Local Mode Analysis: Decoding IR Spectra by Visualizing Molecular Details
文献类型：期刊论文
| 作者 | Massarczyk, M.2; Rudack, T.2; Schlitter, J.2; Kuhne, J.2; Koetting, C.2; Gerwert, K.2,3; Rudack, T.1,3,4; , |
| 刊名 | JOURNAL OF PHYSICAL CHEMISTRY B
 |
| 出版日期 | 2017 |
| 卷号 | 121期号:15页码:3483-3492 |
| 关键词 | Prediction modeling 3 ' untranslated region Alternative polyadenylation Triple-negative breast cancer Lymph node |
| ISSN号 | 1520-6106 |
| DOI | 10.1021/acs.jpcb.6b09343 |
| 文献子类 | Article |
| 英文摘要 | Integration of experimental and computational approaches to investigate chemical reactions in proteins has proven to be very successful. Experimentally, time-resolved FTIR difference-spectroscopy monitors chemical reactions at atomic detail. To, decode detailed structural information encoded in IR spectra, QM/MM calculations are performed. Here, we present a novel method which we call local mode analysis (LMA) for calculating IR spectra and assigning spectral IR-bands on the basis of movements of nuclei and partial charges from just a single QM/MM trajectory. Through LMA the decoding of IR spectra no longer requires several simulations or optimizations. The novel, approach correlates,the motions of atoms Of a single simulation with the corresponding IR bands and provides direct access to the structural information encoded in IR spectra. Either the contributions of a particular atom or atom group to the complete IR spectrum of the molecule are visualized, or an IR-band is selected to visualize the corresponding structural motions. Thus, LMA decodes the detailed information contained in IR spectra and provides an intuitive approach for structural biologists and biochemists The unique feature of LMA is the bidirectional analysis connecting structural details to spectral features and vice versa spectral features to molecular motions. |
| 学科主题 | Chemistry |
| WOS关键词 | N-METHYLACETAMIDE ; DYNAMICS SIMULATIONS ; WATER-MOLECULES ; VIBRATIONAL-SPECTRA ; QM/MM CALCULATIONS ; ARGININE FINGER ; FORCE-FIELD ; PROTEIN ; SPECTROSCOPY ; GTP |
| 语种 | 英语 |
| WOS记录号 | WOS:000400039500026 |
| 出版者 | AMER CHEMICAL SOC |
| 版本 | 出版稿 |
| 源URL | [http://202.127.25.144/handle/331004/1207]  |
| 专题 | 中国科学院上海生命科学研究院营养科学研究所 |
| 作者单位 | 1.Univ Illinois, Beckman Inst Adv Sci & Technol, Champaign, IL 61801 USA; 2.Ruhr Univ Bochum, Dept Biophys, D-44801 Bochum, Germany; 3.Chinese Acad Sci, Max Planck Partner Inst Computat Biol PICB, SIBS, Shanghai 200031, Peoples R China; 4.Univ Illinois, Beckman Inst Adv Sci & Technol, Urbana, IL 61801 USA, |
| 推荐引用方式 GB/T 7714 | Massarczyk, M.,Rudack, T.,Schlitter, J.,et al. Local Mode Analysis: Decoding IR Spectra by Visualizing Molecular Details[J]. JOURNAL OF PHYSICAL CHEMISTRY B,2017,121(15):3483-3492. |
| APA | Massarczyk, M..,Rudack, T..,Schlitter, J..,Kuhne, J..,Koetting, C..,...&,.(2017).Local Mode Analysis: Decoding IR Spectra by Visualizing Molecular Details.JOURNAL OF PHYSICAL CHEMISTRY B,121(15),3483-3492. |
| MLA | Massarczyk, M.,et al."Local Mode Analysis: Decoding IR Spectra by Visualizing Molecular Details".JOURNAL OF PHYSICAL CHEMISTRY B 121.15(2017):3483-3492. |
入库方式： OAI收割
来源：上海营养与健康研究所
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