SURFNET identifies voids between two or more molecules as well as internal cavities and pockets by fitting virtual spheres into the solvent-accessible space between protein atoms.
In this case, mass spectroscopic mapping experiments detected peptides that corresponded to αN-terminal ubiquitination products, as well as isopeptide-linked Ub molecules at internal Lys residues 45, 50, and less frequently to Lys residues 85, 218, 284, and 372 (see Supplementary Fig S7B, caption).
Internal cavitations at the nano/microscale can be utilized in transporting small molecules as well [40-42] [40-42]
Having excluded other options, we then concluded that SM d18 1/17:0 is endogenously present in plasma and we tested other exogenous lipid molecules potentially suitable as internal standards for sphingomyelins (see ESM Fig. S1).
Serial dilutions of plasmid DNA containing the SOX2 and β-actin fragments over eight log scales (10 10 molecules per capillary) were used as internal template standards (calculation via LC quantification software version 3.5; Roche Diagnostics).
In fact, flavonoids are not thought to have been immediately effective as UV protection before the emergence of complex structures allowing for their accumulation in large quantities, and it has been proposed that they were initially used as internal signaling molecules [ 7].
Different computational procedures are compared for numerical solution of equations of motion for molecular dynamics of semi-rigid polymeric molecules with internal coordinates as general variables and an optimal method is proposed.
Because part of a fluid that is forced to move carries along to some extent adjacent parts, viscosity may be thought of as internal friction between the molecules; such friction opposes the development of velocity differences within a fluid.
Overall, the FTIR differences reveal fundamental differences between the structural changes during the primary phototransition of these two ChRs from Chlamydomonas involving the retinylidene chromophore, peptide backbone, Asp/Glu residues, cysteine residues, and internal water molecules as summarized below.
