1
|
Mei LC, Hao GF, Yang GF. Computational methods for predicting hotspots at protein-RNA interfaces. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1675. [PMID: 34080311 DOI: 10.1002/wrna.1675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 11/10/2022]
Abstract
Protein-RNA interactions play essential roles in many critical biological events. A comprehensive understanding of the mechanisms underlying these interactions is helpful when studying cellular activities and therapeutic applications. Hotspots are a small portion of residues contributing much toward protein-RNA binding affinity. In pharmaceutical research, the hotspot residues are seen as the best option for designing small molecules to target proteins of therapeutic interest. With the accumulation of experimental data about protein-RNA interactions, computational methods have been produced for hotspot prediction on a large scale. In this review, we first present an overview of the existing databases for protein-RNA binding data. Furthermore, we outline the most adopted computational methods for hotspots prediction in protein-RNA interactions. Finally, we discuss the applications of hotspot prediction. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Methods > RNA Analyses In Vitro and In Silico.
Collapse
Affiliation(s)
- Long-Can Mei
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, China.,International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, China
| | - Ge-Fei Hao
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, China.,International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, China.,State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang, China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, China.,International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, China.,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| |
Collapse
|
2
|
Ragucci S, Pacifico S, Ruocco MR, Crescente G, Nasso R, Simonetti M, Masullo M, Piccolella S, Pedone PV, Landi N, Di Maro A. Ageritin from poplar mushrooms: scale-up purification and cytotoxicity towards undifferentiated and differentiated SH-SY5Y cells. Food Funct 2019; 10:6342-6350. [DOI: 10.1039/c9fo01483g] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Ageritin from poplar mushroom is a valuable selective neurotoxin towards undifferentiated neuroblastoma SH-SY5Y cells.
Collapse
|
3
|
Castaño-Rodríguez C, Olombrada M, Partida-Hanon A, Lacadena J, Oñaderra M, Gavilanes JG, García-Ortega L, Martínez-Del-Pozo Á. Involvement of loops 2 and 3 of α-sarcin on its ribotoxic activity. Toxicon 2015; 96:1-9. [PMID: 25598497 DOI: 10.1016/j.toxicon.2015.01.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Revised: 12/21/2014] [Accepted: 01/14/2015] [Indexed: 01/07/2023]
Abstract
Ribotoxins are a family of fungal ribosome-inactivating proteins displaying highly specific ribonucleolytic activity against the sarcin/ricin loop (SRL) of the larger rRNA, with α-sarcin as its best-characterized member. Their toxicity arises from the combination of this activity with their ability to cross cell membranes. The involvement of α-sarcin's loops 2 and 3 in SRL and ribosomal proteins recognition, as well as in the ribotoxin-lipid interactions involving cell penetration, has been suggested some time ago. In the work presented now different mutants have been prepared in order to study the role of these loops in their ribonucleolytic and lipid-interacting properties. The results obtained confirm that loop 3 residues Lys 111, 112, and 114 are key actors of the specific recognition of the SRL. In addition, it is also shown that Lys 114 and Tyr 48 conform a network of interactions which is essential for the catalysis. Lipid-interaction studies show that this Lys-rich region is indeed involved in the phospholipids recognition needed to cross cell membranes. Loop 2 is shown to be responsible for the conformational change which exposes the region establishing hydrophobic interactions with the membrane inner leaflets and eases penetration of ribotoxins target cells.
