Molecular dynamics simulation of HIV-1 protease in a crystalline environment and in solution

A de novo GRIN1 Variant Associated With Myoclonus and Developmental Delay: From Molecular Mechanism to Rescue Pharmacology

N-Methyl-D-aspartate receptors (NMDARs) are highly expressed in brain and play important roles in neurodevelopment and various neuropathologic conditions. Here, we describe a new phenotype in an individual associated with a novel de novo deleterious variant in GRIN1 (c.1595C>A, p.Pro532His). The clinical phenotype is characterized with developmental encephalopathy, striking stimulus-sensitive myoclonus, and frontal lobe and frontal white matter hypoplasia, with no apparent seizures detected. NMDARs that contained the P532H within the glycine-binding domain of GluN1 with either the GluN2A or GluN2B subunits were evaluated for changes in their pharmacological and biophysical properties, which surprisingly revealed only modest changes in glycine potency but a significant decrease in glutamate potency, an increase in sensitivity to endogenous zinc inhibition, a decrease in response to maximally effective concentrations of agonists, a shortened synaptic-like response time course, a decreased channel open probability, and a reduced receptor cell surface expression. Molecule dynamics simulations suggested that the variant can lead to additional interactions across the dimer interface in the agonist-binding domains, resulting in a more open GluN2 agonist-binding domain cleft, which was also confirmed by single-molecule fluorescence resonance energy transfer measurements. Based on the functional deficits identified, several positive modulators were evaluated to explore potential rescue pharmacology.

N6-Adenosine methylation on mRNA is recognized by YTH2 domain protein of human malaria parasite Plasmodium falciparum

Background

Plasmodium falciparum exhibits high translational plasticity during its development in RBCs, yet the regulation at the post-transcriptional level is not well understood. The N⁶-methyl adenosine (m6A) is an important epigenetic modification primarily present on mRNA that controls the levels of transcripts and efficiency of translation in eukaryotes. Recently, the dynamics of m6A on mRNAs at all three developmental stages of P. falciparum in RBCs have been profiled; however, the proteins that regulate the m6A containing mRNAs in the parasites are unknown.

Results

Using sequence analysis, we computationally identified that the P. falciparum genome encodes two putative YTH (YT521-B Homology) domain-containing proteins, which could potentially bind to m6A containing mRNA. We developed a modified methylated RNA immunoprecipitation (MeRIP) assay using PfYTH2 and find that it binds selectively to m6A containing transcripts. The PfYTH2 has a conserved aromatic amino acid cage that forms the methyl-binding pocket. Through site-directed mutagenesis experiments and molecular dynamics simulations, we show that F98 residue is important for m6A binding on mRNA. Fluorescence depolarization assay confirmed that PfYTH2 binds to methylated RNA oligos with high affinity. Further, MeRIP sequencing data revealed that PfYTH2 has more permissive sequence specificity on target m6A containing mRNA than other known eukaryotic YTH proteins. Taken together, here we identify and characterize PfYTH2 as the major protein that could regulate m6A containing transcripts in P. falciparum.

Conclusion

Plasmodium spp. lost the canonical m6A-specific demethylases in their genomes, however, the YTH domain-containing proteins seem to be retained. This study presents a possibility that the YTH proteins are involved in post-transcriptional control in P. falciparum, and might orchestrate the translation of mRNA in various developmental stages of P. falciparum. This is perhaps the first characterization of the methyl-reading function of YTH protein in any parasites.

NMR and MD studies combined to elucidate inhibitor and water interactions of HIV-1 protease and their modulations with resistance mutations

Over the last two decades, both the sensitivity of NMR and the time scale of molecular dynamics (MD) simulation have increased tremendously and have advanced the field of protein dynamics. HIV-1 protease has been extensively studied using these two methods, and has presented a framework for cross-evaluation of structural ensembles and internal dynamics by integrating the two methods. Here, we review studies from our laboratories over the last several years, to understand the mechanistic basis of protease drug-resistance mutations and inhibitor responses, using NMR and crystal structure-based parallel MD simulations. Our studies demonstrate that NMR relaxation experiments, together with crystal structures and MD simulations, significantly contributed to the current understanding of structural/dynamic changes due to HIV-1 protease drug resistance mutations.

