ArticlebioRxiv : the preprint server for biology2025
Blind prediction of complex water and ion ensembles around RNA in CASP16.
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51 authors.
Rachael C KretschBiophysics Program, Stanford University School of Medicine, Stanford, California, USA.ORCID 0000-0002-6935-518X
Elisa PosaniScuola Internazionale Superiore di Studi Avanzati (SISSA), via Bonomea 265, 34136 Trieste, Italy.ORCID 0000-0002-0217-5125
Eugene F BaulinLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland.ORCID 0000-0003-4694-9783
Janusz M BujnickiLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland.ORCID 0000-0002-6633-165X
Giovanni BussiScuola Internazionale Superiore di Studi Avanzati (SISSA), via Bonomea 265, 34136 Trieste, Italy.ORCID 0000-0001-9216-5782
Thomas E CheathamUniversity of Utah, Medicinal Chemistry Department, Salt Lake City, Utah, USA.ORCID 0000-0003-0298-3904
Shi-Jie ChenDepartment of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA.ORCID 0000-0002-8093-7244
Arne ElofssonDep of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University Box 1031, 171 21 Solna, Sweden.ORCID 0000-0002-7115-9751
Masoud Amiri FarsaniLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland.ORCID 0000-0001-5116-0483
Olivia N FisherUniversity of Utah, Medicinal Chemistry Department, Salt Lake City, Utah, USA.ORCID 0000-0002-0862-8367
M Michael GromihaDepartment of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India.ORCID 0000-0002-1776-4096
Ayush GuptaWilliam A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, 4226 Martin Luther King Boulevard, Houston, TX, 77204, USA.ORCID 0009-0006-1702-6946
Michiaki HamadaFaculty of Science and Engineering, Waseda University, 169-8555, Tokyo, Japan.ORCID 0000-0001-9466-1034
K HariniDepartment of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India.
Gang HuNITFID, School of Statistics and Data Science, AAIS, LPMC and KLMDASR, Nankai University, Tianjin 300071, China.ORCID 0000-0002-7134-3380
David HuangDepartment of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.
Junichi IwakiriGraduate School of Frontier Sciences, The University of Tokyo, 277-8561, Chiba, Japan.ORCID 0000-0002-4611-2142
Anika JainDepartment of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.ORCID 0000-0002-0249-875X
Yuki KagayaDepartment of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.ORCID 0000-0003-0146-1709
Daisuke KiharaDepartment of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.ORCID 0000-0003-4091-6614
Sebastian KmiecikUniversity of Warsaw, Biological and Chemical Research Centre, Faculty of Chemistry, Warsaw, Poland.ORCID 0000-0001-7623-0935
Sowmya Ramaswamy KrishnanDepartment of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India.ORCID 0000-0001-5404-3266
Ikuo KurisakiWaseda Research Institute for Science and Engineering, Waseda University, 169-8555, Tokyo, Japan.ORCID 0000-0003-4519-1093
Olivier Languin-CattoënScuola Internazionale Superiore di Studi Avanzati (SISSA), via Bonomea 265, 34136 Trieste, Italy.
Jun LiSchool of Sciences, Great Bay University, Great Bay Institute for Advanced Study, Guangdong Provincial Key Laboratory of Mathematical and Neural Dynamical Systems, Dongguan, Guangdong 523000, China.ORCID 0000-0002-7011-1991
Shanshan LiDivision of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China.ORCID 0000-0002-7041-5960
Karim MalekzadehWilliam A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, 4226 Martin Luther King Boulevard, Houston, TX, 77204, USA.ORCID 0009-0004-8185-4995
Tsukasa NakamuraDepartment of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.ORCID 0000-0002-6312-3070
Wentao NiNITFID, School of Statistics and Data Science, AAIS, LPMC and KLMDASR, Nankai University, Tianjin 300071, China.ORCID 0009-0002-7355-0073
Chandran NithinUniversity of Warsaw, Biological and Chemical Research Centre, Faculty of Chemistry, Warsaw, Poland.ORCID 0000-0001-8212-6093
Michael Z PaloDepartment of Structural Biology, Stanford University School of Medicine, CA USA.ORCID 0000-0003-4883-6766
Joon Hong ParkDepartment of Computer Science, Purdue University, West Lafayette, IN, 47907, USA.
Smita P PillaUniversity of Warsaw, Biological and Chemical Research Centre, Faculty of Chemistry, Warsaw, Poland.ORCID 0000-0002-4520-3210
Simón PobleteFacultad de Ingeniería, Universidad San Sebastián, Bellavista 7, 8420524 Santiago, Chile.ORCID 0000-0001-7793-0570
Fabrizio PucciComputational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium.ORCID 0000-0003-2916-022X
Pranav PunuruDepartment of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.
