基本信息
邵强  男  硕导  中国科学院上海药物研究所
电子邮件: qshao@simm.ac.cn
通信地址: 中科院上海药物所,张江祖冲之路555号
邮政编码: 201203

研究领域

1. 针对生物体系的理论计算模拟方法发展
  经典的分子模拟可用于多个领域的理论研究,然而其需要的计算资源巨大,计算时间很长。本人开发增强取样的分子动力学模拟方法,加速模拟体系的动态运动过程,从而显著地减少复杂体系的计算时间。目前开发的多个增强取样方法已被成功地应用于生物体系的动态运动(蛋白质折叠、蛋白质功能性构象变化等)的理论模拟。

2. 药物靶标蛋白质的功能性构象变化及与药物分子相互作用机制研究、药物设计
  蛋白质发挥功能时通常伴随着大幅度的构象变化,此外药物分子通过与药物受体(主要是蛋白质)结合进而促进或抑制蛋白质的构象变化并因此改变其生理功能,从而实现对疾病的治疗效果。本人运用自主开发的增强取样分子动力学模拟方法来实现对蛋白质体系的大规模构象变化、蛋白-药物分子相互作用的快速模拟,并将之应用于药物设计研究,为药物设计提供新的研究思路和模拟手段。

3. 蛋白质的折叠、错误折叠机制研究以及蛋白质结构设计
  蛋白质折叠问题被列为“21世纪的生物物理学”的重要课题,是分子生物学中心法则尚未解决的一个重大生物学问题。本人将增强取样的分子模拟方法应用于蛋白质的折叠模拟,预测蛋白质的结构信息,研究氨基酸序列与蛋白质折叠机制的关联性,为蛋白质分子设计提供新颖的信息。

4. 环境因素对蛋白质结构的影响研究
  氨基酸序列决定蛋白质结构,而蛋白质的折叠过程及其结构稳定性亦会受到溶液环境的影响。在蛋白质的体外实验中多种有机小分子与水的共溶剂用于蛋白质的折叠/去折叠研究。本人通过分子动力学模拟研究各种有机共溶剂对蛋白质折叠的热力学、动力学影响,探索外在溶液环境影响蛋白质结构的机制,寻找有利于蛋白质折叠及稳定性的溶液,为实验研究蛋白质折叠、蛋白质结晶提供更有效的溶剂选择。


招生信息

   
招生专业
100720-药物设计学
070320-计算机化学

教育背景

2004-08--2009-12 TexasA&M University, Texas, USA 博士
2003-08--2004-05 College of William & Mary, Virginia, USA 硕士
1999-09--2003-06 南京大学化学与化工学院 研究生毕业
1995-09--1999-06 南京大学化学与化工学院 学士

工作经历

   
工作简历
2011-10--今 中科院上海药物研究所 副研究员
2010-01--2011-09 北京大学化学与分子工程学院 博士后

发表论文

2016年
1. Yu Yuqi, Wang Jinan, Shao Qiang*, Shi Jiye*, Zhu Weiliang*. The effects of organic solvents on the folding pathway and associated thermodynamics of proteins: a microscopic view.  Sci. Rep. 2016, 5:19500.(*通讯作者)

2015年
1. Yang Lijiang, Liu Chengwen, Shao Qiang, Zhang Jun, Gao Yi Qin*. From thermodynamics to kinetics: enhanced sampling of rare events. Acc. Chem. Res. 2015, 48:947-955
2. Yu Yuqi, Wang Jinan, Shao Qiang*, Shi Jiye*, Zhu Weiliang*. Effects of drug-resistant mutations on the dynamic properties of HIV-1 protease and inhibition by Amprenavir and Darunavir. Sci. Rep. 2015, 5:10517.
3. Yu Yuqi, Wang Jinan, Shao Qiang*, Shi Jiye*, Zhu Weiliang*. Increasing the sampling efficiency of protein conformational transition using velocity-scaling optimized hybrid explicit/implicit solvent REMD simulation. J. Chem. Phys. 2015, 142, 125105.
4. Wang Jinan, Shao Qiang*, Crossins Benjamin, Shi Jiye*, Chen Kaixian, Zhu Weiliang*. Thermodynamics calculation of protein-ligand interactions by QM/MM polarizable charge parameters. J. Biomol. Struct. Dyn. 2015, accepted
5. Shao Qiang*. Folding or misfolding: The choice of βhairpin. J. Phys. Chem. B 2015, 119:3893-3900.
6. Shao Qiang*. Important roles of hydrophobic interactions in folding and charge interactions in misfolding of α-helix bundle protein. ASC Adv. 2015, 5, 4191-4199.
7. Xiong Xiuming, Chen Zhaoqiang, Cossins Benjamin, Xu Zhijian, Shao Qiang, Ding K., Zhu Weiliang*, Shi Jiye*. Force fields and scoring functions for carbohydrate simulation. Carbohydr. Res. 2015, 401:73-81.

