{"title":"x射线晶体学和核磁共振残余偶极偶联在蛋白质动力学表征中的协同作用。","authors":"Yang Shen, Ad Bax","doi":"10.1063/4.0000192","DOIUrl":null,"url":null,"abstract":"<p><p>The important role of structural dynamics in protein function is widely recognized. Thermal or B-factors and their anisotropy, seen in x-ray analysis of protein structures, report on the presence of atomic coordinate heterogeneity that can be attributed to motion. However, their quantitative evaluation in terms of protein dynamics by x-ray ensemble refinement remains challenging. NMR spectroscopy provides quantitative information on the amplitudes and time scales of motional processes. Unfortunately, with a few exceptions, the NMR data do not provide direct insights into the atomic details of dynamic trajectories. Residual dipolar couplings, measured by solution NMR, are very precise parameters reporting on the time-averaged bond-vector orientations and may offer the opportunity to derive correctly weighted dynamic ensembles of structures for cases where multiple high-resolution x-ray structures are available. Applications to the SARS-CoV-2 main protease, M<sup>pro</sup>, and ubiquitin highlight this complementarity of NMR and crystallography for quantitative assessment of internal motions.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.3000,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10338066/pdf/","citationCount":"0","resultStr":"{\"title\":\"Synergism between x-ray crystallography and NMR residual dipolar couplings in characterizing protein dynamics.\",\"authors\":\"Yang Shen, Ad Bax\",\"doi\":\"10.1063/4.0000192\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>The important role of structural dynamics in protein function is widely recognized. Thermal or B-factors and their anisotropy, seen in x-ray analysis of protein structures, report on the presence of atomic coordinate heterogeneity that can be attributed to motion. However, their quantitative evaluation in terms of protein dynamics by x-ray ensemble refinement remains challenging. NMR spectroscopy provides quantitative information on the amplitudes and time scales of motional processes. Unfortunately, with a few exceptions, the NMR data do not provide direct insights into the atomic details of dynamic trajectories. Residual dipolar couplings, measured by solution NMR, are very precise parameters reporting on the time-averaged bond-vector orientations and may offer the opportunity to derive correctly weighted dynamic ensembles of structures for cases where multiple high-resolution x-ray structures are available. Applications to the SARS-CoV-2 main protease, M<sup>pro</sup>, and ubiquitin highlight this complementarity of NMR and crystallography for quantitative assessment of internal motions.</p>\",\"PeriodicalId\":48683,\"journal\":{\"name\":\"Structural Dynamics-Us\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":2.3000,\"publicationDate\":\"2023-07-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10338066/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Structural Dynamics-Us\",\"FirstCategoryId\":\"101\",\"ListUrlMain\":\"https://doi.org/10.1063/4.0000192\",\"RegionNum\":2,\"RegionCategory\":\"物理与天体物理\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"CHEMISTRY, PHYSICAL\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Structural Dynamics-Us","FirstCategoryId":"101","ListUrlMain":"https://doi.org/10.1063/4.0000192","RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"CHEMISTRY, PHYSICAL","Score":null,"Total":0}
Synergism between x-ray crystallography and NMR residual dipolar couplings in characterizing protein dynamics.
The important role of structural dynamics in protein function is widely recognized. Thermal or B-factors and their anisotropy, seen in x-ray analysis of protein structures, report on the presence of atomic coordinate heterogeneity that can be attributed to motion. However, their quantitative evaluation in terms of protein dynamics by x-ray ensemble refinement remains challenging. NMR spectroscopy provides quantitative information on the amplitudes and time scales of motional processes. Unfortunately, with a few exceptions, the NMR data do not provide direct insights into the atomic details of dynamic trajectories. Residual dipolar couplings, measured by solution NMR, are very precise parameters reporting on the time-averaged bond-vector orientations and may offer the opportunity to derive correctly weighted dynamic ensembles of structures for cases where multiple high-resolution x-ray structures are available. Applications to the SARS-CoV-2 main protease, Mpro, and ubiquitin highlight this complementarity of NMR and crystallography for quantitative assessment of internal motions.
Structural Dynamics-UsCHEMISTRY, PHYSICALPHYSICS, ATOMIC, MOLECU-PHYSICS, ATOMIC, MOLECULAR & CHEMICAL
CiteScore
5.50
自引率
3.60%
发文量
24
审稿时长
16 weeks
期刊介绍:
Structural Dynamics focuses on the recent developments in experimental and theoretical methods and techniques that allow a visualization of the electronic and geometric structural changes in real time of chemical, biological, and condensed-matter systems. The community of scientists and engineers working on structural dynamics in such diverse systems often use similar instrumentation and methods.
The journal welcomes articles dealing with fundamental problems of electronic and structural dynamics that are tackled by new methods, such as:
Time-resolved X-ray and electron diffraction and scattering,
Coherent diffractive imaging,
Time-resolved X-ray spectroscopies (absorption, emission, resonant inelastic scattering, etc.),
Time-resolved electron energy loss spectroscopy (EELS) and electron microscopy,
Time-resolved photoelectron spectroscopies (UPS, XPS, ARPES, etc.),
Multidimensional spectroscopies in the infrared, the visible and the ultraviolet,
Nonlinear spectroscopies in the VUV, the soft and the hard X-ray domains,
Theory and computational methods and algorithms for the analysis and description of structuraldynamics and their associated experimental signals.
These new methods are enabled by new instrumentation, such as:
X-ray free electron lasers, which provide flux, coherence, and time resolution,
New sources of ultrashort electron pulses,
New sources of ultrashort vacuum ultraviolet (VUV) to hard X-ray pulses, such as high-harmonic generation (HHG) sources or plasma-based sources,
New sources of ultrashort infrared and terahertz (THz) radiation,
New detectors for X-rays and electrons,
New sample handling and delivery schemes,
New computational capabilities.