When incubated under simulated microgravity (s-microg), endothelial cells (EC) form tubular structures that resemble vascular intimas. This delayed formation of 3D EC structures begins between the 5th and 7th day of culturing EC under conditions of s-microg, when double-row cell assemblies become visible. With the aim of learning about this initial phase of tubular structure formation, we found that NFkappaBp65 protein content was similar in all cell populations, but gene and protein expression of phosphokinase A catalytic subunit, phosphokinase Calpha, and extracellular signal-regulated kinases 1 and 2 was altered in cells cultured under s-microg. Apoptosis remained below 30% in all EC cultures. In contrast to controls, the 7-day-old s-microg cultures contained 3D aggregates with proliferating cells, enhanced numbers of necrotic cells, and osteopontin-negative EC as well as supernatants with reduced quantities of vascular endothelial growth factor (VEGF), basic fibroblast growth factor (bFGF), soluble TNFRSF5, TNFSF5, intercellular adhesion molecule-1, tumor necrosis factor receptor 2, IL-18, complement C3, and von Willebrand factor. VEGF and/or bFGF (10 ng/mL) application influenced the accumulation of proteins in supernatants more profoundly under 1 g than under s-microg. These findings provide evidence that phosphokinase Calpha plays a key role in tube formation. Improving the interaction of VEGF and/or bFGF with EC under s-microg could enhance the engineering of vascular intimas.