Collapse
Affiliation(s)
- Carlos Castaño-Rodríguez
- Departamento de Bioquímica y Biología Molecular I, Facultades de Química y Biología, Universidad Complutense, 28040 Madrid, Spain
| | - Miriam Olombrada
- Departamento de Bioquímica y Biología Molecular I, Facultades de Química y Biología, Universidad Complutense, 28040 Madrid, Spain
| | - Angélica Partida-Hanon
- Departamento de Bioquímica y Biología Molecular I, Facultades de Química y Biología, Universidad Complutense, 28040 Madrid, Spain
| | - Javier Lacadena
- Departamento de Bioquímica y Biología Molecular I, Facultades de Química y Biología, Universidad Complutense, 28040 Madrid, Spain
| | - Mercedes Oñaderra
- Departamento de Bioquímica y Biología Molecular I, Facultades de Química y Biología, Universidad Complutense, 28040 Madrid, Spain
| | - José G Gavilanes
- Departamento de Bioquímica y Biología Molecular I, Facultades de Química y Biología, Universidad Complutense, 28040 Madrid, Spain.
| | - Lucía García-Ortega
- Departamento de Bioquímica y Biología Molecular I, Facultades de Química y Biología, Universidad Complutense, 28040 Madrid, Spain
| | - Álvaro Martínez-Del-Pozo
- Departamento de Bioquímica y Biología Molecular I, Facultades de Química y Biología, Universidad Complutense, 28040 Madrid, Spain.
| |
Collapse
|
4
|
Ingle S, Azad RN, Jain SS, Tullius TD. Chemical probing of RNA with the hydroxyl radical at single-atom resolution. Nucleic Acids Res 2014; 42:12758-67. [PMID: 25313156 PMCID: PMC4227780 DOI: 10.1093/nar/gku934] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 09/17/2014] [Accepted: 09/24/2014] [Indexed: 12/02/2022] Open
Abstract
While hydroxyl radical cleavage is widely used to map RNA tertiary structure, lack of mechanistic understanding of strand break formation limits the degree of structural insight that can be obtained from this experiment. Here, we determine how individual ribose hydrogens of sarcin/ricin loop RNA participate in strand cleavage. We find that substituting deuterium for hydrogen at a ribose 5'-carbon produces a kinetic isotope effect on cleavage; the major cleavage product is an RNA strand terminated by a 5'-aldehyde. We conclude that hydroxyl radical abstracts a 5'-hydrogen atom, leading to RNA strand cleavage. We used this approach to obtain structural information for a GUA base triple, a common tertiary structural feature of RNA. Cleavage at U exhibits a large 5' deuterium kinetic isotope effect, a potential signature of a base triple. Others had noted a ribose-phosphate hydrogen bond involving the G 2'-OH and the U phosphate of the GUA triple, and suggested that this hydrogen bond contributes to backbone rigidity. Substituting deoxyguanosine for G, to eliminate this hydrogen bond, results in a substantial decrease in cleavage at G and U of the triple. We conclude that this hydrogen bond is a linchpin of backbone structure around the triple.
Collapse
Affiliation(s)
- Shakti Ingle
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Robert N Azad
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Swapan S Jain
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Thomas D Tullius
- Department of Chemistry, Boston University, Boston, MA 02215, USA Program in Bioinformatics, Boston University, Boston, MA 02215, USA
| |
Collapse
|
5
|
Parker MS, Sah R, Balasubramaniam A, Sallee FR, Park EA, Parker SL. On the expansion of ribosomal proteins and RNAs in eukaryotes. Amino Acids 2014; 46:1589-604. [PMID: 24633358 DOI: 10.1007/s00726-014-1704-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 02/18/2014] [Indexed: 01/11/2023]
Abstract
While the ribosome constitution is similar in all biota, there is a considerable increase in size of both ribosomal proteins (RPs) and RNAs in eukaryotes as compared to archaea and bacteria. This is pronounced in the large (60S) ribosomal subunit (LSU). In addition to enlargement (apparently maximized already in lower eukarya), the RP changes include increases in fraction, segregation and clustering of basic residues, and decrease in hydrophobicity. The acidic fraction is lower in eukaryote as compared to prokaryote RPs. In all eukaryote groups tested, the LSU RPs have significantly higher content of basic residues and homobasic segments than the SSU RPs. The vertebrate LSU RPs have much higher sequestration of basic residues than those of bacteria, archaea and even of the lower eukarya. The basic clusters are highly aligned in the vertebrate, but less in the lower eukarya, and only within families in archaea and bacteria. Increase in the basicity of RPs, besides helping transport to the nucleus, should promote stability of the assembled ribosome as well as the association with translocons and other intracellular matrix proteins. The size and GC nucleotide bias of the expansion segments of large LSU rRNAs also culminate in the vertebrate, and should support ribosome association with the endoplasmic reticulum and other intracellular networks. However, the expansion and nucleotide bias of eukaryote LSU rRNAs do not clearly correlate with changes in ionic parameters of LSU ribosomal proteins.
