Molecular dynamics analysis of biomolecular systems including nucleic acids
With the recent progress in structural biology and genome biology, structural dynamics of molecular systems that include nucleic acids has attracted attention in the context of gene regulation. The structure–function relationship is an important topic that highlights the importance of the physicoche...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
The Biophysical Society of Japan
2022-09-01
|
| Series: | Biophysics and Physicobiology |
| Subjects: | |
| Online Access: | https://doi.org/10.2142/biophysico.bppb-v19.0027 |
| _version_ | 1798000172737757184 |
|---|---|
| author | Takeru Kameda Akinori Awazu Yuichi Togashi |
| author_facet | Takeru Kameda Akinori Awazu Yuichi Togashi |
| author_sort | Takeru Kameda |
| collection | DOAJ |
| description | With the recent progress in structural biology and genome biology, structural dynamics of molecular systems that include nucleic acids has attracted attention in the context of gene regulation. The structure–function relationship is an important topic that highlights the importance of the physicochemical properties of nucleotides, as well as that of amino acids in proteins. Simulations are a useful tool for the detailed analysis of molecular dynamics that complement experiments in molecular biology; however, molecular simulation of nucleic acids is less well developed than that of proteins partly due to the physical nature of nucleic acids. In this review, we briefly describe the current status and future directions of the field as a guide to promote collaboration between experimentalists and computational biologists. |
| first_indexed | 2024-04-11T11:15:56Z |
| format | Article |
| id | doaj.art-3128a6156d29490b99ef9bbce1bed068 |
| institution | Directory Open Access Journal |
| issn | 2189-4779 |
| language | English |
| last_indexed | 2024-04-11T11:15:56Z |
| publishDate | 2022-09-01 |
| publisher | The Biophysical Society of Japan |
| record_format | Article |
| series | Biophysics and Physicobiology |
| spelling | doaj.art-3128a6156d29490b99ef9bbce1bed0682022-12-22T04:27:12ZengThe Biophysical Society of JapanBiophysics and Physicobiology2189-47792022-09-011910.2142/biophysico.bppb-v19.0027Molecular dynamics analysis of biomolecular systems including nucleic acidsTakeru Kameda0Akinori Awazu1Yuichi Togashi2College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, JapanGraduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, JapanCollege of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, JapanWith the recent progress in structural biology and genome biology, structural dynamics of molecular systems that include nucleic acids has attracted attention in the context of gene regulation. The structure–function relationship is an important topic that highlights the importance of the physicochemical properties of nucleotides, as well as that of amino acids in proteins. Simulations are a useful tool for the detailed analysis of molecular dynamics that complement experiments in molecular biology; however, molecular simulation of nucleic acids is less well developed than that of proteins partly due to the physical nature of nucleic acids. In this review, we briefly describe the current status and future directions of the field as a guide to promote collaboration between experimentalists and computational biologists.https://doi.org/10.2142/biophysico.bppb-v19.0027dna/rnanucleosomemolecular modelingsimulationstructural dynamics |
| spellingShingle | Takeru Kameda Akinori Awazu Yuichi Togashi Molecular dynamics analysis of biomolecular systems including nucleic acids Biophysics and Physicobiology dna/rna nucleosome molecular modeling simulation structural dynamics |
| title | Molecular dynamics analysis of biomolecular systems including nucleic acids |
| title_full | Molecular dynamics analysis of biomolecular systems including nucleic acids |
| title_fullStr | Molecular dynamics analysis of biomolecular systems including nucleic acids |
| title_full_unstemmed | Molecular dynamics analysis of biomolecular systems including nucleic acids |
| title_short | Molecular dynamics analysis of biomolecular systems including nucleic acids |
| title_sort | molecular dynamics analysis of biomolecular systems including nucleic acids |
| topic | dna/rna nucleosome molecular modeling simulation structural dynamics |
| url | https://doi.org/10.2142/biophysico.bppb-v19.0027 |
| work_keys_str_mv | AT takerukameda moleculardynamicsanalysisofbiomolecularsystemsincludingnucleicacids AT akinoriawazu moleculardynamicsanalysisofbiomolecularsystemsincludingnucleicacids AT yuichitogashi moleculardynamicsanalysisofbiomolecularsystemsincludingnucleicacids |