Heidelberg Institute for Theoretical Studies, Heidelberg, Germany; Hamburg Unit c/o DESY, European Molecular Biology Laboratory, Hamburg, Germany.
Heidelberg Institute for Theoretical Studies, Heidelberg, Germany; Max Planck School Matter-to-Life (MtL), Heidelberg, Germany; Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg, Germany.
Biophys J. 2021 Sep 7;120(17):3544-3549. doi: 10.1016/j.bpj.2021.07.009. Epub 2021 Jul 13.
Type I collagen is the main structural component of many tissues in the human body. It provides excellent mechanical properties to connective tissue and acts as a protein interaction hub. There is thus a wide interest in understanding the properties and diverse functions of type I collagen at the molecular level. A precondition is an atomistic collagen I structure as it occurs in native tissue. To this end, we built full-atom models of cross-linked collagen fibrils by integrating the low-resolution structure of collagen fibril available from x-ray fiber diffraction with high-resolution structures of short collagen-like peptides from x-ray crystallography and mass spectrometry data. We created a Web resource of collagen models for 20 different species with a large variety of cross-link types and localization within the fibril to facilitate structure-based analyses and simulations of type I collagen in health and disease. To easily enable simulations, we provide parameters of the modeled cross-links for an Amber force field. The repository of collagen models is available at https://colbuilder.h-its.org.
I 型胶原蛋白是人体许多组织的主要结构成分。它为结缔组织提供了极好的机械性能，并充当蛋白质相互作用的枢纽。因此，人们广泛关注在分子水平上了解 I 型胶原蛋白的特性和多种功能。一个前提条件是原子 I 型胶原蛋白结构，因为它存在于天然组织中。为此，我们通过将来自 X 射线纤维衍射的胶原纤维的低分辨率结构与来自 X 射线晶体学和质谱数据的短胶原样肽的高分辨率结构整合，构建了交联胶原纤维的全原子模型。我们创建了一个具有 20 种不同物种的胶原模型的网络资源，其中包含大量不同类型的交联和在纤维内的定位，以促进基于结构的 I 型胶原蛋白在健康和疾病中的分析和模拟。为了方便模拟，我们为建模的交联提供了 Amber 力场的参数。胶原模型的存储库可在 https://colbuilder.h-its.org 获得。
