Please wait a minute...
Chin. Phys. B, 2022, Vol. 31(6): 068704    DOI: 10.1088/1674-1056/ac560e
INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY Prev   Next  

Force-constant-decayed anisotropic network model: An improved method for predicting RNA flexibility

Wei-Bu Wang(王韦卜)1,†, Xing-Yuan Li(李兴元)1,†, and Ji-Guo Su(苏计国)1,2,‡
1 Key Laboratory for Microstructural Material Physics of Hebei Province, School of Science, Yanshan University, Qinhuangdao 066004, China;
2 The Sixth Laboratory, National Vaccine and Serum Institute, Beijing 101111, China
Abstract  RNA is an important biological macromolecule, which plays an irreplaceable role in many life activities. RNA functions are largely determined by its tertiary structure and the intrinsic dynamics encoded in the structure. Thus, how to effective extract structure-encoded dynamics is of great significance for understanding RNA functions. Anisotropic network model (ANM) is an efficient method to investigate macromolecular dynamical properties, which has been widely used in protein studies. However, the performance of the conventional ANM in describing RNA flexibility is not as good as that on proteins. In this study, we proposed a new approach, named force-constant-decayed anisotropic network model (fcd-ANM), to improve the performance in investigating the dynamical properties encoded in RNA structures. In fcd-ANM, nucleotide pairs in RNA structure were connected by springs and the force constant of springs was decayed exponentially based on the separation distance to describe the differences in the inter-nucleotide interaction strength. The performance of fcd-ANM in predicting RNA flexibility was evaluated using a non-redundant structure database composed of 51 RNAs. The results indicate that fcd-ANM significantly outperforms the conventional ANM in reproducing the experimental B-factors of nucleotides in RNA structures, and the Pearson correlation coefficient between the predicted and experimental nucleotide B-factors was distinctly improved by 21.05% compared to the conventional ANM. Fcd-ANM can serve as a more effective method for analysis of RNA dynamical properties.
Keywords:  anisotropic network model      B-factor      RNA  
Received:  07 January 2022      Revised:  05 February 2022      Accepted manuscript online:  17 February 2022
PACS:  87.15.ad (Analytical theories)  
  87.14.gn (RNA)  
  87.15.hp (Conformational changes)  
Corresponding Authors:  Ji-Guo Su     E-mail:  jiguosu@ysu.edu.cn

Cite this article: 

Wei-Bu Wang(王韦卜), Xing-Yuan Li(李兴元), and Ji-Guo Su(苏计国) Force-constant-decayed anisotropic network model: An improved method for predicting RNA flexibility 2022 Chin. Phys. B 31 068704

