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Mechanism of action of cyclophilin a explored by metadynamics simulations.

Leone V, Lattanzi G, Molteni C, Carloni P - PLoS Comput. Biol. (2009)

Bottom Line: Trans/cis prolyl isomerisation is involved in several biological processes, including the development of numerous diseases.In the HIV-1 capsid protein (CA), such a process takes place in the uncoating and recruitment of the virion and is catalyzed by cyclophilin A (CypA).Our results allow us to propose a novel mechanistic hypothesis, which is finally consistent with all of the available molecular biology data.

View Article: PubMed Central - PubMed

Affiliation: International School for Advanced Studies (SISSA), Trieste, Italy.

ABSTRACT
Trans/cis prolyl isomerisation is involved in several biological processes, including the development of numerous diseases. In the HIV-1 capsid protein (CA), such a process takes place in the uncoating and recruitment of the virion and is catalyzed by cyclophilin A (CypA). Here, we use metadynamics simulations to investigate the isomerization of CA's model substrate HAGPIA in water and in its target protein CypA. Our results allow us to propose a novel mechanistic hypothesis, which is finally consistent with all of the available molecular biology data.

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Related in: MedlinePlus

Human CypA in complex with CA.Human CypA is a cytoplasmatic single peptide chain, 165 amino acids long. Top: The X-ray structure shows that it is a β-barrel with eight antiparallel β-strands and two α-helices flanking the β-barrel [13]. These secondary structures are connected by several flexible loops. The β-barrel contains the active site for cis/trans prolyl isomerization. The CA protein is composed by two helices connected by a loop. This contains the G89-P90 target peptide bond (Bottom, right). Bottom, left: Transition state of the cis-trans isomerisation, emerging from this and previous [14],[18],[22] calculations.
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pcbi-1000309-g001: Human CypA in complex with CA.Human CypA is a cytoplasmatic single peptide chain, 165 amino acids long. Top: The X-ray structure shows that it is a β-barrel with eight antiparallel β-strands and two α-helices flanking the β-barrel [13]. These secondary structures are connected by several flexible loops. The β-barrel contains the active site for cis/trans prolyl isomerization. The CA protein is composed by two helices connected by a loop. This contains the G89-P90 target peptide bond (Bottom, right). Bottom, left: Transition state of the cis-trans isomerisation, emerging from this and previous [14],[18],[22] calculations.

Mentions: The best characterized isomerization in vivo and in vitro occurs in the uncoating and recruitment of the human HIV-1 capsid (CA) protein in the virions [7], and it is catalyzed by cyclophilin A isomerase (CypA, [12]). At the structural level, CypA features α-helices flanking a beta-barrel, while CA is made of several α-helices connected by loops (Figure 1). In the X-ray structure of the complex [13], the targeted proline-containing backbone unit (G89-P90), is accommodated in a hydrophobic pocket of CypA (residues F60, F113, L122, and H126 in Figure 1). Although the backbone unit is in trans conformation in the X-ray structure [13], NMR studies have shown that 45% of conformers are cis for CA-CypAR55A in aqueous solution [12]. The rather significant population of cis conformers could arise not only by the replacement of R55 with Ala, but also by crystal packing forces, different temperature conditions (100 K and 298 K for the X-ray and NMR experiments, respectively), along with different hydration and ionic strength in the two experiments. Free energy calculations further support the hypothesis that CypA promotes a significant population of cis conformation [14],[15]. Thus, the cis population is likely to increase substantially from water – where it is ∼10% [12] – to the complex in aqueous solution.


Mechanism of action of cyclophilin a explored by metadynamics simulations.

Leone V, Lattanzi G, Molteni C, Carloni P - PLoS Comput. Biol. (2009)

Human CypA in complex with CA.Human CypA is a cytoplasmatic single peptide chain, 165 amino acids long. Top: The X-ray structure shows that it is a β-barrel with eight antiparallel β-strands and two α-helices flanking the β-barrel [13]. These secondary structures are connected by several flexible loops. The β-barrel contains the active site for cis/trans prolyl isomerization. The CA protein is composed by two helices connected by a loop. This contains the G89-P90 target peptide bond (Bottom, right). Bottom, left: Transition state of the cis-trans isomerisation, emerging from this and previous [14],[18],[22] calculations.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2643488&req=5

pcbi-1000309-g001: Human CypA in complex with CA.Human CypA is a cytoplasmatic single peptide chain, 165 amino acids long. Top: The X-ray structure shows that it is a β-barrel with eight antiparallel β-strands and two α-helices flanking the β-barrel [13]. These secondary structures are connected by several flexible loops. The β-barrel contains the active site for cis/trans prolyl isomerization. The CA protein is composed by two helices connected by a loop. This contains the G89-P90 target peptide bond (Bottom, right). Bottom, left: Transition state of the cis-trans isomerisation, emerging from this and previous [14],[18],[22] calculations.
Mentions: The best characterized isomerization in vivo and in vitro occurs in the uncoating and recruitment of the human HIV-1 capsid (CA) protein in the virions [7], and it is catalyzed by cyclophilin A isomerase (CypA, [12]). At the structural level, CypA features α-helices flanking a beta-barrel, while CA is made of several α-helices connected by loops (Figure 1). In the X-ray structure of the complex [13], the targeted proline-containing backbone unit (G89-P90), is accommodated in a hydrophobic pocket of CypA (residues F60, F113, L122, and H126 in Figure 1). Although the backbone unit is in trans conformation in the X-ray structure [13], NMR studies have shown that 45% of conformers are cis for CA-CypAR55A in aqueous solution [12]. The rather significant population of cis conformers could arise not only by the replacement of R55 with Ala, but also by crystal packing forces, different temperature conditions (100 K and 298 K for the X-ray and NMR experiments, respectively), along with different hydration and ionic strength in the two experiments. Free energy calculations further support the hypothesis that CypA promotes a significant population of cis conformation [14],[15]. Thus, the cis population is likely to increase substantially from water – where it is ∼10% [12] – to the complex in aqueous solution.

Bottom Line: Trans/cis prolyl isomerisation is involved in several biological processes, including the development of numerous diseases.In the HIV-1 capsid protein (CA), such a process takes place in the uncoating and recruitment of the virion and is catalyzed by cyclophilin A (CypA).Our results allow us to propose a novel mechanistic hypothesis, which is finally consistent with all of the available molecular biology data.

View Article: PubMed Central - PubMed

Affiliation: International School for Advanced Studies (SISSA), Trieste, Italy.

ABSTRACT
Trans/cis prolyl isomerisation is involved in several biological processes, including the development of numerous diseases. In the HIV-1 capsid protein (CA), such a process takes place in the uncoating and recruitment of the virion and is catalyzed by cyclophilin A (CypA). Here, we use metadynamics simulations to investigate the isomerization of CA's model substrate HAGPIA in water and in its target protein CypA. Our results allow us to propose a novel mechanistic hypothesis, which is finally consistent with all of the available molecular biology data.

Show MeSH
Related in: MedlinePlus