title: Smyd3 open & closed lock mechanism for substrate recruitment: The hinge motion of C-terminal domain inferred from μ-second molecular dynamics simulations.
abstract: BACKGROUND
  The human lysine methyltransferase Smyd3, a member of the SET and MYND domain containing protein family, harbors methylation activity on both histone and non-histone targets in a tightly regulated manner. The mechanism of how Smyd3 dynamically regulates substrate recognition is still not fully unveiled.
  
  
  METHODS
  Here, we employed molecular dynamics simulations on full length human Smyd3, performed to a total of 1.2 μ-second, in the presence (holo) and absence (apo) of the S-Adenosyl methionine (AdoMet) cofactor. The dynamical features of Smyd3 in apo and holo states have been examined and compared via examining geometrical and electrostatic properties.
  
  
  RESULTS
  The results show a distinct dynamics of the C-terminal domain (CTD) in the two states. In the apo state, the CTD undergoes a large hinge like motion and samples more opened configurations, thus acting like a loosened clamp and resulting in expanded substrate binding crevice. In the holo state, the CTD exhibits a restricted motion while the overall structure remains compact, mimicking a closed clamp. This leads to a localized increase in the negative potential at the substrate binding cleft. Further, solvent accessibility of critical residues at the target lysine access channel, important for methylation activity, is increased.
  
  
  CONCLUSIONS
  We postulate that AdoMet cofactor acts like a key and locks Smyd3 in a closed conformation. In effect, the cofactor binding restricts the elasticity of the CTD, presenting a compact substrate binding cleft with high negative potential, which may have implications on substrate recruitment via long range electrostatics.
  
  
  CONCLUSIONS
  The deletion of the CTD from Smyd3 has been shown to abolish the basal histone methylation activity. Our study highlights the importance of the CTD elasticity in shaping the substrate binding site for recognition and supports the previously proposed role of the CTD in stabilizing the active site for methylation activity.
authors.affiliation: Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy. Electronic address: bala.chandramouli@sns.it.
authors.forename: Balasubramanian
authors.initials: B
authors.lastname: Chandramouli
authors.affiliation: Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy.
authors.forename: Valentina
authors.initials: V
authors.lastname: Silvestri
authors.affiliation: CINECA, SCAI - SuperComputing Applications and Innovation Department, Via dei Tizii 6, 00185 Rome, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Scarno
authors.affiliation: Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy.
authors.forename: Laura
authors.initials: L
authors.lastname: Ottini
authors.affiliation: CINECA, SCAI - SuperComputing Applications and Innovation Department, Via dei Tizii 6, 00185 Rome, Italy. Electronic address: giochillemi@gmail.com.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Chillemi
mesh_terms: D001665:Binding Sites; D020134:Catalytic Domain; D003067:Coenzymes / Q000737:chemistry / Q000378:metabolism*; D004789:Enzyme Activation; D011495:Histone-Lysine N-Methyltransferase / Q000737:chemistry / Q000378:metabolism*; D006801:Humans; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D012436:S-Adenosylmethionine / Q000737:chemistry / Q000378:metabolism*; D013329:Structure-Activity Relationship; D013379:Substrate Specificity
chemical_list: D003067:Coenzymes; D012436:S-Adenosylmethionine; D011495:Histone-Lysine N-Methyltransferase; C506278:SMYD3 protein, human
keywords: AdoMet; CTD hinge motion; Histone methylation; Lysine methyltransferase; SET and MYND domain; Smyd3