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Author:

Su, Ji-Guo (Su, Ji-Guo.) | Zhang, Xiao (Zhang, Xiao.) | Han, Xiao-Ming (Han, Xiao-Ming.) | Zhao, Shu-Xin (Zhao, Shu-Xin.) | Li, Chun-Hua (Li, Chun-Hua.) (Scholars:李春华)

Indexed by:

Scopus SCIE PubMed

Abstract:

Antibodies have been increasingly used as pharmaceuticals in clinical treatment. Thermal stability and unfolding process are important properties that must be considered in antibody design. In this paper, the structure-encoded dynamical properties and the unfolding process of the Fab fragment of the phosphocholine-binding antibody McPC603 are investigated by use of the normal mode analysis of Gaussian network model (GNM). Firstly, the temperature factors for the residues of the protein were calculated with GNM and then compared with the experimental measurements. A good result was obtained, which provides the validity for the use of GNM to study the dynamical properties of the protein. Then, with this approach, the mean-square fluctuation (MSF) of the residues, as well as the MSF in the internal distance (MSFID) between all pairwise residues, was calculated to investigate the mobility and flexibility of the protein, respectively. It is found that the mobility and flexibility of the constant regions are higher than those of the variable regions, and the six complementarity-determining regions (CDRs) in the variable regions also exhibit relative large mobility and flexibility. The large amplitude motions of the CDRs are considered to be associated with the immune function of the antibody. In addition, the unfolding process of the protein was simulated by iterative use of the GNM. In our method, only the topology of protein native structure is taken into account, and the protein unfolding process is simulated through breaking the native contacts one by one according to the MSFID values between the residues. It is found that the flexible regions tend to unfold earlier. The sequence of the unfolding events obtained by our method is consistent with the hydrogen-deuterium exchange experimental results. Our studies imply that the unfolding behavior of the Fab fragment of antibody McPc603 is largely determined by the intrinsic dynamics of the protein.

Keyword:

fab fragment of antibody McPC603 intrinsic dynamics native structural topology Gaussian network model unfolding process

Author Community:

  • [ 1 ] [Su, Ji-Guo]Yanshan Univ, Coll Sci, Qinhuangdao 066004, Peoples R China
  • [ 2 ] [Zhang, Xiao]Yanshan Univ, Coll Sci, Qinhuangdao 066004, Peoples R China
  • [ 3 ] [Han, Xiao-Ming]Yanshan Univ, Coll Sci, Qinhuangdao 066004, Peoples R China
  • [ 4 ] [Zhao, Shu-Xin]Yanshan Univ, Coll Sci, Qinhuangdao 066004, Peoples R China
  • [ 5 ] [Li, Chun-Hua]Beijing Univ Technol, Coll Life Sci & Bioengn, Beijing 100024, Peoples R China

Reprint Author's Address:

  • [Su, Ji-Guo]Yanshan Univ, Coll Sci, Qinhuangdao 066004, Peoples R China

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Source :

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

ISSN: 1422-0067

Year: 2015

Issue: 12

Volume: 16

Page: 29720-29731

5 . 6 0 0

JCR@2022

ESI Discipline: CHEMISTRY;

ESI HC Threshold:253

JCR Journal Grade:2

CAS Journal Grade:3

Cited Count:

WoS CC Cited Count: 4

SCOPUS Cited Count: 5

ESI Highly Cited Papers on the List: 0 Unfold All

WanFang Cited Count:

Chinese Cited Count:

30 Days PV: 9

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