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Enhancing human spermine synthase activity by engineered mutations.

Zhang Z, Zheng Y, Petukh M, Pegg A, Ikeguchi Y, Alexov E - PLoS Comput. Biol. (2013)

Bottom Line: It is confirmed experimentally that the variant, bearing four amino acid substitutions, is catalytically more active than the wild type.The study demonstrates that wild type SMS is not particularly evolutionarily optimized with respect to the reaction spermidine → spermine.Having in mind that currently there are no variations (non-synonymous single nucleotide polymorphism, nsSNP) detected in healthy individuals, it can be speculated that the human SMS function is precisely tuned toward its wild type and any deviation is unwanted and disease-causing.

View Article: PubMed Central - PubMed

Affiliation: Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, South Carolina, United States of America.

ABSTRACT
Spermine synthase (SMS) is an enzyme which function is to convert spermidine into spermine. It was shown that gene defects resulting in amino acid changes of the wild type SMS cause Snyder-Robinson syndrome, which is a mild-to-moderate mental disability associated with osteoporosis, facial asymmetry, thin habitus, hypotonia, and a nonspecific movement disorder. These disease-causing missense mutations were demonstrated, both in silico and in vitro, to affect the wild type function of SMS by either destabilizing the SMS dimer/monomer or directly affecting the hydrogen bond network of the active site of SMS. In contrast to these studies, here we report an artificial engineering of a more efficient SMS variant by transferring sequence information from another organism. It is confirmed experimentally that the variant, bearing four amino acid substitutions, is catalytically more active than the wild type. The increased functionality is attributed to enhanced monomer stability, lowering the pKa of proton donor catalytic residue, optimized spatial distribution of the electrostatic potential around the SMS with respect to substrates, and increase of the frequency of mechanical vibration of the clefts presumed to be the gates toward the active sites. The study demonstrates that wild type SMS is not particularly evolutionarily optimized with respect to the reaction spermidine → spermine. Having in mind that currently there are no variations (non-synonymous single nucleotide polymorphism, nsSNP) detected in healthy individuals, it can be speculated that the human SMS function is precisely tuned toward its wild type and any deviation is unwanted and disease-causing.

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Related in: MedlinePlus

3D structure of HsSMS dimer in ribbon presentation.Four mutation sites are shown with ball representation: Yellow: S165D; Magenta: C206R; Cyan: L175E; and Orange: T178H.
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pcbi-1002924-g005: 3D structure of HsSMS dimer in ribbon presentation.Four mutation sites are shown with ball representation: Yellow: S165D; Magenta: C206R; Cyan: L175E; and Orange: T178H.

Mentions: The mutant structures were built in silico by side chain replacement through the program SCAP in Jackal package [31]. Several mutant structures were generated in both C chain and D chain: a) the mutant with a single mutation S165D, which is named “SDmut”; b) the mutant with a single mutation C206R, which is named “CRmut”; c) the double mutant with two mutations L175E and T178H together. Making such “PAIR” mutations was prompted by the analysis of multiple sequence alignment (MSA), which will be introduced in a latter section. This mutant is named “Pmut”; d) the mutant with all of the above four mutations S165D, C206R, L175E and T178H. This mutant was named “Fmut”. The mutation sites are shown in Figure 5.


Enhancing human spermine synthase activity by engineered mutations.

Zhang Z, Zheng Y, Petukh M, Pegg A, Ikeguchi Y, Alexov E - PLoS Comput. Biol. (2013)

3D structure of HsSMS dimer in ribbon presentation.Four mutation sites are shown with ball representation: Yellow: S165D; Magenta: C206R; Cyan: L175E; and Orange: T178H.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3585406&req=5

pcbi-1002924-g005: 3D structure of HsSMS dimer in ribbon presentation.Four mutation sites are shown with ball representation: Yellow: S165D; Magenta: C206R; Cyan: L175E; and Orange: T178H.
Mentions: The mutant structures were built in silico by side chain replacement through the program SCAP in Jackal package [31]. Several mutant structures were generated in both C chain and D chain: a) the mutant with a single mutation S165D, which is named “SDmut”; b) the mutant with a single mutation C206R, which is named “CRmut”; c) the double mutant with two mutations L175E and T178H together. Making such “PAIR” mutations was prompted by the analysis of multiple sequence alignment (MSA), which will be introduced in a latter section. This mutant is named “Pmut”; d) the mutant with all of the above four mutations S165D, C206R, L175E and T178H. This mutant was named “Fmut”. The mutation sites are shown in Figure 5.

Bottom Line: It is confirmed experimentally that the variant, bearing four amino acid substitutions, is catalytically more active than the wild type.The study demonstrates that wild type SMS is not particularly evolutionarily optimized with respect to the reaction spermidine → spermine.Having in mind that currently there are no variations (non-synonymous single nucleotide polymorphism, nsSNP) detected in healthy individuals, it can be speculated that the human SMS function is precisely tuned toward its wild type and any deviation is unwanted and disease-causing.

View Article: PubMed Central - PubMed

Affiliation: Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, South Carolina, United States of America.

ABSTRACT
Spermine synthase (SMS) is an enzyme which function is to convert spermidine into spermine. It was shown that gene defects resulting in amino acid changes of the wild type SMS cause Snyder-Robinson syndrome, which is a mild-to-moderate mental disability associated with osteoporosis, facial asymmetry, thin habitus, hypotonia, and a nonspecific movement disorder. These disease-causing missense mutations were demonstrated, both in silico and in vitro, to affect the wild type function of SMS by either destabilizing the SMS dimer/monomer or directly affecting the hydrogen bond network of the active site of SMS. In contrast to these studies, here we report an artificial engineering of a more efficient SMS variant by transferring sequence information from another organism. It is confirmed experimentally that the variant, bearing four amino acid substitutions, is catalytically more active than the wild type. The increased functionality is attributed to enhanced monomer stability, lowering the pKa of proton donor catalytic residue, optimized spatial distribution of the electrostatic potential around the SMS with respect to substrates, and increase of the frequency of mechanical vibration of the clefts presumed to be the gates toward the active sites. The study demonstrates that wild type SMS is not particularly evolutionarily optimized with respect to the reaction spermidine → spermine. Having in mind that currently there are no variations (non-synonymous single nucleotide polymorphism, nsSNP) detected in healthy individuals, it can be speculated that the human SMS function is precisely tuned toward its wild type and any deviation is unwanted and disease-causing.

Show MeSH
Related in: MedlinePlus