Document text
Principal Investigator: Jinwei Zhang
Organization: NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES
Fiscal Year: 2023
Award: $2,136,574
Funding agency: National Institute of Diabetes and Digestive and Kidney Diseases
We have made significant progresses in all three branches of the project: (a) T-box riboswitches, (b) tRNA-like structures in lncRNAs, and (c) Nucleic acid recognition by antibodies.
(a) To gain insights into the T-box structural dynamics before and during tRNA binding, we carried out SAXS, fluorescence lifetime and mutational analyses, as well as single-molecule FRET analyses in collaboration with Hoi Sung Chungs lab at NIDDK. Our data suggest that free T-boxes assume several flexible, open conformations and tRNA binding triggers nearly instantaneous domain closure and guides the folding of the T-box structure. We further show that the pseudoknot structure acts as a geometric hub that organizes the overall T-box architecture to facilitate tRNA binding and domain closure. This work has been provisionally accepted for publication in Nature Communications.
b) To gain insights into the maturation of MALAT1 lncRNA and biogenesis of mascRNA, we have solved the first crystal structures of human mascRNA before and after RNase P processing. mascRNA employs a novel, unusually streamlined mode of partial tRNA mimicry to recruit tRNA-processing enzymes. Using in vitro RNase P, ELAC2, and aminoacylation assays, we have defined the structural determinants of mascRNA that drive its processing and identified its non-tRNA features that escape aminoacylation, preventing interference with translation.
(c) To elucidate how S9.6 antibody recognizes R-loops, we recently reported the first crystal structures of a S9.6 antigen-binding fragment (Fab) free and bound to a 13-bp hybrid duplex. The structures and attendant biophysical and mutational analyses detail how S9.6 achieves specific recognition of hybrids in R-loops, and provide a framework for S9.6 protein engineering. This work was published in Nat. Commun. To understand how the J2 antibody recognize dsRNA, we have determined its first co-crystal structure bound to a dsRNA duplex and are currently characterizing its binding interface and specificity.
Terms: <Affinity><Amino Acids><Amino Acylation><Aminoacylation><Antibiotic Agents><Antibiotic Drugs><Antibiotics><Antibodies><Antigen Binding Fragment><Antigenic Determinants><Architecture><Assay><Autoimmune Diseases><Autoregulation><Bacteria><Bacterial Infections><Binding><Binding Determinants><Bioassay><Biogenesis><Biologic Assays><Biological Assay><Cancers><Cellular Stress><Cellular Stress Response><Clinical Treatment Moab><Collaborations><Communication><DNA><Data><Deoxyribonucleic Acid><Development><Double-Stranded RNA><Elements><Engineering / Architecture><Enzyme Gene><Enzymes><Epitopes><Fab Fragments><Fab Immunoglobulins><Fluorescence><Functional RNA><Gene Action Regulation><Gene Expression><Gene Expression Regulation><Gene Regulation><Gene Regulation Process><Genome><Gram-Positive Bacteria><Homeostasis><Human><Hybrids><Immunity><Immunization><Immunoglobulin, F(ab) Fragment><In Vitro><Intermediary Metabolism><Lupus Erythematosus Disseminatus><MALAT1><MALAT1 gene><Malignant Neoplasms><Malignant Tumor><Metabolic><Metabolic Diseases><Metabolic Disorder><Metabolic Processes><Metabolism><Miscellaneous Antibiotic><Modeling><Modern Man><Molecular Configuration><Molecular Conformation><Molecular Interaction><Molecular Stereochemistry><Monoclonal Antibodies><Mutation Analysis><NIAID><NIDDK><National Institute of Allergy and Infectious Disease><National Institute of Diabetes and Digestive and Kidney Diseases><Nature><Non-Coding><Non-Coding RNA><Non-Polyadenylated RNA><Non-translated RNA><Noncoding RNA><Nontranslated RNA><Nucleic Acid Binding><Nucleic Acids><Nutritional><Origin of Life><Physiological Homeostasis><Plant Viruses><Play><Protein Engineering><Proteins><Publications><Publishing><RNA><RNA Gene Products><RNA targeting drug><RNA targeting therapeutics><RNA vaccine><RNA-based vaccine><RNA-targeting therapy><RNase P><Regulator Genes><Reporting><Research><Resolution><Retroviridae><Retroviruses><Ribonuclease P><Ribonucleic Acid><SLE><Scientific Publication><Specificity><Starvation><Stress><Structure><System><Systemic Lupus Erythematosus><Systemic Lupus Erythematous><Systemic Lupus Erythmatosus><Thesaurismosis><Transcriptional Regulatory Elements><Transfer RNA><Translation Initiation><Translations><Triplet Codon-Amino Acid Adaptor><Untranslated RNA><Vaccine Production><Viral Diseases><Virus Diseases><Virus-Retrovirus><Work><aminoacid><autoimmune condition><autoimmune disorder><autoimmunity disease><bacteria infection><bacterial disease><biophysical analysis><biophysical studies><cell stress><conformation><conformational><conformational state><conformationally><conformations><dark matter><develop therapy><developmental><disseminated lupus erythematosus><dsRNA><flexibility><flexible><genetic protein engineering><human pathogen><improved><insight><intervention development><mAbs><mRNA vaccine><mRNA-based vaccine><malignancy><metabolism disorder><metastasis-associated lung adenocarcinoma transcript 1><mimicry><monoclonal Abs><neoplasm/cancer><noncoding><novel><nutritious><prevent><preventing><produce vaccines><protein design><recruit><regulatory gene><resolutions><response><single-molecule FRET><single-molecule fluorescence resonance energy transfer><smFRET><small molecule><structural determinants><structural factors><systemic lupus erythematosis><tRNA><therapy development><tool><trans acting element><transcription termination><transfer Ribonucleic acids><translation><treatment development><triple helix><viral detection><viral infection><virus detection><virus infection><virus-induced disease>