Framework for Conducting and Analyzing Crystal Simulations of Nucleic Acids to Aid in Modern Force Field Evaluation

Crystal simulations provide useful tools, along with solution simulations, to test nucleic acid force fields, but should be interpreted with care owing to the difficulty of establishing the environmental conditions needed to reproduce experimental crystal packing. These challenges underscore the need to construct proper protocols for carrying out crystal simulations and analyzing results to identify the origin of deviations from crystallographic data. Toward this end, we introduce a novel framework for B-factor decomposition into additive intramolecular, rotational, and translational atomic fluctuation components and partitioning of each of these components into individual asymmetric unit and lattice contributions. We apply the framework to a benchmark set of A-DNA, Z-DNA, and B-DNA double helix systems of various chain lengths. Overall, the intramolecular deviations from the crystal were quite small (≤1.0 Å), suggesting high accuracy of the force field, whereas crystal packing was not well reproduced. The present work establishes a framework to conduct and analyze crystal simulations that ultimately take on issues of crystal packing and can provide insight into nucleic acid force fields.

Structural pierce into molecular mechanism underlying Clostridium perfringens Epsilon toxin function

Epsilon toxin of the Clostridium perfringens garnered a lot of attention due to its potential for toxicity in humans, extreme potency for cytotoxicity in mice and lack of any approved therapeutics prescribed for human. However, the intricacies of the Epsilon toxin action mechanism are yet to be understood. In this regard, various in silico tools have been exploited to model and refine the 3D structure of the toxin and its two receptors. The receptor proteins were embedded into designed lipid membranes within an aqueous and ionized environment. Thereafter, the modeled structures subjected to series of consecutive molecular dynamics runs to achieve the most natural like coordination for each model. Ultimately, protein-protein interaction analyses were performed to understand the probable action mechanism. The obtained results successfully confirmed the accuracy of employed methods to achieve high quality models for the toxin and its receptors within their lipid bilayers. Molecular dynamics analyses lead the structures to a more native like coordination. Moreover, the results of previous empirical studies were confirmed, while new insights for action mechanisms including the detailed roles of Hepatitis A virus cellular receptor 1 (HAVCR1) and Myelin and lymphocyte protein (MAL) proteins were achieved. In light of previous and our observations, we suggested novel models which elucidated the existing interplay between potential players of Epsilon toxin action mechanism with detailed structural evidences. These models would pave the way to have more robust understanding of the Epsilon toxin biology, more precise vaccine construction and more successful drug (inhibitor) design.

Transporter occluded-state conformation-induced endocytosis: Amino acid transporter ATB0,+-mediated tumor targeting of liposomes for docetaxel delivery for hepatocarcinoma therapy

Rapidly proliferating tumor cells upregulate specific amino acid transporters, which hold great potential for tumor-selective drug delivery. Published reports have focused primarily on blocking these transporters as a means of starving the tumor cells of amino acids, but their potential in drug delivery remains understudied. In the present study, we developed liposomes functionalized with lysine and polyoxyethylene stearate conjugate (LPS) to interact with ATB^0,+, an amino acid transporter overexpressed in hepatocarcinoma and the liver cancer cell line HepG2. The LPS modified liposomes (LPS-Lips) were ~100nm in size and exhibited high drug encapsulation efficiency as 94.7%. The uptake of LPS-Lips in HepG2 cells was dependent on Na⁺ and Cl^-. Molecular dynamic simulation showed that a sustained occluded state of the transporter upon binding to co-transported ions was formed and LPS-Lips triggered the cellular internalization of liposomes. We loaded these LPS-Lips with docetaxel and evaluated the potential of ATB^0,+-mediated endocytosis of the drug-loaded LPS-Lips in HepG2 cells in vitro and in syngeneic mouse transplants in vivo. Compared with unmodified liposomes, which did not interact with ATB^0,+, LPS-Lips exhibited the ability to deliver docetaxel more efficiently into tumor cells with consequent greater antitumor efficacy and less systemic toxicity. These studies provide first evidences that ATB^0,+ can be used as a novel and effective target for drug delivery system in tumor cells using chemically modified liposomes for loading with chemotherapeutics and targeting them for the transporter-mediated endocytosis. As ATB^0,+ is highly upregulated in several cancers, this approach holds potential for tumor-selective delivery of drugs to treat these cancer types.

