Comparison of metal-binding strength between methionine and cysteine residues: Implications for the design of metal-binding motifs in proteins

• Published in: Biophysical chemistry Vol. 224; pp. 32 - 39
• Main Authors: Krishna Deepak, R.N.V., Chandrakar, Brijesh, Sankararamakrishnan, Ramasubbu
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.05.2017
• Subjects: Binding Sites; Copper - chemistry; Cysteine - chemistry; Design of metal-binding motifs; Drug Design; Metal interactions in proteins; Metal ligand; Metalloproteins - chemistry; Metals - chemistry; Methionine - chemistry; Methionine-metal interactions; Models, Molecular; Protein Interaction Domains and Motifs; Quantum chemical calculations; Quantum Theory; Sulfur as metal ligand; Sulfur as metal ligand; Quantum chemical calculations; Methionine-metal interactions; Metal interactions in proteins; Metal ligand; Design of metal-binding motifs
• ISSN: 0301-4622; 1873-4200
• DOI: 10.1016/j.bpc.2017.02.007

Metals play vital role in various physiological processes and are bound to biomolecules. Although cysteine sulfur is more frequently found as metal-binding ligand, methionine prefers to occur in copper-binding motifs of some proteins. To address methionine's lower preference in copper-binding sites in comparison to cysteine, we have considered copper-binding motifs (His-Cys-His-Met) from seven different high-resolution protein structures. We performed quantum chemical calculations to find out the strength of interactions between sulfur and metal ion in both Met and Cys residues. In the case of Cys, both neutral (CysH) and the deprotonated form (Cys−) were considered. We used two different levels of theory (B3LYP and M06-2X) and the model compounds methyl propyl sulfide, ethanethiol and ethanethiolate were used to represent Met, CysH and Cys− respectively. To compare the metal-binding strength, we mutated Met in silico to CysH/Cys− and performed the calculations. We also carried out calculations with wild-type Cys present in the same metal-binding motif. On average, interactions of Met with copper ion are stronger by 13–35kcal/mol compared to CysH. However, Cys− interactions with copper is stronger than that of Met by ~250kcal/mol. We then considered the entire metal-binding motif with four residues and calculated the interaction energies with the copper ion. We also considered Met→Cys− mutation in the motif and repeated the calculations. Interaction of the wild-type motif with the copper ion is ~160kcal/mol weaker than that of mutated motif. Our studies suggest the factors that could explain why Met is not as frequently observed as Cys in the metal-binding motifs. Results of these studies will help in designing metal-binding motifs in proteins with varying interaction strengths. •Unlike cysteine, methionine is found only in few examples as a ligand in copper-binding sites of some proteins•Quantum chemical calculations were carried out to compare the strength of metal-binding between Met-sulfur and Cys-sulfur•Both neutral Cys (CysH) and its deprotonated form (Cys-) were considered for the calculations•Met-sulfur interacts strongly with copper than that of CysH while the interaction of cysteinate-sulfur is the strongest•Met as a ligand can be used to modulate the strength of metal-binding motifs and can aid in designing new motifs [Display omitted]