2014年
1. Wang Jinan, Shao Qiang*, Xu Zhijian, Liu Yingtao, Yang Zhuo, Cossins Benjamin, Jiang Hualiang, Chen Kaixian, Shi Jiye*, Zhu Weiliang*. Exploring transition pathway and free energy profile of large-scale protein conformational change by combining normal mode analysis and umbrella sampling molecular dynamics. J. Phys. Chem. B 2014, 118: 134-143.
2. Wang Jinan, Peng Shaoliang, Cossins Benjamin, Liao Xiangke, Chen Kaixian, Shao Qiang*, Zhu X*, Shi Jiye*, Zhu Weiliang. Mapping central α-helix linker mediated conformational transition pathway of calmodulin via simple computational approach. J. Phys. Chem. B 2014, 118, 9677-9685.
3. Shao Qiang*, Wang Jinan, Zhu Weiliang. On the influence of the mixture of denaturants on protein structure stability: A molecular dynamics study.  Chem. Phys. 2014, 441, 38-46.
4. Shao Qiang*. Probing sequence dependence of folding pathway of α-helix bundle proteins through free energy landscape analysis. J. Phys. Chem. B 2014, 118: 5891-5900.
5. Shao Qiang*. Methanol concentration dependent protein denaturing ability of guanidinium/methanol mixed solution. J. Phys. Chem. B 2014, 118: 6175-6185.
6. Shao Qiang*. The addition of 2,2,2-trifluoroethanol prevents the aggregation of guanidinium around protein and impairs its denaturation ability: A molecular dynamics simulation study. Proteins, 2014, 82: 944-953.

2013年
1. Shao Qiang*, Wang Jinan, Shi Jiye, Zhu Weiliang. The universality of β-hairpin misfolding indicated by molecular dynamics simulations. J. Chem. Phys. 2013, 139: 165103/1-165103/8.
2. Shao Qiang*, Shi Jiye*, Zhu Weiliang. Molecular dynamics simulation indicating cold denaturation of β-hairpins. J. Chem. Phys. 2013, 138: 085102/1-085102/10.
3. Zhang Zhengyan, Xu Zhijian, Yang Zhuo, Liu Yingtao, Wang Jinan, Shao Qiang, Li Shujin, Lu Yunxiang, Zhu Weiliang.* The stabilization effect of dielectric constant and acidic amino acids on arginine-arginine (Arg-Arg) pairings: Database survey and computational studies. J. Phys. Chem. B, 2013, 117: 4827-4835. 
4.  Wu Tianmin, Yang Lijiang, Zhang Ruiting, Shao Qiang, Zhuang Wei.* Modeling the thermal unfolding 2DIR spectra of a β-hairpin peptide based on the implicit solvent MD simulation.  J. Phys. Chem. A, 2013, 117: 6256-6263.
5. Shao Qiang*. On the influence of hydrated imidazolium-based ionic liquid on protein structure stability: A molecular dynamics simulation study. J. Chem. Phys. 2013, 139: 115102/1-115102/8.
6. Wang Jinan, Fulford Tim, Shao Qiang, Javelle Arnaud, Yang Huaiyu, Zhu Weiliang,* Merrick Mike.* Ammonium transport proteins with changes in one of the conserved pore histidines have different performance in ammonia and methylamine conduction. Plos One 2013, 8: e62745


2012年
1. Shao Qiang, Zhu Weiliang, Gao Yi Qin.* Robustness in protein folding revealed by thermodynamics calculation. J. Phys. Chem. B 2012, 116: 13848-13856.
2. Shao Qiang*, Shi Jiye, Zhu Weiliang.* Enhanced sampling molecular dynamics simulation captures experimentally suggested intermediate and unfolded states in the folding pathway of Trp-cage miniprotein. J. Chem. Phys. 2012, 137: 125013/1-125013/10.
3. Shao Qiang*, Gao Yi Qin.* Water plays an important role in osmolyte-induced hairpin structure change: A molecular dynamics simulation study. J. Chem. Phys. 2012, 137: 145101/1-145101/10.
4. Shao Qiang, Fan Yubo, Yang Lijiang, Gao Yi Qin.* Counterion effects on the denaturing activity of guanidinium cation to protein. J. Chem. Theory Comput. 2012, 8: 4364-4373.
5. Shao Qiang, Fan Yubo, Yang Lijiang, Gao Yi Qin.* From protein denaturant to protectant: Comparative molecular dynamics study of alcohol/protein interactions, J. Chem. Phys. 2012, 136, 115101/1-115101/9 (封面文章, research highlights).
6. Lyu Zhi-Xin, Shao Qiang, Gao Yi Qin,* Zhao Xin Sheng.* Direct observation of the uptake of outer membrane proteins by the periplasmic chaperone Skp, Plos One 2012, 7: e46068.
7. Shao Qiang, Gao Yi Qin.* The protein folding mechanism revealed by the folding free energy landscape analysis and denaturation simulations, Curr. Phys. Chem. 2012, 2: 33-44.
8. Yang Lijiang, Shao Qiang, Gao Yi Qin.* Enhanced sampling method in molecular simulations, Prog. Chem. 2012, 24: 1199-1213.

