Tavşanlı Ayşenaz, Balta Bülent
Department of Molecular Biology and Genetics, Istanbul Technical University, Maslak 34469 Istanbul, Turkey.
ACS Omega. 2023 Feb 10;8(7):7191-7200. doi: 10.1021/acsomega.3c00212. eCollection 2023 Feb 21.
Cellular prion protein PrP consists of three α-helices, one β-sheet, and an unstructured N-terminal domain. Misfolding of this protein into the scrapie form (PrP) increases dramatically the β-sheet content. H1 is the most stable helix on PrP and contains an unusual number of hydrophilic amino acids. Its fate in PrP is not clear. We performed replica exchange molecular dynamics simulations on H1 alone, H1 together with an N-terminally flanking H1B1 loop and H1 in complex with other hydrophilic regions of the prion protein. In the presence of the HSQWNKPSKPKTNMK sequence, H1 is almost completely converted to a loop structure stabilized by a network of salt bridges. On the other hand, H1 retains its helical structure alone or together with the other sequences considered in this study. We carried out an additional simulation by restraining the distance between the two ends of H1, mimicking a possible geometric restriction by the rest of the protein. Even though the loop was the major conformation, a significant amount of helical structure was also observed. This suggests that the interaction with HSQWNKPSKPKTNMK is necessary for complete helix-to-loop conversion.
细胞朊蛋白PrP由三个α螺旋、一个β折叠和一个无结构的N端结构域组成。该蛋白错误折叠成瘙痒病形式(PrP)会显著增加β折叠含量。H1是PrP上最稳定的螺旋,含有异常数量的亲水性氨基酸。其在PrP中的命运尚不清楚。我们对单独的H1、与N端侧翼H1B1环一起的H1以及与朊蛋白其他亲水区复合的H1进行了复制交换分子动力学模拟。在HSQWNKPSKPKTNMK序列存在的情况下,H1几乎完全转变为通过盐桥网络稳定的环结构。另一方面,H1单独或与本研究中考虑的其他序列一起时保留其螺旋结构。我们通过限制H1两端之间的距离进行了额外的模拟,模拟了蛋白质其余部分可能的几何限制。尽管环是主要构象,但也观察到大量的螺旋结构。这表明与HSQWNKPSKPKTNMK的相互作用对于完全的螺旋到环的转变是必要的。