Anouka SahaDepartment of Mathematics, The University of Texas at Austin, Austin, TX, 78712, USA.
Kengo SatoSchool of Life Science and Technology, Institute of Science Tokyo, 152-8550, Tokyo, Japan.ORCID 0000-0001-6744-7390
Ambuj SrivastavaDepartment of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India.
Genki TerashiDepartment of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.ORCID 0000-0002-5339-909X
Emilia TugolukovaDepartment of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.
Jacob VerburgtDepartment of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.ORCID 0000-0002-8524-1342
Qiqige WuyunDepartment of Computer Science and Engineering, Michigan State University, East Lansing, Michigan 48824, USA.ORCID 0000-0002-7228-903X
Gül H ZerzeWilliam A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, 4226 Martin Luther King Boulevard, Houston, TX, 77204, USA.ORCID 0000-0002-3074-3521
Kaiming ZhangDivision of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China.ORCID 0000-0003-0414-4776
Sicheng ZhangDepartment of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA.ORCID 0009-0009-9851-5451
Wei ZhengNITFID, School of Statistics and Data Science, AAIS, LPMC and KLMDASR, Nankai University, Tianjin 300071, China.ORCID 0000-0002-2984-9003
Yuanzhe ZhouDepartment of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA.ORCID 0000-0003-1858-3067
Wah ChiuBiophysics Program, Stanford University School of Medicine, Stanford, California, USA.ORCID 0000-0002-8910-3078
David A CaseDepartment of Chemistry & Chemical Biology, Rutgers University, Piscataway, New Jersey, USA.ORCID 0000-0003-2314-2346
Rhiju DasBiophysics Program, Stanford University School of Medicine, Stanford, California, USA.ORCID 0000-0001-7497-0972
Funding
The Stanford-SLAC CryoEM Center supplementU24GM129541 · NIGMS · STANFORD UNIVERSITY · PI CHIU, WAH, HEDMAN, BRITT · 2018 to 2023
$54.8MCenter for Structural Biology of HIV RNAU54AI170660 · NIAID · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI ALICE TELESNITSKY · 2022 to 2026
$32.1MUnified Data Resource for Large Complexes Determined by Cryo-Electron MicroscopyR01GM079429 · NIGMS · STANFORD UNIVERSITY · PI CHIU, WAH · 2007 to 2021
$11.6MNext-generation computational/chemical methods for complex RNA structuresR35GM122579 · NIGMS · STANFORD UNIVERSITY · PI Rhiju Das · 2017 to 2026
$7.2MNew methods for computational modeling of RNA structuresR35GM134919 · NIGMS · UNIVERSITY OF MISSOURI-COLUMBIA · PI SHI-JIE CHEN · 2020 to 2026
$3.3MBiomolecular simulation for the end-stage refinement of nucleic acid structureR01GM081411 · NIGMS · UNIVERSITY OF UTAH · PI CHEATHAM, THOMAS E. · 2008 to 2022
$2.7MPurdue University Molecular Biophysics Training ProgramT32GM132024 · NIGMS · PURDUE UNIVERSITY · PI Angeline Marie Lyon, John Tesmer · 2019 to 2026
$2.0MBuilding protein structure models for intermediate resolution cryo-electron microscopy mapsR01GM133840 · NIGMS · PURDUE UNIVERSITY · PI KIHARA, DAISUKE · 2020 to 2023
$1.6MData-driven biomolecular structure modeling for cryo-EM mapsR35GM158267 · NIGMS · PURDUE UNIVERSITY · PI Daisuke Kihara · 2025 to 2026
$791kNIAID NIH HHS U54 AI170660NIGMS NIH HHS R01 GM079429NIGMS NIH HHS R01 GM081411NIGMS NIH HHS R01 GM133840NIGMS NIH HHS R35 GM122579NIGMS NIH HHS R35 GM134919NIGMS NIH HHS R35 GM158267NIGMS NIH HHS T32 GM132024NIGMS NIH HHS U24 GM129541
Abstract
Biomolecules rely on water and ions for stable folding, but these interactions are often transient, dynamic, or disordered and thus hidden from experiments and evaluation challenges that represent biomolecules as single, ordered structures. Here, we compare blindly predicted ensembles of water and ion structure to the cryo-EM densities observed around the
Indexed as
cryo-EMensemble predictionionsmolecular dynamicsribozymeRNAsolvationwater
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