title: Structural basis for regulation of stability and activity in glyceraldehyde-3-phosphate dehydrogenases. Differential scanning calorimetry and molecular dynamics.
abstract: Tissue specific isoforms of human glyceraldehyde-3-phosphate dehydrogenase, somatic (GAPD) and sperm-specific (GAPDS), have been reported to display different levels of both stability and catalytic activity. Here we apply MD simulations to investigate molecular basis of this phenomenon. The protein is a tetramer where each subunit consists of two domains - catalytic and NAD-binding one. We demonstrated key residues responsible for intersubunit and interdomain interactions. Effect of several residues was studied by point mutations. Overall we considered three mutations (Glu96Gln, Glu244Gln and Asp311Asn) disrupting GAPDS-specific salt bridges. Comparison of calculated interaction energies with calorimetric enthalpies confirmed that intersubunit interactions were responsible for enhanced thermostability of GAPDS whereas interdomain interactions had indirect influence on intersubunit contacts. Mutation Asp311Asn was around 10Å far from the active center and corresponded to the closest natural substitution in the isoenzymes. MD simulations revealed that this residue had slight interaction with catalytic residues but influenced the hydrogen bond net and dynamics in active site. These effects can be responsible for a strong influence of this residue on catalytic activity. Overall, our results provide new insight into glyceraldehyde-3-phosphate dehydrogenase structure-function relationships and can be used for the engineering of mutant proteins with modified properties and for development of new inhibitors with indirect influence on the catalytic site.
authors: Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Center, Russian Academy of Sciences, Kazan, Russia. Electronic address: makshakova@gmail.com.
authors: Olga N
authors: ON
authors: Makshakova
authors: Belozersky Institute of Physico-Chemical Biology of Lomonosov Moscow State University, Moscow, Russia.
authors: Pavel I
authors: PI
authors: Semenyuk
authors: Belozersky Institute of Physico-Chemical Biology of Lomonosov Moscow State University, Moscow, Russia.
authors: Mikhail L
authors: ML
authors: Kuravsky
authors: Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Center, Russian Academy of Sciences, Kazan, Russia.
authors: Elena A
authors: EA
authors: Ermakova
authors: Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Center, Russian Academy of Sciences, Kazan, Russia.
authors: Yuriy F
authors: YF
authors: Zuev
authors: Belozersky Institute of Physico-Chemical Biology of Lomonosov Moscow State University, Moscow, Russia.
authors: Vladimir I
authors: VI
authors: Muronetz
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D002152:Calorimetry, Differential Scanning; D002384:Catalysis; D005987:Glyceraldehyde-3-Phosphate Dehydrogenases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D007527:Isoenzymes / Q000737:chemistry / Q000378:metabolism; D008297:Male; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D017354:Point Mutation / Q000235:genetics; D011487:Protein Conformation; D015202:Protein Engineering / Q000379:methods; D055550:Protein Stability; D017422:Sequence Analysis, DNA; D013094:Spermatozoa / Q000201:enzymology*
chemical_list: D007527:Isoenzymes; D005987:Glyceraldehyde-3-Phosphate Dehydrogenases
keywords: Differential scanning calorimetry; Glyceraldehyde-3-phosphate dehydrogenase; Molecular dynamic simulations; Structural factors of stability