Forces of the Antigen Antibody Reaction The forces are hydrophobic,and Van der Waals forces which are spherical symmetrical. Hydrogen bonds are also involved which are directional and require matching reactants Antigen and antibody reactions only take place when the epitope and paratope fit tightly. Antigen with four different epitopes 》 The hydrophilic regions of protein surface are the most likely to be antigenic: however the entire exposed surface could be antigenic.Normally the functional epitopes are exposed epitopes and are hydrophilic.These protruding parts of the molecular surface are generally most accessible to antibody molecules. Some components of an epitope are more immunodominant than others.When the epitope is a terminal sequence,the terminal residue of that sequence is almost invariably the immunodominant subunit.Some amino acids contribute to the epitope more than others. Some Amino Acids Are More Important Than Others Since antibodies bind to antigen by noncovalent binding through charged groups and hydrophobi c groups then amino acids like lysine and glutamic id (charged amino acid and alanine leucine,tyrosine,phenylalanine,and valine (hydrophobic amino acids) are important in the formation of the epitope. Table 1 Abbreviations for amino acids. Amino Acid Three-letter One-letter abbreviation Alanine Ala Arginine Arg R Asparagine Asn M Aspartic Acid Asp 0 Asparagine or aspartic acid Asx 6 Cysteine Cys Glutamine GIn Glutamic acid Glu E Glutamine or glutamic acid GIx 10 Glycine Gly Histidine His HForces of the Antigen Antibody Reaction The forces are hydrophobic, and Van der Waals forces which are spherical symmetrical. Hydrogen bonds are also involved which are directional and require matching reactants. Antigen and antibody reactions only take place when the epitope and paratope fit tightly. The hydrophilic regions of protein surface are the most likely to be antigenic; however the entire exposed surface could be antigenic. Normally the functional epitopes are exposed epitopes and are hydrophilic. These protruding parts of the molecular surface are generally most accessible to antibody molecules. Some components of an epitope are more immunodominant than others. When the epitope is a terminal sequence, the terminal residue of that sequence is almost invariably the immunodominant subunit. Some amino acids contribute to the epitope more than others. Some Amino Acids Are More Important Than Others Since antibodies bind to antigen by noncovalent binding through charged groups and hydrophobic groups then amino acids like lysine and glutamic acid (charged amino acids) and alanine leucine, tyrosine, phenylalanine, and valine (hydrophobic amino acids) are important in the formation of the epitope. Table 1 Abbreviations for amino acids. _____________________________________________________________________________ Amino Acid Three-letter One-letter abbreviation symbol _____________________________________________________________________________ 1 Alanine Ala A 2 Arginine Arg R 3 Asparagine Asn N 4 Aspartic Acid Asp D 5 Asparagine or aspartic acid Asx B 6 Cysteine Cys C 7 Glutamine Gln Q 8 Glutamic acid Glu E 9 Glutamine or glutamic acid Glx Z 10 Glycine Gly G 11 Histidine His H