Department of Pathology, New York Harbor VA Medical Center, 800 Poly Place, Brooklyn, NY 11209, USA.
Protein J. 2013 Jan;32(1):58-67. doi: 10.1007/s10930-012-9459-9.
Using the chain build-up procedure based on the program ECEPP, we have computed the lowest energy structures for two terminally blocked subsequences from the antigenic circumsporozoite protein of Plasmodium berghei, that is known to cause malaria in animals. The full antigenic sequence is an octapeptide proline-rich tandem repeat, (Pro-Pro-Pro-Pro-Asn-Pro-Asn-Asp)(2). We computed the structures for the first octapeptide plus one Pro from the second octapeptide, terminally blocked CH(3)CO-Pro-Pro-Pro-Pro-Asn-Pro-Asn-Asp-Pro-NHCH(3) as well as the first octpeptide with an additional three Pro residues from the adjoining unit, i.e., CH(3)CO-Pro-Pro-Pro-Pro-Asn-Pro-Asn-Asp-Pro-Pro-Pro-NHCH(3). We find that the first sequence adopts a number of different low energy structures, the most probable of which has a probability of occurrence of 56 %. Addition of two more Pro residues results in the adoption a single, unique lowest energy structure that has a probability of occurrence of over 95 % without solvation effects and 86 % when solvation effects are included in the calculations. We predict that this structure may be the one recognized as a major antigenic determinant.
我们使用基于 ECEPP 程序的链增长程序，计算了来自疟原虫环子孢子蛋白的两个末端封闭子序列的最低能量结构，该蛋白已知会导致动物疟疾。完整的抗原序列是一个八肽脯氨酸富含串联重复序列，（Pro-Pro-Pro-Pro-Asn-Pro-Asn-Asp）（2）。我们计算了第一个八肽加第二个八肽中从第一个八肽末端封闭的 CH(3)CO-Pro-Pro-Pro-Pro-Asn-Pro-Asn-Asp-Pro-NHCH(3)以及从相邻单元添加的三个脯氨酸残基的结构，即 CH(3)CO-Pro-Pro-Pro-Pro-Asn-Pro-Asn-Asp-Pro-Pro-Pro-NHCH(3)。我们发现第一个序列采用了许多不同的低能量结构，其中最可能的结构出现的概率为 56%。再添加两个脯氨酸残基导致采用单个独特的最低能量结构，其出现的概率在没有溶剂化效应时超过 95%，在包括溶剂化效应的计算时为 86%。我们预测该结构可能是被识别为主要抗原决定簇的结构。
