Department of Molecular Virology, Immunology and Medical Genetics, The College of Medicine, The Ohio State University, Columbus, OH 43210, USA.
Orig Life Evol Biosph. 2013 Apr;43(2):161-87. doi: 10.1007/s11084-013-9331-8. Epub 2013 May 29.
The distributions of amino acids at most-conserved sites nearest catalytic/active centers (C/AC) in 4,645 sequences of ten enzymes of the glycolytic Embden-Meyerhof-Parnas pathway in Archaea, Bacteria and Eukaryota are similar to the proposed temporal order of their appearance on Earth. Glycine, isoleucine, leucine, valine, glutamic acid and possibly lysine often described as prebiotic, i.e., existing or occurring before the emergence of life, were localized in positional and conservational defined aggregations in all enzymes of all Domains. The distributions of all 20 biologic amino acids in most-conserved sites nearest their C/ACs were quite different either from distributions in sites less-conserved and further from their C/ACs or from all amino acids regardless of their position or conservation. The major concentrations of glycine, e.g., perhaps the earliest prebiotic amino acid, occupies ≈ 16 % of all the most-conserved sites within a volume of ≈ 7-8 Å radius from their C/ACs and decreases linearly towards the molecule's peripheries. Spatially localized major concentrations of isoleucine, leucine and valine are in the mid-conserved and mid-distant sites from their C/ACs in protein interiors. Lysine and glutamic acid comprise ≈ 25-30 % of all amino acids within an irregular volume bounded by ≈ 24-28 Å radii from their C/ACs at the most-distant least-conserved sites. The unreported characteristics of these amino acids: their spatially and conservationally identified concentrations in Archaea, Bacteria and Eukaryota, suggest some common structural organization of glycolytic enzymes that may be relevant to their evolution and that of other proteins. We discuss our data in relation to enzyme evolution, their reported prebiotic putative temporal appearances on Earth, abundances, biological "cost", neighbor-sequence preferences or "ordering" and some thermodynamic parameters.
在古菌、细菌和真核生物中，糖酵解 EMP 途径的 10 种酶的 4645 个序列中，最接近催化/活性中心 (C/AC) 的大多数保守位点的氨基酸分布类似于它们在地球上出现的时间顺序。甘氨酸、异亮氨酸、亮氨酸、缬氨酸、谷氨酸和可能的赖氨酸通常被描述为前生物的，即在生命出现之前存在或发生的，它们在所有领域的所有酶中都定位于位置和保守性定义的聚集处。在最接近其 C/AC 的大多数保守位点的所有 20 种生物氨基酸的分布与在不太保守的位点和离 C/AC 更远的位点以及与所有氨基酸（无论其位置或保守性如何）的分布非常不同。甘氨酸的主要浓度，例如，也许是最早的前生物氨基酸，占据了 ≈ 16%的所有最保守的位点，其体积约为 C/AC 半径的 7-8 Å，并向分子的外围线性减少。在蛋白质内部，异亮氨酸、亮氨酸和缬氨酸的空间局部主要浓度位于中保守和中距离位点，距离 C/AC 较远。赖氨酸和谷氨酸在 C/AC 最远的最不保守位点，在其半径约为 24-28 Å 的不规则体积内约占所有氨基酸的 25-30%。这些氨基酸的未报告特征：它们在古菌、细菌和真核生物中的空间和保守性浓度，表明糖酵解酶具有一些共同的结构组织，这可能与它们的进化以及其他蛋白质的进化有关。我们讨论了我们的数据与酶进化、它们在地球上报告的前生物假定的时间出现、丰度、生物“成本”、邻居序列偏好或“排序”以及一些热力学参数的关系。
