Biology subjects

Mulkidjanian, A. Y.

Publications and source records attributed to Mulkidjanian, A. Y..

5 recordsLinked to original sources

bioRxiv2026

Evolution of membrane rotary ATP synthases: A trade-off between the net productivity and mechanistic stability?

We scrutinized the evolution of rotary membrane ATPases/ATP synthases by combining phylogenomic and comparative structural analyses. Regarding F-type ATPases, we found that organisms with more subunits in the membrane-embedded "proteolipid" c-rings tend to have shorter or absent {delta}-subunits. Organisms with such F-ATPases branch earlier in the phylogenetic tree of catalytic {beta}-subunits. Additionally, we discovered that archaeal-type A-ATPases form at least three distinct branches, including both archaeal and bacterial A-ATPases. This finding suggests that A-ATPase genes have undergone several lateral transfers from archaea to bacteria. We posit that the common ancestor of rotary membrane ATPases possessed six catalytic subunits and over 20 subunits in their Na-transporting c-rings. This ancestor likely had two ion-translocating peripheral stalks and was optimized for low membrane potentials. The loss of half the catalytic subunits, which occurred separately in bacterial and archaeal lineages, enabled the number of c-subunits to be halved without losing efficiency. As cell membranes gained the ability to hold increasingly high membrane voltages, the loss of one of the ion-translocating peripheral stalks, separately in A- and F-ATPases, doubled their efficiency. The mechanism of this loss differed between the two types of ATPases; in F-ATPases, the gain in efficiency came at the cost of mechanistic stability. Thus, the large-scale lateral gene transfer of A-ATPases to bacteria may have been caused by the lower mechanical stability of prokaryotic F-ATPases. The concomitant acquisition of novel subunits resulted in the now-typical Na- and H-transporting A- and F-ATPases geared toward high membrane potentials. Overall, rotary ATP synthases evolved to produce more net ATP.

evolutionary biology↗

bioRxiv2022

Patterns of hydrolysis initiation in P-loop fold nucleoside triphosphatases - united in diversity

In ubiquitous P-loop fold nucleoside triphosphatases (also known as Walker NTPases), hydrolysis of ATP or GTP is initiated by interaction with an activating partner (usually another protein domain), which is accompanied by insertion of stimulatory moiety(ies) (usually arginine or lysine residues) into the catalytic site. After inspecting over 3600 Mg-NTP-containing structures of P-loop NTPases, we identified those with stimulator(s) inserted into catalytic sites and analysed the patterns of stimulatory interactions. In most cases, at least one stimulator twists gamma-phosphate counter-clockwise by linking the oxygen atoms of alpha- and gamma-phosphates; the twisted gamma-phosphate is stabilized by a hydrogen bond with the backbone amino group of the fourth residue of the Walker A motif. In the remaining cases, the stimulators only interact with gamma-phosphate. The ubiquitous mechanistic interaction of diverse stimulators with the gamma phosphate group suggests its twist/rotation as the trigger for NTP hydrolysis.

biochemistry↗

bioRxiv2022

Common mechanism of activated catalysis in P-loop fold nucleoside triphosphatases - in varietate concordia

Though P-loop fold nucleoside triphosphatases (also known as Walker NTPases) are widespread, their catalytic mechanism remains unclear. Based on a comparative structure analysis of 3136 Mg-NTP-containing catalytic sites, we propose a common scheme of activated catalysis for P-loop NTPases. In this scheme, a hydrogen bond (H-bond) between the strictly conserved, Mg-coordinating Ser/Thr of the Walker A motif ([Ser/Thr]WA) and the conserved aspartate of the Walker B motif (AspWB) plays the key role. We found that this H-bond is very short in the structures with bound transition state analogs. Given that a short hydrogen bond (also known as a low-barrier hydrogen bond) implies parity of pK values of the H-bond partners, we suggest that the proton affinities of these two residues reverse upon activation so that the proton relocates from [Ser/Thr]WA to AspWB. The anionic [Ser/Thr]WA alkoxide withdraws then a proton from the would-be nucleophile (either a water molecule or a sugar moiety in some P-loop kinases), and the nascent anion attacks the gamma-phosphate group. When gamma-phosphate breaks away, the trapped proton relays from AspWB, via [Ser/Thr]WA, to beta-phosphate and compensates for its developing negative charge.

biochemistry↗

bioRxiv2021

Spectroscopic glimpses of the transition state of ATP hydrolysis trapped in a bacterial DnaB helicase

The ATP hydrolysis transition state of motor proteins is a weakly populated protein state that can be stabilized and investigated by replacing ATP with chemical mimics. We present atomic-level structural and dynamic insights on a state created by ADP aluminum fluoride binding to the bacterial DnaB helicase from Helicobacter pylori. We determined the positioning of the metal ion cofactor within the active site using electron paramagnetic resonance, and identified the protein protons coordinating to the phosphate groups of ADP and DNA using proton-detected 31P,1H solid-state nuclear magnetic resonance spectroscopy at fast magic-angle spinning > 100 kHz, as well as temperature-dependent proton chemical-shift values to prove their engagements in hydrogen bonds. 19F and 27Al MAS NMR spectra reveal a highly mobile, fast-rotating aluminum fluoride unit pointing to the capture of a late ATP hydrolysis translation state in which the phosphoryl unit is already detached from the arginine and lysine fingers.

biophysics↗

bioRxiv2018

Comparative analysis of active sites in P-loop nucleoside triphosphatases suggests an ancestral activation mechanism

P-loop nucleoside triphosphatases (NTPases) share common Walker A (P-loop) and Walker B sequence motifs and depend on activating moieties (Arg or Lys fingers or a K+ ion). In search for a common catalytic mechanism, we combined structure comparisons of active sites in major classes of P-loop NTPases with molecular dynamics (MD) simulations of the Ras GTPase, a well-studied oncoprotein. Comparative structure analysis showed that positively charged activating moieties interact with gamma-phosphate groups of NTP substrates in all major classes of P-loop NTPases. In MD simulations, interaction of the activating Arg finger with the Mg-GTP-Ras complex led to the rotation of the gamma-phosphate group by 40 degrees enabling its interaction with the backbone amide group of Gly13. In all analyzed structures, the residue that corresponds to Gly13 of Ras was in a position to stabilize gamma-phosphate after its rotation, suggesting a common ancestral activation mechanism within the entire superfamily.

evolutionary biology↗