crosslinking to study RNA-protein interactions in multicomponent ribonucleoprotein complexes. Methods Mol. Biol. 1086: 193-207.
  • Esakova O, Perederina A, Berezin I, Krasilnikov AS (2013). Conserved regions of ribonucleoprotein ribonuclease MRP are involved in interactions with its substrate. Nucleic Acids Research 41: 7084-7091.
  • Khanova E, Esakova O, Perederina A, Berezin I, Krasilnikov AS (2012). Structural organizations of yeast RNase P and RNase MRP holoenzymes as revealed by UV-crosslinking studies of RNA-protein interactions. RNA 18: 720-728.
  • Perederina A, Krasilnikov AS (2012). Crystallization of RNA-protein complexes: from synthesis and purification of individual components to crystals. Methods Mol. Biol. 905: 123-143.
  • Perederina A, Khanova E, Quan C, Berezin I, Esakova O, Krasilnikov AS (2011). Interactions of a Pop5/Rpp1 heterodimer with the catalytic domain of RNase MRP. RNA 17: 1922-1931.
  • Krasilnikov AS (2011). Ribonucleoprotein ribonucleases P and MRP. In Ribonucleases (ed. Nicholson AW), pp 319-342. Springer, New York, NY, doi: 10.1007/978-3-642-21078-5_13
  • Esakova O, Perederina A, Quan C, Berezin I, Krasilnikov AS (2011). Substrate recognition by ribonucleoprotein Ribonuclease MRP. RNA 17: 356-364.
  • Esakova O, Krasilnikov AS (2010). Of proteins and RNA: the RNase P/MRP family. RNA 16: 1725-1747.
  • Perederina A, Krasilnikov AS (2010). The P3 domain of eukaryotic RNases P/MRP: Making a protein-rich RNA-based enzyme. RNA Biology 7: 534-539.
  • Perederina A, Esakova O, Quan, C, Khanova E, Krasilnikov AS (2010). Eukaryotic Ribonucleases P/MRP: the crystal structure of the P3 domain. EMBO J. 29: 761-769.
  • Lu Q, Wierzbicki S, Krasilnikov AS, Schmitt ME (2010). Comparison of mitochondrial and nucleolar RNase MRP reveals identical RNA components with distinct enzymatic activities and protein components. RNA 16: 529-537.
  • Perederina A, Esakova O, Quan C, Khanova E, Krasilnikov AS (2010). Crystallization and preliminary X-ray diffraction analysis of the P3 RNA domain of yeast Ribonuclease MRP in a complex with RNase P/ MRP protein components Pop6 and Pop7. Acta Crystallographica F66: 76-80.
  • Esakova O, Perederina A, Quan C, Schmitt ME, Krasilnikov AS (2008). Footprinting analysis demonstrates extensive similarity between eukaryotic RNase P and RNase MRP holoenzymes. RNA14: 1558-1567.
  • Perederina A, Esakova O, Koc H, Schmitt ME, Krasilnikov AS (2007). Specific binding of a Pop6/Pop7 heterodimer to the P3 stem of yeast RNase MRP and RNase P RNAs. RNA 13: 1648-1655.
  • Baird NJ, Srividya N, Krasilnikov AS, Mondragon A, Sosnick TR, Pan T (2006). Structural basis for altering the stability of homologous RNAs from a mesophilic and a thermophilic bacterium. RNA 12: 598-606.
  • Torres-Larios A, Swinger, KK, Krasilnikov AS, Pan T, Mondragon A (2005). Crystal structure of the RNA component of bacterial Ribonuclease P. Nature 437: 584-587.
  • Krasilnikov AS, Xiao Y, Pan T, Mondragon A (2004). Basis for structural diversity in homologous RNAs. Science 306: 104-107.
  • Krasilnikov AS, Mondragon A (2003). On the occurrence of the T-loop RNA folding motif in large RNA molecules. RNA 9:640-643.
  • Krasilnikov AS, Yang XJ, Pan T, Mondragon A (2003). Crystal structure of the specificity domain of ribonuclease P. Nature 421: 760-764.