Nucleotide-dependent conformational states of actin

Pfaendtner, Jim; Branduardi, Davide; Parrinello, Michele; Pollard, Thomas D.; Voth, Gregory A.

doi:10.1073/pnas.0902092106

Cited by 114 publications

(133 citation statements)

References 50 publications

Supporting

Mentioning

122

Contrasting

Unclassified

Order By: Relevance

“…In the ADA case, assuming that the initial and the final state correspond to ADA with the H3 α-helix in the closed and open conformation, respectively, a PCV is constructed with the cartesian coordinates of the alpha carbons of the residues that determine the α-helix movement. This type of CV has been successfully applied in recent studies on complex protein motion (29,30) and ligand/protein docking (20).…”

Section: Resultsmentioning

confidence: 99%

Sampling protein motion and solvent effect during ligand binding

Limongelli

Marinelli

Cosconati³

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

110

105

View full text Add to dashboard Cite

An exhaustive description of the molecular recognition mechanism between a ligand and its biological target is of great value because it provides the opportunity for an exogenous control of the related process. Very often this aim can be pursued using high resolution structures of the complex in combination with inexpensive computational protocols such as docking algorithms. Unfortunately, in many other cases a number of factors, like protein flexibility or solvent effects, increase the degree of complexity of ligand/protein interaction and these standard techniques are no longer sufficient to describe the binding event. We have experienced and tested these limits in the present study in which we have developed and revealed the mechanism of binding of a new series of potent inhibitors of Adenosine Deaminase. We have first performed a large number of docking calculations, which unfortunately failed to yield reliable results due to the dynamical character of the enzyme and the complex role of the solvent. Thus, we have stepped up the computational strategy using a protocol based on metadynamics. Our approach has allowed dealing with protein motion and solvation during ligand binding and finally identifying the lowest energy binding modes of the most potent compound of the series, 4-decyl-pyrazolo[1,5-a]pyrimidin-7-one.ADA | well-tempered metadynamics | ligand/protein docking | path collective variables | reweighting algorithm A denosine Deaminase (ADA) regulates the purine metabolism by catalyzing the irreversible hydrolysis of adenosine to inosine and 2′-deoxyadenosine to 2′-deoxyinosine. Thus, this enzyme plays a crucial role in many pathologies such as inflammation, some types of cancer, and others which are strictly connected to the physiological level of these nucleosides (1-5). Despite great efforts in developing ADA inhibitors, only Pentostatin is currently in clinical use (I in Fig. S1) (3). However, recent progress has been reported by Terasaka et al. and by some of us who have developed a new generation of nonnucleoside ADA inhibitors (II, III, and IV in Fig. S1) (6-11). Unfortunately, the understanding at molecular level of the ligand/ADA interaction is hampered by the pronounced ability of the active site to accommodate different inhibitors and by the crucial role played by water molecules during ligand binding. A rational drug design is further complicated by the fact that in response to different inhibitors, ADA can assume either an open or a closed conformation by changing the position of the H3 α-helix (Thr57-Ala73). The open conformation corresponds to the apo-form (PDB ID code 3iar) and is preferred when a nonnucleoside inhibitor is bound (12, 13). In this case, the active site presents a hydrophilic subsite S0 and three hydrophobic subsites F0, F1, and F2 (Fig. 1A) (13). The S0 subsite is defined by the structural gate formed by a β-strand (Leu182-Asp185) and two leucine side chains attached to the H3 α-helix while the F0 site is formed by the hydrophobic side chains of the H3 α-helix. In the op...

show abstract

Section: Resultsmentioning

confidence: 99%

Sampling protein motion and solvent effect during ligand binding

Limongelli

Marinelli

Cosconati³

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

110

105

View full text Add to dashboard Cite

show abstract

“…Furthermore, most crystal structures of ADP-actin as well as ATP-actin are in the closed state, with a single exception of the ␤-actin-profilin complex, which was solved in the open conformation (13). A recent report utilizing dynamic fluorescence quenching supports the opening and closing of the cleft upon profilin and cofilin binding, respectively (14), whereas the results of several molecular dynamic simulation studies are inconclusive (1,(15)(16)(17)(18). Thus, it appears that additional experiments involving direct measurements of intercleft distance are required to resolve this ambiguity.…”