Understanding the effects on constitutive activation and drug binding of a D130N mutation in the β2 adrenergic receptor via molecular dynamics simulation

G-protein-coupled receptors (GPCRs) are currently one of the largest families of drug targets. The constitutive activation induced by mutation of key GPCR residues is associated closely with various diseases. However, the structural basis underlying such activation and its role in drug binding has remained unclear. Herein, we used all-atom molecular dynamics simulations and free energy calculations to study the effects of a D130N mutation on the structure of β2 adrenergic receptor (β2AR) and its binding of the agonist salbutamol. The results indicate that the mutation caused significant changes in some key helices. In particular, the mutation leads to the departure of transmembrane 3 (TM3) from transmembrane 6 (TM6) and marked changes in the NPxxY region as well as the complete disruption of a key ionic lock, all of which contribute to the observed constitutive activation. In addition, the D130N mutation weakens some important H-bonds, leading to structural changes in these regions. Binding free energy calculations indicate that van der Waals and electrostatic interactions are the main driving forces in binding salbutamol; however, binding strength in the mutant β2AR is significantly enhanced mainly through modifying electrostatic interactions. Further analysis revealed that the increase in binding energy upon mutation stems mainly from the H-bonds formed between the hydroxyl group of salbutamol and the serine residues of TM5. This observation suggests that modifications of the H-bond groups of this drug could significantly influence drug efficacy in the treatment of diseases associated with this mutation.

Antigen exposure leads to rigidification of germline antibody combining site

Immune complexes involving diverse antigens and corresponding antibodies were analyzed for mapping conformational transitions of an antibody before antigen binding, upon antigen binding and after antigen release. Molecular dynamics simulations of the two comprehensive datasets consisting of the antigen-free and antigen-bound structures of the germline antibodies 36-65 and BBE6.12H3 provided mechanistic model of antigen encounter by primary antibodies. While native germline antibodies exhibit substantial mobility in the antigen-combining sites, their antigen-bound states exhibit relatively rigid conformations, even in the absence of the antigen suggesting preservation of the structural state after antigen release. It is proposed that acquired rigidity by a germline antibody upon antigen binding may be the first step in affinity maturation in favor of that antigen.

Inhibition of HIV-1 protease: the rigidity perspective

MOTIVATION

HIV-1 protease is a key drug target due to its role in the life cycle of the HIV-1 virus. Rigidity analysis using the software First is a computationally inexpensive method for inferring functional information from protein crystal structures. We evaluate the rigidity of 206 high-resolution (2 Å or better) X-ray crystal structures of HIV-1 protease and compare the effects of different inhibitors binding to the enzyme.

RESULTS

Inhibitor binding has little effect on the overall rigidity of the protein homodimer, including the rigidity of the active site. The principal effect of inhibitor binding on rigidity is to constrain the flexibility of the β-hairpin flaps, which move to allow access to the active site of the enzyme. We show that commercially available antiviral drugs which target HIV-1 protease can be divided into two classes, those which significantly affect flap rigidity and those which do not. The non-peptidic inhibitor tipranavir is distinctive in its consistently strong effect on flap rigidity.

CONTACT

jack.heal@warwick.ac.uk; r.roemer@warwick.ac.uk

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

An insight into the opening path to semi-open conformation of HIV-1 protease by molecular dynamics simulation

Investigation of the opening process of HIV-1 protease is highly useful for understanding its functional mechanism and substrate/inhibitor binding dynamics, and for facilitating inhibitor drug design. Previous molecular dynamics simulations have revealed some opening paths and conformations, but they appear to be insufficient to explain some experimentally detected opening behaviors. We evaluated the possibility of the existence of alternative opening paths to the semi-open conformation by performing the molecular dynamics simulation of the early opening process of an inhibitor-free HIV-1 protease with explicit solvation. The closed form of the HIV-1 protease transforms to the semi-open form in 2500 ps via a path significantly different from those detected by other reported molecular dynamics simulations of the same protein. Some characteristics of this alternative path are consistent with the experimentally detected opening behavior. Our study combined with earlier studies suggested the existence of multiple opening paths.