Collapse
Affiliation(s)
- Michael S Parker
- Department of Microbiology and Molecular Cell Sciences, University of Memphis, Memphis, TN, 38152, USA
| | | | | | | | | | | |
Collapse
|
6
|
Abstract
Ricin and Shiga toxins designated as ribosome inactivating proteins (RIPs) are RNA N-glycosidases that depurinate a specific adenine (A₄₃₂₄ in rat 28S rRNA) in the conserved α-sarcin/ricin loop of the large rRNA, inhibiting protein synthesis. Evidence obtained from a number of studies suggests that interaction with ribosomal proteins plays an important role in the catalytic activity and ribosome specificity of RIPs. This review summarizes the recent developments in identification of the ribosomal proteins that interact with ricin and Shiga toxins and the principles governing these interactions.
Collapse
Affiliation(s)
- Nilgun E Tumer
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, 59 Dudley Road, New Brunswick, NJ 08901-8520, USA.
| | | |
Collapse
|
7
|
Álvarez-García E, Diago-Navarro E, Herrero-Galán E, García-Ortega L, López-Villarejo J, Olmo N, Díaz-Orejas R, Gavilanes JG, Martínez-del-Pozo Á. The ribonucleolytic activity of the ribotoxin α-sarcin is not essential for in vitro protein biosynthesis inhibition. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1377-82. [DOI: 10.1016/j.bbapap.2011.06.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 06/21/2011] [Accepted: 06/29/2011] [Indexed: 11/16/2022]
|
8
|
Herrero-Galán E, García-Ortega L, Lacadena J, Martínez-Del-Pozo A, Olmo N, Gavilanes JG, Oñaderra M. Implication of an Asp residue in the ribonucleolytic activity of hirsutellin A reveals new electrostatic interactions at the active site of ribotoxins. Biochimie 2011; 94:427-33. [PMID: 21871524 DOI: 10.1016/j.biochi.2011.08.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 08/15/2011] [Indexed: 10/17/2022]
Abstract
Ribotoxins are fungal extracellular ribonucleases that specifically cleave ribosomes leading to cell-death via apoptosis. α-Sarcin is the ribotoxin studied in deepest detail, and therefore constitutes the referential protein for the whole family. It has been demonstrated that ribotoxin activity depends on a very precise structural microenvironment in which electrostatic interactions among residues in the active site are of the highest importance. Hirsutellin A (HtA) has been recently described as the smallest ribotoxin known to date, encompassing all the abilities of previously characterized members of this family into a shorter sequence. Comparison of HtA and α-sarcin three-dimensional structures suggested that residues presumably forming the catalytic triad of HtA would be His 42, Glu 66, and His 113. Within this same idea, the presence of an Asp residue (Asp 40) in a position equivalent to α-sarcin Tyr 48 is highlighted as a novelty in this field. In this work, substitution mutants H42Q, E66Q and H113Q, as well as double and triple mutants in all possible combinations, are studied regarding their ribonucleolytic activity and cytotoxicity. Implication of these three residues in the ribotoxin activity of HtA is confirmed, though none of them is strictly essential for ribosomal cleavage. Studies with mutants D40N and D40N/E66Q demonstrate an important role for Asp 40 in the activity of HtA and establish a new set of electrostatic interactions different from the one described for already known ribotoxins.
Collapse
Affiliation(s)
- Elías Herrero-Galán
- Departamento de Bioquímica y Biología Molecular I, Facultad de Química, Universidad Complutense, 28040 Madrid, Spain
| | | | | | | | | | | | | |
Collapse
|