Protein-protein　interactions　(PPIs)　are　fundamental　to　all　biological　processes.　Recently,　the　CK2　beta-derived　cyclic　peptide　Pc　has　been　demonstrated　to　efficiently　antagonize　the　CK2　alpha/CK2　beta　interaction　and　strongly　affect　the　phosphorylation　of　CK2　beta-dependent　CK2　substrate　specificity.　The　binding　affinity　of　Pc　to　CK2　alpha　is　destroyed　to　different　extents　by　two　single-point　mutations　of　Tyr188　to　Ala　(Upsilon　188A)　and　Phe190　to　Ala　(F190A),　which　exert　negative　effects　on　the　inhibitory　activity　(IC50)　of　Pc　against　the　CK2　alpha/CK2　beta　interaction　from　3.0　mu　M　to　54.0　mu　M　and　＞＞　100　mu　M,　respectively.　However,　the　structural　influences　of　Upsilon　188A　and　F190A　mutations　on　the　CK2　alpha-Pc　complex　remain　unclear.　In　this　study,　comparative　molecular　dynamics　(MD)　simulations,　principal　component　analysis　(PCA),　domain　cross-correlation　map　(DCCM)　analysis　and　energy　calculations　were　performed　on　wild　type　(WT),　Upsilon　188A　mutant,　and　F190A　mutant　systems.　The　results　revealed　that　ordered　communications　between　hydrophobic　and　polar　interactions　were　essential　for　CK2　alpha-Pc　binding　in　the　WT　system.　In　addition　to　the　loss　of　the　hydrogen　bond　between　Gln36　of　CK2　alpha　and　Gly189　of　Pc　in　the　two　mutants,　the　improper　recognition　mechanisms　occurred　through　different　pathways.　These　pathways　included　the　weakened　hydrophobic　interactions　in　the　Upsilon　188A　mutant　as　well　as　decreased　polar　and　hydrophobic　interactions　in　the　F190A　mutant.　The　energy　analysis　results　qualitatively　elucidated　the　instability　of　the　two　mutants　and　energetic　contributions　of　the　key　residues.　This　study　not　only　revealed　the　structural　mechanisms　for　the　decreased　binding　affinity　of　Upsilon　188A　and　F190A　mutant　CK2　alpha-Pc　complexes,　but　also　provided　valuable　clues　for　the　rational　design　of　CK2　alpha/CK2　beta　subunit　interaction　inhibitors　with　high　affinity　and　specificity.