[1] Sharp P A 2009 Cell 136 577
[2] Warf M B and Berglund J A 2010 Trends in Biochemical Sciences 35 169
[3] McManus C J and Graveley B R 2011 Current Opinion in Genetics & Development 21 373
[4] Kozak M 2005 Gene 361 13
[5] Mauger D M, Siegfried N A and Weeks K M 2013 FEBS Letters 587 1180
[6] Walter N G 2009 Methods (San Diego, Calif.) 49 85
[7] Lilley D M J 2017 Biochemical Society Transactions 45 683
[8] Serganov A and Nudler E 2013 Cell 152 17
[9] Doudna J A and Cech T R 2002 Nature 418 222
[10] Korostelev A, Ermolenko D N and Noller H F 2008 Current Opinion in Chemical Biology 12 674
[11] Zhuang X, Kim H, Pereira M J B, Babcock H P, Walter N G and Chu S 2002 Science 296 1473
[12] Solem A C, Halvorsen M, Ramos S B V and Laederach A 2015 Wiley Interdisciplinary Reviews: RNA 6 517
[13] Tan Y L, Feng C J, Wang X X, Zhang W B and Tan Z J 2021 Chin. Phys. B 30 28705
[14] Dror R O, Dirks R M, Grossman J P, Xu H and Shaw D E 2012 Annual Review of Biophysics 41 429
[15] Mlýnský V C and Bussi G 2018 The Journal of Physical Chemistry Letters 9 313
[16] Sklenovský P, Florová P, Banaá P, Réblová K, Lankas F, Otyepka M and Sponer J i 2011 Journal of Chemical Theory and Computation 7 2963
[17] Mustoe A M, Brooks C L and Al-Hashimi H M 2014 Annual Review of Biochemistry 83 441
[18] Drozdetski A V, Tolokh I S, Pollack L, Baker N and Onufriev A V 2016 Phys. Rev. Lett. 117 028101
[19] Bao L, Zhang X, Shi Y Z, Wu Y Y and Tan Z J 2017 Biophysical Journal 112 1094
[20] Deng N J and Cieplak P 2010 Biophysical Journal 98 627
[21] Henzler-Wildman K and Kern D 2007 Nature 450 964
[22] Chennubhotla C, Rader A J, Yang L W and Bahar I 2005 Physical Biology 2 S173
[23] Sanejouand Y H 2013 Methods Mol. Biol. 924 601
[24] Tirion M M 1996 Phys. Rev. Lett. 77 1905
[25] Hu G, Michielssens S, Moors S L C and Ceulemans A 2012 Journal of Molecular Graphics and Modelling 34 28
[26] Li X Y, Zhang J C, Zhu Y Y and Su J G 2015 International Journal of Molecular Sciences 16 29383
[27] Yang L, Song G and Jernigan R L 2009 Proteins: Structure, Function, and Bioinformatics 76 164
[28] Soheilifard R, Makarov D E and Rodin G J 2008 Physical Biology 5 026008
[29] Kundu S, Melton J S, Sorensen D C and Phillips Jr G N 2002 Biophysical Journal 83 723
[30] Bahar I, Atilgan A R and Erman B 1997 Folding and Design 2 173
[31] Atilgan A R, Durell S R, Jernigan R L, Demirel M C, Keskin O and Bahar I 2001 Biophysical Journal 80 505
[32] Bahar I, Lezon T R, Bakan A and Shrivastava I H 2010 Chemical Reviews 110 1463
[33] Gur M, Zomot E and Bahar I 2013 The Journal of Chemical Physics 139 121912
[34] Yu M, Chen Y, Wang Z L and Liu Z 2019 Physical Chemistry Chemical Physics 21 5200
[35] Huang Q, Song P, Chen Y, Liu Z and Lai L 2021 The Journal of Physical Chemistry Letters 12 5404
[36] Zimmermann M T and Jernigan R L 2014 RNA 20 792
[37] Wang Y, Rader A J, Bahar I and Jernigan R L 2004 Journal of Structural Biology 147 302
[38] Wang Y and Jernigan R L 2005 Biophysical Journal 89 3399
[39] González Á L, Teixidó J, Borrell J I and Estrada-Tejedor R 2016 PLoS One 11 e0152049
[40] Wang W J and Su J G 2021 Chin. Phys. B 30 058701
[41] Berman H M, Westbrook J, Feng Z, Gilliland G, Bhat T N, Weissig H, Shindyalov I N and Bourne P E 2000 Nucleic Acids Research 28 235
[42] Tama F, Valle M, Frank J and Brooks C L 2003 Proc. Natl. Acad. Sci. USA 100 9319
[43] Leontis N B and Zirbel C L 2012 RNA 3D Structure Analysis and Prediction (Berlin, Heidelberg: Springer) pp. 281-298
[44] Morgan C E, Huang W, Rudin S D, Taylor D J, Kirby J E, Bonomo R A and Yu E W 2020 Mbio 11 e03117
[45] Isami S, Sakamoto N, Nishimori H and Awazu A 2015 PLoS One 10 e0143760
[46] Matsumoto A and Olson W K 2002 Biophysical Journal 83 22
