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Rabdano SO, Shannon MD, Izmailov SA, Gonzalez Salguero N, Zandian M, Purusottam RN, Poirier MG, Skrynnikov NR, Jaroniec CP. Histone H4 Tails in Nucleosomes: a Fuzzy Interaction with DNA. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Sevastyan O. Rabdano
- Laboratory of Biomolecular NMR St. Petersburg State University St. Petersburg 199034 Russian Federation
| | - Matthew D. Shannon
- Department of Chemistry and Biochemistry The Ohio State University Columbus OH 43210 USA
| | - Sergei A. Izmailov
- Laboratory of Biomolecular NMR St. Petersburg State University St. Petersburg 199034 Russian Federation
| | | | - Mohamad Zandian
- Department of Chemistry and Biochemistry The Ohio State University Columbus OH 43210 USA
| | - Rudra N. Purusottam
- Department of Chemistry and Biochemistry The Ohio State University Columbus OH 43210 USA
| | | | - Nikolai R. Skrynnikov
- Laboratory of Biomolecular NMR St. Petersburg State University St. Petersburg 199034 Russian Federation
- Department of Chemistry Purdue University West Lafayette IN 47906 USA
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Rabdano SO, Shannon MD, Izmailov SA, Gonzalez Salguero N, Zandian M, Purusottam RN, Poirier MG, Skrynnikov NR, Jaroniec CP. Histone H4 Tails in Nucleosomes: a Fuzzy Interaction with DNA. Angew Chem Int Ed Engl 2021; 60:6480-6487. [PMID: 33522067 DOI: 10.1002/anie.202012046] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/15/2020] [Indexed: 12/21/2022]
Abstract
The interaction of positively charged N-terminal histone tails with nucleosomal DNA plays an important role in chromatin assembly and regulation, modulating their susceptibility to post-translational modifications and recognition by chromatin-binding proteins. Here, we report residue-specific 15 N NMR relaxation rates for histone H4 tails in reconstituted nucleosomes. These data indicate that H4 tails are strongly dynamically disordered, albeit with reduced conformational flexibility compared to a free peptide with the same sequence. Remarkably, the NMR observables were successfully reproduced in a 2-μs MD trajectory of the nucleosome. This is an important step toward resolving an apparent inconsistency where prior simulations were generally at odds with experimental evidence on conformational dynamics of histone tails. Our findings indicate that histone H4 tails engage in a fuzzy interaction with nucleosomal DNA, underpinned by a variable pattern of short-lived salt bridges and hydrogen bonds, which persists at low ionic strength (0-100 mM NaCl).
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Affiliation(s)
- Sevastyan O Rabdano
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, 199034, Russian Federation
| | - Matthew D Shannon
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
| | - Sergei A Izmailov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, 199034, Russian Federation
| | | | - Mohamad Zandian
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
| | - Rudra N Purusottam
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
| | - Michael G Poirier
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
| | - Nikolai R Skrynnikov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, 199034, Russian Federation.,Department of Chemistry, Purdue University, West Lafayette, IN, 47906, USA
| | - Christopher P Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
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Shi X, Prasanna C, Nagashima T, Yamazaki T, Pervushin K, Nordenskiöld L. Structure and Dynamics in the Nucleosome Revealed by Solid-State NMR. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804707] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Xiangyan Shi
- School of Physical and Mathematical Sciences; Nanyang Technological University; 21 Nanyang Link Singapore 637371 Singapore
| | - Chinmayi Prasanna
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
| | - Toshio Nagashima
- RIKEN Center for Life Science Technologies; Yokohama City Kanagawa 230-0045 Japan
| | - Toshio Yamazaki
- RIKEN Center for Life Science Technologies; Yokohama City Kanagawa 230-0045 Japan
| | - Konstantin Pervushin
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
| | - Lars Nordenskiöld
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
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Shi X, Prasanna C, Nagashima T, Yamazaki T, Pervushin K, Nordenskiöld L. Structure and Dynamics in the Nucleosome Revealed by Solid-State NMR. Angew Chem Int Ed Engl 2018; 57:9734-9738. [DOI: 10.1002/anie.201804707] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 05/23/2018] [Indexed: 02/01/2023]
Affiliation(s)
- Xiangyan Shi
- School of Physical and Mathematical Sciences; Nanyang Technological University; 21 Nanyang Link Singapore 637371 Singapore
| | - Chinmayi Prasanna
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
| | - Toshio Nagashima
- RIKEN Center for Life Science Technologies; Yokohama City Kanagawa 230-0045 Japan
| | - Toshio Yamazaki
- RIKEN Center for Life Science Technologies; Yokohama City Kanagawa 230-0045 Japan
| | - Konstantin Pervushin
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
| | - Lars Nordenskiöld
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
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