Results 41 to 50 of about 6,175 (141)

Correcting pervasive errors in RNA crystallography through enumerative structure prediction

, 2012
Three-dimensional RNA models fitted into crystallographic density maps exhibit pervasive conformational ambiguities, geometric errors and steric clashes. To address these problems, we present enumerative real-space refinement assisted by electron density
AT Brunger, DJ Mandell, F DiMaio, F DiMaio, Fang-Chieh Chou, J Praznikar, JA Cruz, JJ Headd, JS Richardson, KS Keating, M Forconi, MD Winn, N Ban, P Gendron, P Sripakdeevong, Parin Sripakdeevong, PD Adams, PV Afonine, R Das, R Das, Rhiju Das, RJ Read, Sergey M Dibrov, SM Dibrov, Thomas Hermann, VB Chen, VB Chen, X Wang   +27 more
core   +1 more source

Mirror‐Image Random Nonstandard Peptides Integrated Discovery (MI‐RaPID) Technology Yields Highly Stable and Selective Macrocyclic Peptide Inhibitors for Matrix Metallopeptidase 7

Angewandte Chemie, Volume 137, Issue 8, February 17, 2025.
Mirror‐image RaPID (MI‐RaPID) technology was developed for the discovery of innate protease‐resistant macrocyclic peptides. Metalloproteinase 7 (MMP7) plays a crucial role in cancer, making it an attractive target for therapeutic development. Using MI‐RaPID technology, we identified a highly selective and stable macrocyclic peptide, which consists of D‐
Hiba Ghareeb, Choi Yi Li, Anjana Shenoy, Naama Rotenberg, Julia M. Shifman, Takayuki Katoh, Irit Sagi, Hiroaki Suga, Norman Metanis   +8 more
wiley   +2 more sources

Comparison of the Structures and Mechanisms of the Pistol and Hammerhead Ribozymes [PDF]

, 2019
Comparison of the secondary and three-dimensional structures of the hammerhead and pistol ribozymes reveals many close similarities, so in this work we have asked if they are mechanistically identical.
Dai, Qing, Li, Nan-Sheng, Lilley, David M. J., Liu, Yijin, Piccirilli, Joseph A., Wilson, Timothy J.   +5 more
core   +3 more sources

High yield production of the antifungal proteins PeAfpA and PdAfpB by vacuole targeting in a TMV‐based expression vector

Plant Biotechnology Journal, EarlyView.
Summary Antifungal proteins (AFPs) derived from filamentous fungi show great potential against economically significant fungi that cause plant diseases and consequently threat food safety and security. This study focuses on the Penicillium expansum PeAfpA and Penicillium digitatum PdAfpB proteins and their activity against several phytopathogens.
Adrià Bugeda, Xiaoqing Shi, Laia Castillo, Jose F. Marcos, Paloma Manzanares, Juan José López‐Moya, María Coca   +6 more
wiley   +1 more source

Biophysical and biochemical investigations of RNA catalysis in the hammerhead ribozyme [PDF]

, 1999
1. How do ribozymes work? 241 2. The hammerhead RNA as a prototype ribozyme 242 2.1 RNA enzymes 242 2.2 Satellite self-cleaving RNAs 242 2.3 Hammerhead RNAs and hammerhead ribozymes 244 3.
Scott, William G
core   +2 more sources

Engineering of Small Ribozymes Acting on RNA: What is Needed to Make a New Function Work with an Existing Catalyst?

ChemBioChem, Volume 26, Issue 10, May 27, 2025.
Rational design is a potent strategy for developing ribozymes with advanced functionalities. Engineered variants of the hairpin ribozyme impressively demonstrate how function can be tuned through structural manipulation. The engineering of nucleic acids has been a longstanding objective in research, with the field gaining significant attention ...
Constanze Ebermann, Sabine Müller
wiley   +1 more source

Efficient trans-cleavage of a stem-loop RNA substrate by a ribozyme derived from neurospora VS RNA. [PDF]

The EMBO Journal, 1995
We have constructed a ribozyme containing 144 nucleotides of Neurospora VS RNA that can catalyze the cleavage of a separate RNA in a true enzymatic manner (Km approximately 0.13 microM, kcat approximately 0.7/min). Comparison of the rates of cis- and trans-cleavage, as well as the lack of effect of pH on the rate of cleavage, suggest that a rate ...
Richard A. Collins, H. C. T. Guo
openaire   +3 more sources

Nanosecond Hyperquenching for Electron Cryo‐Microscopy Without Air‐Water Interface Artifacts

Chemistry – A European Journal, Volume 31, Issue 29, May 22, 2025.
A novel method for the ultrafast vitrification of the biological assemblies is assayed by the electron cryotomography. Protein specimens prepared by this method inherently lack the spatial/structural artifacts, which derive from the surface tension at the air‐water interface (AWI).
Utz H. Ermel, Harald Schwalbe, Alexey V. Cherepanov   +2 more
wiley   +1 more source

A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination [PDF]

, 2010
RNA crystallization and phasing represent major bottlenecks in RNA structure determination. Seeking to exploit antibody fragments as RNA crystallization chaperones, we have used an arginine-enriched synthetic Fab library displayed on phage to obtain Fabs
A Desmyter, A Ke, A Serganov, AA Kossiakoff, AC Messias, AL Edwards, Anthony A Kossiakoff, AR Ferré-D'Amaré, AR Ferré-D'Amaré, AY Keel, BL Golden, BM Lunde, BS Saville, C Eigenbrot, C Höbartner, C Keryer-Bibens, CG Hoogstraten, D Piekna-Przybylska, David M Shechner, David P Bartel, DM Shechner, EA Kabat, EH Ekland, Erica M Duguid, FA Fellouse, FA Fellouse, FA Fellouse, IA Laird-Offringa, J-D Ye, JA Chao, JA Doudna, Jingdong Ye, Joseph A Piccirilli, JR Hogg, JR Hogg, JS Mattick, JS Mattick, K Decanniere, M Jinek, MJ Fedor, MP Robertson, N Carrasco, NH Bergman, Nikolai B Suslov, P Kapranov, PJ Carter, R Dutzler, RJ Taft, RK Montange, S Birtalan, S Iwata, S Jones, S Koide, S Koide, S Uysal, Sachdev S Sidhu, SC Bagby, Shohei Koide, SL Reichow, SR Eddy, SS Sidhu, TA Cooper, V Tereshko, Yelena Koldobskaya   +63 more
core   +2 more sources

Simple and Efficient Transformation and Gene Editing of Marchantia polymorpha Spores

Current Protocols, Volume 5, Issue 5, May 2025.
Abstract Marchantia polymorpha (Marchantia) has become a model species for liverwort studies, owing to its rapid growth in vitro, ease of propagation, simple genetics, small genome, haploid‐dominant life cycle, and because it is amenable to genetic transformation.
Rebecca M. Yorker, Simon C. Deroles, Yanfei Zhou, Jennifer A. Tate, Kevin M. Davies, Nick W. Albert   +5 more
wiley   +1 more source