[47] Hu G, He L, Iacovelli F and Falconi M 2017 Molecules 22 145
[48] Jo S, Son J, Lee B H, Dugasani S R, Park S H and Kim M K 2017 RSC Adv. 7 47190
[1] Acoustic propagation uncertainty in internal wave environments using an ocean-acoustic joint model
Fei Gao(高飞), Fanghua Xu(徐芳华), Zhenglin Li(李整林), Jixing Qin(秦继兴), and Qinya Zhang(章沁雅). Chin. Phys. B, 2023, 32(3): 034302.
[2] Long-time evolution of charged grains in plasma under harmonic external force and after being withdrawn
Miao Guan(管苗), Zhi-Dong Chen(陈志东), Meng-Die Li(李梦蝶), Zhong-Mao Liu(刘忠茂), You-Mei Wang(汪友梅), and Ming-Yang Yu(郁明阳). Chin. Phys. B, 2022, 31(2): 025201.
[3] Extraordinary mechanical performance in charged carbyne
Yong-Zhe Guo(郭雍哲), Yong-Heng Wang(汪永珩), Kai Huang(黄凯), Hao Yin(尹颢), and En-Lai Gao(高恩来). Chin. Phys. B, 2022, 31(12): 128102.
[4] RNAGCN: RNA tertiary structure assessment with a graph convolutional network
Chengwei Deng(邓成伟), Yunxin Tang(唐蕴芯), Jian Zhang(张建), Wenfei Li(李文飞), Jun Wang(王骏), and Wei Wang(王炜). Chin. Phys. B, 2022, 31(11): 118702.
[5] Theoretical investigation of ferromagnetic resonance in a ferromagnetic thin film with external stress anisotropy
Jieyu Zhou(周婕妤), Jianhong Rong(荣建红), Huan Wang(王焕), Guohong Yun(云国宏), Yanan Wang(王娅男), and Shufei Zhang(张舒飞). Chin. Phys. B, 2022, 31(1): 017601.
[6] Enhancements of the Gaussian network model in describing nucleotide residue fluctuations for RNA
Wen-Jing Wang(王文静) and Ji-Guo Su(苏计国). Chin. Phys. B, 2021, 30(5): 058701.
[7] Optical polarization characteristics for AlGaN-based light-emitting diodes with AlGaN multilayer structure as well layer
Lu Xue(薛露), Yi Li(李毅), Mei Ge(葛梅), Mei-Yu Wang(王美玉), and You-Hua Zhu(朱友华). Chin. Phys. B, 2021, 30(4): 047802.
[8] Combined effects of carrier scattering and Coulomb screening on photoluminescence in InGaN/GaN quantum well structure with high In content
Rui Li(李睿), Ming-Sheng Xu(徐明升), Peng Wang(汪鹏), Cheng-Xin Wang(王成新), Shang-Da Qu(屈尚达), Kai-Ju Shi(时凯居), Ye-Hui Wei(魏烨辉), Xian-Gang Xu(徐现刚), and Zi-Wu Ji(冀子武). Chin. Phys. B, 2021, 30(4): 047801.
[9] Structural, mechanical, electronic properties, and Debye temperature of quaternary carbide Ti3NiAl2C ceramics under high pressure: A first-principles study
Diyou Jiang(姜迪友), Wenbo Xiao(肖文波), and Sanqiu Liu(刘三秋). Chin. Phys. B, 2021, 30(3): 036202.
[10] Flow separation control over an airfoil using continuous alternating current plasma actuator
Jian-Guo Zheng(郑建国). Chin. Phys. B, 2021, 30(3): 034702.
[11] Internal friction behavior of Zr59Fe18Al10Ni10Nb3 metallic glass under different aging temperatures
Israa Faisal Ghazi, Israa Meften Hashim, Aravindhan Surendar, Nalbiy Salikhovich Tuguz, Aseel M. Aljeboree, Ayad F. Alkaim, and Nisith Geetha. Chin. Phys. B, 2021, 30(2): 026401.
[12] Statistical potentials for 3D structure evaluation: From proteins to RNAs
Ya-Lan Tan(谭雅岚), Chen-Jie Feng(封晨洁), Xunxun Wang(王勋勋), Wenbing Zhang(张文炳), and Zhi-Jie Tan(谭志杰). Chin. Phys. B, 2021, 30(2): 028705.
[13] Band alignment in SiC-based one-dimensional van der Waals homojunctions
Xing-Yi Tan(谭兴毅), Lin-Jie Ding(丁林杰), and Da-Hua Ren(任达华). Chin. Phys. B, 2021, 30(12): 126102.
[14] A review on the design of ternary logic circuits
Xiao-Yuan Wang(王晓媛), Chuan-Tao Dong(董传涛), Zhi-Ru Wu(吴志茹), and Zhi-Qun Cheng(程知群). Chin. Phys. B, 2021, 30(12): 128402.
[15] Broad gain, continuous-wave operation of InP-based quantum cascade laser at λ~11.8 μm
Huan Wang(王欢), Jin-Chuan Zhang(张锦川), Feng-Min Cheng(程凤敏), Zeng-Hui Gu(顾增辉), Ning Zhuo(卓宁), Shen-Qiang Zhai(翟慎强), Feng-Qi Liu(刘峰奇), Jun-Qi Liu(刘俊岐), Shu-Man Liu(刘舒曼), and Zhan-Guo Wang(王占国). Chin. Phys. B, 2021, 30(12): 124202.
No Suggested Reading articles found!