2011年
1. Shao Qiang, Yang Lijiang, Gao Yi Qin.* Structure change of β-hairpin induced by turn optimization: An enhanced sampling molecular dynamics simulation study, J. Chem. Phys. 2011, 135: 235104/1-235104/10.
 
2. Shao Qiang, Gao Yi Qin.* The relative helix and hydrogen bond stability in the B domain of protein A as revealed by ITS MD simulation, J. Chem. Phys. 2011, 135: 135102/1-135102/12.
3. Hwang Soyoun1, Shao Qiang1, Williams Howard, Hilty Christian,* Gao Yi Qin.* Methanol strengthens hydrogen bonds and weakens hydrophobic interactions in proteins-A combined molecular dynamics and NMR study, J. Phys. Chem. B 2011, 115: 6653-6660. (1共同一作)
4. Chen Liuxi, Shao Qiang, Gao Yi Qin, Russell H. David.* A molecular dynamics and ion mobility spectrometry study of modelβ-hairpin peptide, Trpzip1, J. Phys. Chem. A 2011, 115: 4427-4435.

2010年
1. Shao Qiang, Gao Yi Qin.* Temperature dependence of hydrogen-bond stability in β-hairpin structures, J. Chem. Theory Comput. 2010, 6: 3750-3760.
2. Shao Qiang, Wei Haiyan, Gao Yi Qin.* Effects of turn stability and side-chain hydrophobicity on the folding of β-structures, J. Mol. Biol. 2010, 402: 595-609.
3. Wei Haiyan, Shao Qiang, Gao Yi Qin.* The effects of side chain hydrophobicity on the denaturation of simple β-hairpins, Phys. Chem. Chem. Phys. 2010, 12: 9292-9299.
4. Lund Liliya, Fan Yubo, Shao Qiang, Gao Yi Qin,* and Raushel M. Frank.* Carbamate transport in carbamoyl phosphate synthetase: A theoretical and experimental investigation, J. Am. Chem. Soc. 2010, 132: 3870-3878.

2006~2009年
1. Gao Yi Qin,* Shao Qiang The chemomechanical coupling mechanisms of kinesin and dynein, Proteins Energy Heat & Signal Flow 2009, Book chapter.
2.  Fan Yubo, Lund Liliya, Shao Qiang, Gao Yi Qin,* and Raushel M. Frank.* A combined theoretical and experimental study of the ammonia tunnel in carbamoyl phosphate synthetase, J. Am. Chem. Soc. 2009, 131:10211-10219.
3. Shao Qiang, Yang Lijiang, Gao Yi Qin.* A test of implicit solvent models on the folding simulation of the GB1 peptide, J. Chem. Phys. 2009, 130:195104/1-195104/6.
4. Yang Lijiang, Shao Qiang, Gao Yi Qin.* Thermodynamics and folding pathways of trpzip2: An accelerated molecular dynamics simulation study, J. Phys. Chem. B 2009, 113: 803-808.
5. Yang Lijiang, Shao Qiang, Gao Yi Qin.* Comparison between integrated and parallel tempering methods in enhanced sampling simulations, J. Chem. Phys. 2009, 130:124111/1-124111/8.
6. Gao Yi Qin,* Yang Lijiang, Fan Yubo, Shao Qiang. Thermodynamics and kinetics simulations of multi-time-scale processes for complex systems, Int. Rev. Phys. Chem. 2008, 27: 201-227.
7. Shao Qiang, Gao Yi Qin.* Asymmetry in kinesin walking, Biochemistry 2007, 46: 9098-9106.
8. Shao Qiang, Gao Yi Qin.* On the hand-over-hand mechanism of kinesin, Proc. Natl. Acad. Sci. USA 2006, 103: 8072-8077.

科研活动

   
科研项目
(1) 蛋白质大规模构象变化的模拟方法发展及应用研究,主持,国家级,2014-01--2017-12
(2) 蛋白质复合体和膜蛋白结构生物学中的新技术和新方法研究,参与,国家级,2014-01--2018-12
(3) 自组装的理论与模拟,参与,国家级,2011-01--2014-12
(4) 核糖体对新生肽链,蛋白质与蛋白质之间的相互反应对蛋白质的折叠影响的理论模拟研究,主持,国家级,2011-01--2013-12