Molecular Dynamics Simulations of the First Steps of the Reaction Catalyzed by HIV-1 Protease

Trylska, Joanna; Bała, Piotr; Geller, Maciej; Grochowski, Paweł

doi:10.1016/s0006-3495(02)75209-0

Cited by 21 publications

(33 citation statements)

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“…The cleavage site has been studied at the DFT-BLYP level of theory with a PW basis set. The two reaction coordinates that were constrained in order to simulate the hydrolysis reaction were (i) the C (SUB) -O (WAT) distance, which has already been suggested in previous studies, 6,7,15 and (ii) the N (INT) -H (Asp25) distance, which has been identified in this work by performing an unbiased scan of the free-energy surface with the CAFES method. 42 The reaction is characterized by two distinct energy barriers, one for the nucleophilic attack of the water molecule (TS1) and the second for the protonation of the peptide bond nitrogen (TS2) that leads A comparison of our QM/MM results with previous studies and with the analogous QM/MM simulations in which the protein electric field is switched off indicates that, at least for the first reaction step, the electrostatic field generated by the residues surrounding the cleavage site plays a fundamental role in stabilizing the Asp dyad.…”

Section: Discussionmentioning

confidence: 99%

“…Previous studies have established that CO ) d(C-(SUB) -O (WAT) ) is an appropriate reaction coordinate for describing this part of the reaction. 6,7,15 For chemical step 2, several reaction coordinates are possible. For this reason, 3.0 ps of QM/MM-CAFES 42 simulation were performed to obtain qualitative information about the possible reaction coordinates.…”

Section: Methodsmentioning

confidence: 99%

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Reaction Mechanism of HIV-1 Protease by Hybrid Car-Parrinello/Classical MD Simulations

et al. 2004

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We present a QM/MM ab initio molecular dynamics study of the peptide hydrolysis reaction catalyzed by HIV-1 protease. The QM/MM calculations are based on previous extensive classical MD simulations on the protein in complex with a model substrate Rothlisberger, U. Protein Sci. 2002, 11, 2393-2402. Gradient-corrected BLYP density functional theory (DFT) describes the reactive part of the active site, and the AMBER force field describes the rest of the protein, the solvent, and the counterions. An unbiased enhanced sampling of the QM/MM free-energy surface is performed to identify a plausible reaction coordinate for the second step of the reaction. The enzymatic reaction is characterized by two reaction freeenergy barriers of ∼18 and ∼21 kcal mol -1 separated by a metastable gem-diol intermediate. In both steps, a proton transfer that involves the substrate and the two catalytic Asp molecules is observed. The orientation and the flexibility of the reactants, governed by the surrounding protein frame, are the key factors in determining the activation barrier. The calculated value for the barrier of the second step is slightly larger than the value expected from experimental data (∼16 kcal mol -1 ). An extensive comparison with calculations on gas-phase model systems at the Hartree-Fock, DFT-BP, DFT-BLYP, DFT-B3LYP, MP2, CCD, and QM/MM DFT-BLYP levels of theory suggests that the DFT-BLYP functional has the tendency to underestimate the energy of the gem-diol intermediate by ∼5-7 kcal mol -1 .The aspartyl protease from human immunodeficiency virus type 1 (HIV-1 PR) targets the AIDS epidemic. The enzyme is essential for viral metabolism 1 because it cleaves the long polypeptide chain that is expressed in infected host cells in specific positions to generate the active proteins that are required for viral maturation.HIV-1 PR is a homodimer with the active site located at the interface between the two subunits. The cleavage site is an Asp dyad (Asp25 and Asp25′, Figure 1), located inside a large activesite pocket that allows the enzyme to recognize and cleave sequences of six amino acids selectively. 2 Several aspects of the enzymatic reaction mechanism have been the focus of a variety of computational techniques, including molecular mechanics, 3-5 tight-binding, 6 semiempirical, 7,8 and ab initio 9-15 methods. This theoretical work has been complemented by kinetic, thermodynamic, and structural data. 8,[16][17][18][19][20][21][22][23][24][25][26][27][28][29] The picture emerging from these studies can be summarized as follows. The free form of the enzyme (E) is stabilized by a low-barrier H bond (LBHB) 30 locking the Asp dyad in an almost coplanar conformation. In a first physical step, E binds to substrate SUB to form the enzyme-substrate complex ESUB, which might (ESUB(a), Figure 1) or might not (ESUB(b), Figure 1) maintain the LBHB. 2 H and 15 N kinetic isotope effect measurements 17,18,28 have established that in HIV-1 PR (i) a hydrated intermediate is reversibly formed and (ii) protonation of the peptide bond nit...

