Coarse-Grained Model of Glycosaminoglycans for Biomolecular Simulations

被引:1
|
作者
Shivgan, Aishwary T. [1 ,2 ]
Marzinek, Jan K. [2 ]
Krah, Alexander [2 ]
Matsudaira, Paul [1 ]
Verma, Chandra S. [1 ,2 ,3 ]
Bond, Peter J. [1 ,2 ]
机构
[1] Natl Univ Singapore, Dept Biol Sci, Singapore 117543, Singapore
[2] Bioinformat Inst A STAR, Singapore 138671, Singapore
[3] Nanyang Technol Univ, Sch Biol Sci, Singapore 637551, Singapore
关键词
FIBROBLAST-GROWTH-FACTOR; MARTINI FORCE-FIELD; FREE-ENERGY CALCULATIONS; CHONDROITIN SULFATE; MOLECULAR-DYNAMICS; ALPHA-INHIBITOR; PROTEIN INTERACTIONS; TRYPSIN-INHIBITOR; CRYSTAL-STRUCTURE; DERMATAN SULFATE;
D O I
10.1021/acs.jctc.3c01088
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
Proteoglycans contain glycosaminoglycans (GAGs) which are negatively charged linear polymers made of repeating disaccharide units of uronic acid and hexosamine units. They play vital roles in numerous physiological and pathological processes, particularly in governing cellular communication and attachment. Depending on their sulfonation state, acetylation, and glycosidic linkages, GAGs belong to different families. The high molecular weight, heterogeneity, and flexibility of GAGs hamper their characterization at atomic resolution, but this may be circumvented via coarse-grained (CG) approaches. In this work, we report a CG model for a library of common GAG types in their isolated or proteoglycan-linked states compatible with version 2.2 (v2.2) of the widely popular CG Martini force field. The model reproduces conformational and thermodynamic properties for a wide variety of GAGs, as well as matching structural and binding data for selected proteoglycan test systems. The parameters developed here may thus be employed to study a range of GAG-containing biomolecular systems, thereby benefiting from the efficiency and broad applicability of the Martini framework.
引用
收藏
页码:3308 / 3321
页数:14
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