mentioning

confidence: 99%

A Nucleotide State-sensing Region on Actin

Kudryashov

Grintsevich

Rubenstein

et al. 2010

Journal of Biological Chemistry

View full text Add to dashboard Cite

The nucleotide state of actin (ATP, ADP-P i , or ADP) is known to impact its interactions with other actin molecules upon polymerization as well as with multiple actin binding proteins both in the monomeric and filamentous states of actin. Recently, molecular dynamics simulations predicted that a sequence located at the interface of subdomains 1 and 3 (W-loop; residues 165-172) changes from an unstructured loop to a ␤-turn conformation upon ATP hydrolysis (Zheng, X., Diraviyam, K., and Sept, D. (2007) Biophys. J. 93, 1277-1283). This region participates directly in the binding to other subunits in F-actin as well as to cofilin, profilin, and WH2 domain proteins and, therefore, could contribute to the nucleotide sensitivity of these interactions. The present study demonstrates a reciprocal communication between the W-loop region and the nucleotide binding cleft on actin. Point mutagenesis of residues 167, 169, and 170 and their site-specific labeling significantly affect the nucleotide release from the cleft region, whereas the ATP/ADP switch alters the fluorescence of probes located in the W-loop. In the ADP-P i state, the W-loop adopts a conformation similar to that in the ATP state but different from the ADP state. Binding of latrunculin A to the nucleotide cleft favors the ATP-like conformation of the W-loop, whereas ADP-ribosylation of Arg-177 forces the W-loop into a conformation distinct from those in the ADP and ATP-states. Overall, our experimental data suggest that the W-loop of actin is a nucleotide sensor, which may contribute to the nucleotide state-dependent changes in F-actin and nucleotide state-modulated interactions of both G-and F-actin with actin-binding proteins.Actin, one of the most abundant and conserved eukaryotic proteins, is involved in a variety of cellular functions, from cell division and migration to intracellular transport and endo-and exocytosis. Under physiological conditions, monomeric actin (G-actin) 3 and filamentous actin (F-actin) are in a dynamic equilibrium, strongly favoring the latter. Very low basal ATPase activity of G-actin is amplified strongly upon its polymerization, and the release of inorganic P i in general follows the polymerization with some delay (2, 3). Consequently, under equilibrium conditions, a typical actin filament contains ATP protomers at the growing end followed by an ADP-P i -enriched region and then by an extended ADP region in the rest of the filament. The nature of the bound nucleotide influences the properties of G-and F-actin and controls their interactions with a number of actin-binding proteins (ABP), which play key regulatory and structural roles in the dynamics and maintenance of the actin cytoskeleton. Nucleotide-sensitive ABPs regulate nucleotide exchange rates and the polymerization of G-actin, the nucleation of new filaments, and disassembly of mature filaments. Thus, preferential binding of the Arp2/3 nucleating complex to ATP and ADP-P i F-actin, cofilin to ADP-F-actin, and profilin to ATP-G-actin leads to the acceleration of directe...

show abstract

“…31), at least one of which (31) resembles the extended D-loop recently observed in F-actin (24). Independent molecular dynamic modeling studies of monomeric actin and trimeric actin (as a model of F-actin) (32)(33)(34) suggest that folded (helical) and unfolded D-loop conformations co-exist in equilibrium in ADP-G-actin, with equivalent free energy, but in the ADP-trimer the folded D-loop is stable at a free energy minimum (34). In addition to and independent of the structural and modeling data, there is considerable biochemical evidence that the nature of the bound nucleotide affects the conformation of the D-loop.…”

Section: Properties Of Purified Mutantmentioning

confidence: 99%

Mutation of Actin Tyr-53 Alters the Conformations of the DNase I-binding Loop and the Nucleotide-binding Cleft

Liu

Shu

Hong

et al. 2010

Journal of Biological Chemistry

View full text Add to dashboard Cite

All but 11 of the 323 known actin sequences have Tyr at position 53, and the 11 exceptions have the conservative substitution Phe, which raises the following questions. What is the critical role(s) of Tyr-53, and, if it can be replaced by Phe, why has this happened so infrequently? We compared the properties of purified endogenous Dictyostelium actin and mutant constructs with Tyr-53 replaced by Phe, Ala, Glu, Trp, and Leu. The Y53F mutant did not differ significantly from endogenous actin in any of the properties assayed, but the Y53A and Y53E mutants differed substantially; affinity for DNase I was reduced, the rate of nucleotide exchange was increased, the critical concentration for polymerization was increased, filament elongation was inhibited, and polymerized actin was in the form of small oligomers and imperfect filaments. Growth and/or development of cells expressing these actin mutants were also inhibited. The Trp and Leu mutations had lesser but still significant effects on cell phenotype and the biochemical properties of the purified actins. We conclude that either

show abstract

Nucleotide-dependent conformational states of actin

Cited by 114 publications

References 50 publications

Sampling protein motion and solvent effect during ligand binding

Sampling protein motion and solvent effect during ligand binding

A Nucleotide State-sensing Region on Actin

Mutation of Actin Tyr-53 Alters the Conformations of the DNase I-binding Loop and the Nucleotide-binding Cleft

Contact Info

Product

Resources

About