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author:

Cui, Xiaochen (Cui, Xiaochen.) [1] | Zheng, Zhuoqi (Zheng, Zhuoqi.) [2] | Rahman, Mueed Ur (Rahman, Mueed Ur.) [3] | Hong, Xiaokun (Hong, Xiaokun.) [4] (Scholars:洪晓昆) | Ji, Xiaoyue (Ji, Xiaoyue.) [5] | Li, Zhengxin (Li, Zhengxin.) [6] | Chen, Hai-Feng (Chen, Hai-Feng.) [7]

Indexed by:

EI Scopus SCIE

Abstract:

Intrinsically disordered proteins (IDPs) lack stable tertiary structures under physiological conditions, yet play key roles in biological processes and associated with human complex diseases. Their conformational characteristics and high content of charged residues make the use of polarizable force fields an advantageous for simulating IDPs. The Drude2019IDP polarizable force field, previously introduced, has demonstrated comprehensive enhancements and improvements in dipeptides, short peptides, and IDPs, achieving a balanced sampling between IDPs and structured proteins. However, the performance in simulating 5 dipeptides was found to be underestimate. Therefore, we individually performed reweighting and grid-based energy correction map (CMAP) optimization for these 5 dipeptides, resulting in the enhanced Drude2019IDPC force field. The performance of Drude2019IDPC was evaluated with 5 dipeptides, 5 disordered short peptides, and a representative IDP. The results demonstrated a marked improvement comparing with original Drude2019IDP. To further substantiate the capabilities of Drude2019IDPC, MD simulation and Markov state model (MSM) were applied to wild type and mutant for insulin, to elucidate the difference of conformational characteristics and transition path. The findings reveal that mutation can maintain the monomorphic characteristics, providing insights for engineered insulin development. These results indicate that Drude2019IDPC could be used to reveal the structure-function relationship for other proteins.

Keyword:

Drude2019IDPC Markov state model Polarizable force field Reweighting optimization

Community:

  • [ 1 ] [Cui, Xiaochen]Shanghai Jiao Tong Univ, Natl Expt Teaching Ctr Life Sci & Biotechnol, Sch Life Sci & Biotechnol, Joint Int Res Lab Metab & Dev Sci,Dept Bioinformat, Shanghai 200240, Peoples R China
  • [ 2 ] [Zheng, Zhuoqi]Shanghai Jiao Tong Univ, Natl Expt Teaching Ctr Life Sci & Biotechnol, Sch Life Sci & Biotechnol, Joint Int Res Lab Metab & Dev Sci,Dept Bioinformat, Shanghai 200240, Peoples R China
  • [ 3 ] [Rahman, Mueed Ur]Shanghai Jiao Tong Univ, Natl Expt Teaching Ctr Life Sci & Biotechnol, Sch Life Sci & Biotechnol, Joint Int Res Lab Metab & Dev Sci,Dept Bioinformat, Shanghai 200240, Peoples R China
  • [ 4 ] [Ji, Xiaoyue]Shanghai Jiao Tong Univ, Natl Expt Teaching Ctr Life Sci & Biotechnol, Sch Life Sci & Biotechnol, Joint Int Res Lab Metab & Dev Sci,Dept Bioinformat, Shanghai 200240, Peoples R China
  • [ 5 ] [Li, Zhengxin]Shanghai Jiao Tong Univ, Natl Expt Teaching Ctr Life Sci & Biotechnol, Sch Life Sci & Biotechnol, Joint Int Res Lab Metab & Dev Sci,Dept Bioinformat, Shanghai 200240, Peoples R China
  • [ 6 ] [Chen, Hai-Feng]Shanghai Jiao Tong Univ, Natl Expt Teaching Ctr Life Sci & Biotechnol, Sch Life Sci & Biotechnol, Joint Int Res Lab Metab & Dev Sci,Dept Bioinformat, Shanghai 200240, Peoples R China
  • [ 7 ] [Hong, Xiaokun]Fuzhou Univ, Coll Biol Sci & Engn, Fuzhou 350116, Fujian, Peoples R China

Reprint 's Address:

  • [Chen, Hai-Feng]Shanghai Jiao Tong Univ, Natl Expt Teaching Ctr Life Sci & Biotechnol, Sch Life Sci & Biotechnol, Joint Int Res Lab Metab & Dev Sci,Dept Bioinformat, Shanghai 200240, Peoples R China

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Source :

INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

ISSN: 0141-8130

Year: 2024

Volume: 280

7 . 7 0 0

JCR@2023

Cited Count:

WoS CC Cited Count:

SCOPUS Cited Count:

ESI Highly Cited Papers on the List: 0 Unfold All

WanFang Cited Count:

Chinese Cited Count:

30 Days PV: 1

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