物理化学学报
物理化學學報
물이화학학보
ACTA PHYSICO-CHIMICA SINICA
2015年
2期
384-392
,共9页
朱玉风%曹赞霞%赵立岭%王吉华
硃玉風%曹讚霞%趙立嶺%王吉華
주옥풍%조찬하%조립령%왕길화
FlgM蛋白%固有无序蛋白%分子动力学模拟%温度适应性%结构特征
FlgM蛋白%固有無序蛋白%分子動力學模擬%溫度適應性%結構特徵
FlgM단백%고유무서단백%분자동역학모의%온도괄응성%결구특정
FlgM protein%Intrinsical y disordered protein%Molecular dynamics simulation%Temperature adapting%Structure characteristic
基于分子动力学模拟方法比较了超嗜热菌FlgM蛋白在常温(293 K)和生理温度(358 K)下的结构特征.基于GROMACS软件包,采用OPLS-AA分子力场和TIP3P水模型,对超嗜热菌FlgM蛋白在293和358 K进行了2组独立的长时间分子动力学模拟,每组体系模拟时间为1500 ns.主要分析了两种温度下超嗜热菌FlgM蛋白的二级结构特征、整体构象变化及半无序化区域和结构化区域的构象特征.研究结果表明：在常温下,N端具有一定程度的螺旋成分,但在生理温度下,超嗜热菌FlgM蛋白的结构变得松散,螺旋结构减少,构象稳定性减弱, H1螺旋散开, FlgM蛋白构象灵活性增强,不稳定程度增加.这些不同温度的结构变化说明：半无序化区域(N端)在非结合状态下有一定的螺旋结构,但该段螺旋的稳定性随温度升高而降低.超嗜热菌FlgM蛋白会通过增加结构的无序程度使结构更加灵活,以适应高温,从而使该类固有无序蛋白更好地行使其功能,如提高同其他成分的结合速率等.
基于分子動力學模擬方法比較瞭超嗜熱菌FlgM蛋白在常溫(293 K)和生理溫度(358 K)下的結構特徵.基于GROMACS軟件包,採用OPLS-AA分子力場和TIP3P水模型,對超嗜熱菌FlgM蛋白在293和358 K進行瞭2組獨立的長時間分子動力學模擬,每組體繫模擬時間為1500 ns.主要分析瞭兩種溫度下超嗜熱菌FlgM蛋白的二級結構特徵、整體構象變化及半無序化區域和結構化區域的構象特徵.研究結果錶明：在常溫下,N耑具有一定程度的螺鏇成分,但在生理溫度下,超嗜熱菌FlgM蛋白的結構變得鬆散,螺鏇結構減少,構象穩定性減弱, H1螺鏇散開, FlgM蛋白構象靈活性增彊,不穩定程度增加.這些不同溫度的結構變化說明：半無序化區域(N耑)在非結閤狀態下有一定的螺鏇結構,但該段螺鏇的穩定性隨溫度升高而降低.超嗜熱菌FlgM蛋白會通過增加結構的無序程度使結構更加靈活,以適應高溫,從而使該類固有無序蛋白更好地行使其功能,如提高同其他成分的結閤速率等.
기우분자동역학모의방법비교료초기열균FlgM단백재상온(293 K)화생리온도(358 K)하적결구특정.기우GROMACS연건포,채용OPLS-AA분자력장화TIP3P수모형,대초기열균FlgM단백재293화358 K진행료2조독립적장시간분자동역학모의,매조체계모의시간위1500 ns.주요분석료량충온도하초기열균FlgM단백적이급결구특정、정체구상변화급반무서화구역화결구화구역적구상특정.연구결과표명：재상온하,N단구유일정정도적라선성분,단재생리온도하,초기열균FlgM단백적결구변득송산,라선결구감소,구상은정성감약, H1라선산개, FlgM단백구상령활성증강,불은정정도증가.저사불동온도적결구변화설명：반무서화구역(N단)재비결합상태하유일정적라선결구,단해단라선적은정성수온도승고이강저.초기열균FlgM단백회통과증가결구적무서정도사결구경가령활,이괄응고온,종이사해류고유무서단백경호지행사기공능,여제고동기타성분적결합속솔등.
The aim of this work was to compare the structural characteristics of the FlgM protein from the thermophile aquifex aeolicus at room temperature (293 K) and at the physiological temperature (358 K) using molecular dynamics simulations. Two independent long-time molecular dynamics simulations were performed using the GROMACS software package at 293 and 358 K, respectively. The OPLS-AA force field and the TIP3P water model were used. Each simulation was run for 1500 ns. We mainly analyzed the secondary structural characteristics, the overal conformation variation, the conformational characteristics of a semi-disordered region and the structured region of the FlgM protein at two different temperatures. The results indicate that the helix structure of the N terminal increased at room temperature. The FlgM protein had the fol owing characteristics at the physiological temperature:the structure loosed, the helix structure reduced in size, the conformational stability weakened, the H1 helix spread, the conformational flexibility increased, and the degree of instability increased. In summary, the semi-disordered region (N terminal) formed a helical structure in the unbound state and its stability decreased with an increase in temperature. The FlgM protein adapts to temperature by increasing the degree of disorder, creating a more flexible structure by improving the binding rate.
