Measurement of solvent accessibility at protein-protein interfaces.
Methods are presented for monitoring solvent accessibility of protein-ligand and protein-protein interfaces. The kinetics of solvent accessibility at the protein-protein interface is monitored by amide hydrogen/deuterium (H/2H) exchange detected by matrix assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). A straightforward theoretical analysis is presented for determining the concentration of a weakly binding ligand that is required for achieving a situation in which the receptor is essentially 100% bound, and this is verified by control experiments. We show that when the receptor is essentially 100% bound it is possible to distinguish amide exchange as a result of solvent accessibility at the interface from amide exchange caused by complex dissociation. Methods are also presented for the measurement of tightly bound complexes of large interactions such as antibody-antigen complexes. Quantitation of the number of amides sequestered at the interface can be related to the number of H2O molecules excluded from the interface.
Mandell
Jeffrey G
JG
Dept. of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA, USA.
Baerga-Ortiz
Abel
A
Falick
Arnold M
AM
Komives
Elizabeth A
EA
D000577:Amides / Q000737:chemistry; D000936:Antigen-Antibody Complex / Q000737:chemistry / Q000378:metabolism; D003627:Data Interpretation, Statistical; D003903:Deuterium; D006859:Hydrogen; D006863:Hydrogen-Ion Concentration; D066298:In Vitro Techniques; D007700:Kinetics; D008024:Ligands; D010434:Pepsin A; D010446:Peptide Fragments / Q000302:isolation & purification / Q000378:metabolism; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012997:Solvents; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
D000577:Amides; D000936:Antigen-Antibody Complex; D008024:Ligands; D010446:Peptide Fragments; D011506:Proteins; D012997:Solvents; D006859:Hydrogen; D003903:Deuterium; D010434:Pepsin A