Protein engineering: advances in phage display for basic science and medical research

EK Davydova - Biochemistry (Moscow), 2022 - Springer
Abstract Functional Protein Engineering became the hallmark in biomolecule manipulation
in the new millennium, building on and surpassing the underlying structural DNA …

Synthetic antibodies for accelerated RNA crystallography

S DasGupta - Wiley Interdisciplinary Reviews: RNA, 2024 - Wiley Online Library
RNA structure is crucial to a wide range of cellular processes. The intimate relationship
between macromolecular structure and function necessitates the determination of high …

Structural basis for substrate binding and catalysis by a self-alkylating ribozyme

D Krochmal, Y Shao, NS Li, S DasGupta… - Nature Chemical …, 2022 - nature.com
Ribozymes that react with small-molecule probes have important applications in
transcriptomics and chemical biology, such as RNA labeling and imaging. Understanding …

Structural basis for fluorescence activation by Pepper RNA

HC Rees, W Gogacz, NS Li, D Koirala… - ACS chemical …, 2022 - ACS Publications
Pepper is a fluorogenic RNA aptamer tag that binds to a variety of benzylidene-cyanophenyl
(HBC) derivatives with tight affinity and activates their fluorescence. To investigate how …

A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites

D Koirala, Y Shao, Y Koldobskaya, JR Fuller… - Nature …, 2019 - nature.com
Picornaviral IRES elements are essential for initiating the cap-independent viral translation.
However, three-dimensional structures of these elements remain elusive. Here, we report a …

Affinity maturation of a portable Fab–RNA module for chaperone-assisted RNA crystallography

D Koirala, SA Shelke, M Dupont, S Ruiz… - Nucleic Acids …, 2018 - academic.oup.com
Antibody fragments such as Fabs possess properties that can enhance protein and RNA
crystallization and therefore can facilitate macromolecular structure determination. In …

Synthetic antibody binding to a preorganized RNA domain of hepatitis C virus internal ribosome entry site inhibits translation

D Koirala, A Lewicka, Y Koldobskaya… - ACS chemical …, 2019 - ACS Publications
Structured RNA elements within the internal ribosome entry site (IRES) of hepatitis C virus
(HCV) genome hijack host cell machinery for translation initiation through a cap …

Combinatorial design of a nanobody that specifically targets structured RNAs

F Cawez, E Duray, Y Hu, J Vandenameele… - Journal of molecular …, 2018 - Elsevier
Recent advances in transcriptome sequencing and analysis have revealed the complexity of
the human genome. The majority (≈ 98%) of cellular transcripts is not translated into …

Lesson from a Fab-enabled co-crystallization study of TDRD2 and PIWIL1

S Chen, W Zhang, J Min, K Liu - Methods, 2020 - Elsevier
The interaction of Tudor domain-containing proteins (TDRDs) with P-element-induced
wimpy testis (PIWI) proteins plays critical roles in transposon silencing and …

Affinity and structural analysis of the U1A RNA recognition motif with engineered methionines to improve experimental phasing

Y Srivastava, R Bonn-Breach, SS Chavali, GM Lippa… - Crystals, 2021 - mdpi.com
RNA plays a central role in all organisms and can fold into complex structures to orchestrate
function. Visualization of such structures often requires crystallization, which can be a …