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Reaction Mechanism of HIV-1 Protease by Hybrid Car-Parrinello/Classical MD Simulations

et al. 2004

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“…16 The relatively simple structure of the active site is nevertheless the origin of some problems, which are still the source of many scientific debates. Generally, experimental 17, 18, 19, 20 and theoretical 12, 13, 21, 22, 23, 24 studies have provided evidence that peptide bond breaking is the result of a mechanism where a water molecule is activated by an aspartate residue and it then attacks as a nucleophile on a carbonyl carbon of the substrate peptide chain. Nevertheless, in the past 30 years different mechanisms for the reaction catalyzed by aspartic proteases have been suggested.…”

Section: Introductionmentioning

confidence: 99%

Dynamic and Electrostatic Effects on the Reaction Catalyzed by HIV-1 Protease

2016

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HIV-1 Protease (HIV-1 PR) is one of the three enzymes essential for the replication process of HIV-1 virus, which explains why it has been the main target for design of drugs against acquired immunodeficiency syndrome (AIDS). This work is focused on exploring the proteolysis reaction catalyzed by HIV-1 PR, with special attention to the dynamic and electrostatic effects governing its catalytic power. Free energy surfaces for all possible mechanisms have been computed in terms of potentials of mean force (PMFs) within hybrid QM/MM potentials, with the QM sub-set of atoms described at semiempirical (AM1) and DFT (M06-2X) level. The results suggest that the most favorable reaction mechanism involves formation of a gem-diol intermediate, whose decomposition into the product complex would correspond to the rate-limiting step. The agreement between the activation free energy of this step with experimental data, as well as kinetic isotope effects (KIEs), supports this prediction. The role of the protein dynamic was studied by protein isotope labelling in the framework of the Variational Transition State Theory. The predicted enzyme KIEs, also very close to the values measured experimentally, reveal a measurable but small dynamic effect. Our calculations show how the contribution of dynamic effects to the effective activation free energy appears to be below 1 kcal·mol−1. On the contrary, the electric field created by the protein in the active site of the enzyme emerges as being critical for the electronic reorganization required during the reaction. These electrostatic properties of the active site could be used as a mould for future drug design.

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“…In the QM/MM studies of HIV-1pr, the aspartic dyad and model substrates are usually included in the QM representation. 44,45 These studies were successful in clarifying some fundamental aspects of the substrate cleaving reaction. However, the bottleneck steps of the process are the substrate recognition and binding.…”

Section: Multiscale Modeling Of Proteins Tozzinimentioning

confidence: 99%

Multiscale Modeling of Proteins

2009

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The activity within a living cell is based on a complex network of interactions among biomolecules, exchanging information and energy through biochemical processes. These events occur on different scales, from the nano- to the macroscale, spanning about 10 orders of magnitude in the space domain and 15 orders of magnitude in the time domain. Consequently, many different modeling techniques, each proper for a particular time or space scale, are commonly used. In addition, a single process often spans more than a single time or space scale. Thus, the necessity arises for combining the modeling techniques in multiscale approaches. In this Account, I first review the different modeling methods for bio-systems, from quantum mechanics to the coarse-grained and continuum-like descriptions, passing through the atomistic force field simulations. Special attention is devoted to their combination in different possible multiscale approaches and to the questions and problems related to their coherent matching in the space and time domains. These aspects are often considered secondary, but in fact, they have primary relevance when the aim is the coherent and complete description of bioprocesses. Subsequently, applications are illustrated by means of two paradigmatic examples: (i) the green fluorescent protein (GFP) family and (ii) the proteins involved in the human immunodeficiency virus (HIV) replication cycle. The GFPs are currently one of the most frequently used markers for monitoring protein trafficking within living cells; nanobiotechnology and cell biology strongly rely on their use in fluorescence microscopy techniques. A detailed knowledge of the actions of the virus-specific enzymes of HIV (specifically HIV protease and integrase) is necessary to study novel therapeutic strategies against this disease. Thus, the insight accumulated over years of intense study is an excellent framework for this Account. The foremost relevance of these two biomolecular systems was recently confirmed by the assignment of two of the Nobel prizes in 2008: in chemistry for the discovery of GFP and in medicine for the discovery of HIV. Accordingly, these proteins were studied with essentially all of the available modeling techniques, making them ideal examples for studying the details of multiscale approaches in protein modeling.

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Molecular Dynamics Simulations of the First Steps of the Reaction Catalyzed by HIV-1 Protease

Cited by 21 publications

References 50 publications

Reaction Mechanism of HIV-1 Protease by Hybrid Car-Parrinello/Classical MD Simulations

Reaction Mechanism of HIV-1 Protease by Hybrid Car-Parrinello/Classical MD Simulations

Dynamic and Electrostatic Effects on the Reaction Catalyzed by HIV-1 Protease

Multiscale Modeling of Proteins

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