title: Studies on the interactions of SAP-1 (an N-terminal truncated form of cystatin S) with its binding partners by CD-spectroscopic and molecular docking methods.
abstract: SAP-1 is a 113 amino acid long single-chain protein which belongs to the type 2 cystatin gene family. In our previous study, we have purified SAP-1 from human seminal plasma and observed its cross-class inhibitory property. At this time, we report the interaction of SAP-1 with diverse proteases and its binding partners by CD-spectroscopic and molecular docking methods. The circular dichroism (CD) spectroscopic studies demonstrate that the conformation of SAP-1 is changed after its complexation with proteases, and the alterations in protein secondary structure are quantitatively calculated with increase of α-helices and reduction of β-strand content. To get insight into the interactions between SAP-1 and proteases, we make an effort to model the three-dimensional structure of SAP-1 by molecular modeling and verify its stability and viability through molecular dynamics simulations and finally complexed with different proteases using ClusPro 2.0 Server. A high degree of shape complementarity is examined within the complexes, stabilized by a number of hydrogen bonds (HBs) and hydrophobic interactions. Using HB analyses in different protein complexes, we have identified a series of key residues that may be involved in the interactions between SAP-1 and proteases. These findings will assist to understand the mechanism of inhibition of SAP-1 for different proteases and provide intimation for further research.
authors.affiliation: a Department of Biophysics , All India Institute of Medical Sciences , Delhi 110029 , India.
authors.forename: Vikash Kumar
authors.initials: VK
authors.lastname: Yadav
authors.forename: Rahul Shubhra
authors.initials: RS
authors.lastname: Mandal
authors.forename: Bhanwar Lal
authors.initials: BL
authors.lastname: Puniya
authors.forename: Sarman
authors.initials: S
authors.lastname: Singh
authors.forename: Savita
authors.initials: S
authors.lastname: Yadav
mesh_terms: D000595:Amino Acid Sequence; D002942:Circular Dichroism / Q000379:methods*; D006801:Humans; D062105:Molecular Docking Simulation / Q000379:methods*; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D011485:Protein Binding; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D055333:Salivary Cystatins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D017386:Sequence Homology, Amino Acid
chemical_list: D055333:Salivary Cystatins
keywords: binding partners; cystatins; docking; homology modeling; papain