Literature DB >> 31262948

Relating Structure and Dynamics in RNA Biology.

Kevin P Larsen1,2, Junhong Choi1,3, Arjun Prabhakar1,2, Elisabetta Viani Puglisi1, Joseph D Puglisi1.   

Abstract

Recent advances in structural biology methods have enabled a surge in the number of RNA and RNA-protein assembly structures available at atomic or near-atomic resolution. These complexes are often trapped in discrete conformational states that exist along a mechanistic pathway. Single-molecule fluorescence methods provide temporal resolution to elucidate the dynamic mechanisms of processes involving complex RNA and RNA-protein assemblies, but interpretation of such data often requires previous structural knowledge. Here we highlight how single-molecule tools can directly complement structural approaches for two processes--translation and reverse transcription-to provide a dynamic view of molecular function.
Copyright © 2019 Cold Spring Harbor Laboratory Press; all rights reserved.

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Year:  2019        PMID: 31262948      PMCID: PMC6601459          DOI: 10.1101/cshperspect.a032474

Source DB:  PubMed          Journal:  Cold Spring Harb Perspect Biol        ISSN: 1943-0264            Impact factor:   10.005


  110 in total

1.  Effect of RNA secondary structure on the kinetics of DNA synthesis catalyzed by HIV-1 reverse transcriptase.

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Journal:  Biochemistry       Date:  1997-10-14       Impact factor: 3.162

Review 2.  Real-time crystallographic studies of the adenine riboswitch using an X-ray free-electron laser.

Authors:  Jason R Stagno; Yuba R Bhandari; Chelsie E Conrad; Yu Liu; Yun-Xing Wang
Journal:  FEBS J       Date:  2017-08-01       Impact factor: 5.542

3.  Rate-limiting Pyrophosphate Release by HIV Reverse Transcriptase Improves Fidelity.

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Journal:  J Biol Chem       Date:  2016-10-24       Impact factor: 5.157

4.  Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein.

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Journal:  Science       Date:  2014-12-05       Impact factor: 47.728

5.  Atomic accuracy in predicting and designing noncanonical RNA structure.

Authors:  Rhiju Das; John Karanicolas; David Baker
Journal:  Nat Methods       Date:  2010-02-28       Impact factor: 28.547

6.  RNAstructure: software for RNA secondary structure prediction and analysis.

Authors:  Jessica S Reuter; David H Mathews
Journal:  BMC Bioinformatics       Date:  2010-03-15       Impact factor: 3.169

7.  First snapshots of the HIV-1 RNA structure in infected cells and in virions.

Authors:  Jean-Christophe Paillart; Markus Dettenhofer; Xiao-Fang Yu; Chantal Ehresmann; Bernard Ehresmann; Roland Marquet
Journal:  J Biol Chem       Date:  2004-09-08       Impact factor: 5.157

8.  Key Intermediates in Ribosome Recycling Visualized by Time-Resolved Cryoelectron Microscopy.

Authors:  Ziao Fu; Sandip Kaledhonkar; Anneli Borg; Ming Sun; Bo Chen; Robert A Grassucci; Måns Ehrenberg; Joachim Frank
Journal:  Structure       Date:  2016-11-03       Impact factor: 5.006

Review 9.  Crystal structure of eukaryotic ribosome and its complexes with inhibitors.

Authors:  Gulnara Yusupova; Marat Yusupov
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2017-03-19       Impact factor: 6.237

10.  Structures of HIV-1 RT-RNA/DNA ternary complexes with dATP and nevirapine reveal conformational flexibility of RNA/DNA: insights into requirements for RNase H cleavage.

Authors:  Kalyan Das; Sergio E Martinez; Rajiv P Bandwar; Eddy Arnold
Journal:  Nucleic Acids Res       Date:  2014-05-31       Impact factor: 16.971

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  6 in total

1.  Distinct Conformational States Underlie Pausing during Initiation of HIV-1 Reverse Transcription.

Authors:  Kevin P Larsen; Junhong Choi; Lynnette N Jackson; Kalli Kappel; Jingji Zhang; Betty Ha; Dong-Hua Chen; Elisabetta Viani Puglisi
Journal:  J Mol Biol       Date:  2020-06-06       Impact factor: 5.469

2.  NMR Chemical Exchange Measurements Reveal That N6-Methyladenosine Slows RNA Annealing.

Authors:  Honglue Shi; Bei Liu; Felix Nussbaumer; Atul Rangadurai; Christoph Kreutz; Hashim M Al-Hashimi
Journal:  J Am Chem Soc       Date:  2019-12-16       Impact factor: 15.419

Review 3.  FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices.

Authors:  Eitan Lerner; Anders Barth; Jelle Hendrix; Benjamin Ambrose; Victoria Birkedal; Scott C Blanchard; Richard Börner; Hoi Sung Chung; Thorben Cordes; Timothy D Craggs; Ashok A Deniz; Jiajie Diao; Jingyi Fei; Ruben L Gonzalez; Irina V Gopich; Taekjip Ha; Christian A Hanke; Gilad Haran; Nikos S Hatzakis; Sungchul Hohng; Seok-Cheol Hong; Thorsten Hugel; Antonino Ingargiola; Chirlmin Joo; Achillefs N Kapanidis; Harold D Kim; Ted Laurence; Nam Ki Lee; Tae-Hee Lee; Edward A Lemke; Emmanuel Margeat; Jens Michaelis; Xavier Michalet; Sua Myong; Daniel Nettels; Thomas-Otavio Peulen; Evelyn Ploetz; Yair Razvag; Nicole C Robb; Benjamin Schuler; Hamid Soleimaninejad; Chun Tang; Reza Vafabakhsh; Don C Lamb; Claus Am Seidel; Shimon Weiss
Journal:  Elife       Date:  2021-03-29       Impact factor: 8.140

4.  High-resolution view of HIV-1 reverse transcriptase initiation complexes and inhibition by NNRTI drugs.

Authors:  Betty Ha; Kevin P Larsen; Jingji Zhang; Ziao Fu; Elizabeth Montabana; Lynnette N Jackson; Dong-Hua Chen; Elisabetta Viani Puglisi
Journal:  Nat Commun       Date:  2021-05-04       Impact factor: 14.919

Review 5.  Lessons Learned and Yet-to-Be Learned on the Importance of RNA Structure in SARS-CoV-2 Replication.

Authors:  Maclean Bassett; Marco Salemi; Brittany Rife Magalis
Journal:  Microbiol Mol Biol Rev       Date:  2022-07-07       Impact factor: 13.044

Review 6.  Structural Heterogeneities of the Ribosome: New Frontiers and Opportunities for Cryo-EM.

Authors:  Frédéric Poitevin; Artem Kushner; Xinpei Li; Khanh Dao Duc
Journal:  Molecules       Date:  2020-09-17       Impact factor: 4.411

  6 in total

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