Lead expansion and virtual screening of Indinavir derivate HIV-1 protease inhibitors using pharmacophoric - shape similarity scoring function

Indinavir (Crivaxan®) is a potent inhibitor of the HIV (human immunodeficiency virus) protease. This enzyme has an important role in viral replication and is considered to be very attractive target for new antiretroviral drugs. However, it becomes less effective due to highly resistant new viral strains of HIV, which have multiple mutations in their proteases. For this reason, we used a lead expansion method to create a new set of compounds with a new mode of action to protease binding site. 1300 compounds chemically diverse from the initial hit were generated and screened to determine their ability to interact with protease and establish their QSAR properties. Further computational analyses revealed one unique compound with different protease binding ability from the initial hit and its role for possible new class of protease inhibitors is discussed in this report.

(1R, 3S)-(-)-trans-PAT: a novel full-efficacy serotonin 5-HT2C receptor agonist with 5-HT2A and 5-HT2B receptor inverse agonist/antagonist activity

The serotonin 5-HT(2A), 5-HT(2B), and 5-HT(2C) G protein-coupled receptors signal primarily through G alpha(q) to activate phospholipase C (PLC) and formation of inositol phosphates (IP) and diacylglycerol. The human 5-HT(2C) receptor, expressed exclusively in the central nervous system, is involved in several physiological and psychological processes. Development of 5-HT(2C) agonists that do not also activate 5-HT(2A) or 5-HT(2B) receptors is challenging because transmembrane domain identity is about 75% among 5-HT(2) subtypes. This paper reports 5-HT(2) receptor affinity and function of (1R,3S)-(-)-trans-1-phenyl-3-dimethylamino-1,2,3,4-tetrahydronaphthalene (PAT), a small molecule that produces anorexia and weight-loss after peripheral administration to mice. (-)-Trans-PAT is a stereoselective full-efficacy agonist at human 5-HT(2C) receptors, plus, it is a 5-HT(2A)/5-HT(2B) inverse agonist and competitive antagonist. The K(i) of (-)-trans-PAT at 5-HT(2A), 5-HT(2B), and 5-HT(2C) receptors is 410, 1200, and 37 nM, respectively. Functional studies measured activation of PLC/[(3)H]-IP formation in clonal cells expressing human 5-HT(2) receptors. At 5-HT(2C) receptors, (-)-trans-PAT is an agonist (EC(50) = 20 nM) comparable to serotonin in potency and efficacy. At 5-HT(2A) and 5-HT(2B) receptors, (-)-trans-PAT is an inverse agonist (IC(50) = 490 and 1,000 nM, respectively) and competitive antagonist (K(B) = 460 and 1400 nM, respectively) of serotonin. Experimental results are interpreted in light of molecular modeling studies indicating the (-)-trans-PAT protonated amine can form an ionic bond with D3.32 of 5-HT(2A) and 5-HT(2C) receptors, but, not with 5-HT(2B) receptors. In addition to probing 5-HT(2) receptor structure and function, (-)-trans-PAT is a novel lead regarding 5-HT(2C) agonist/5-HT(2A) inverse agonist drug development for obesity and neuropsychiatric disorders.

The solution structure of the simian foamy virus protease reveals a monomeric protein

In contrast to orthoretroviruses, foamy viruses (FVs) express their Pol polyprotein from a separate pol-specific transcript. Only the integrase domain is cleaved off, leading to a protease-reverse transcriptase (PR-RT) protein. We purified the separate PR domain (PRshort) of simian FV from macaques by expressing the recombinant gene in Escherichia coli. Sedimentation analyses and size exclusion chromatography indicate that PRshort is a stable monomer in solution. This allowed us to determine the structure of the PRshort monomer using 1426 experimental restraints derived from NMR spectroscopy. The superposition of 20 conformers resulted in a backbone atom rmsd of 0.55 A for residues Gln8-Leu93. Although the overall folds are similar, the macaque simian FV PRshort reveals significant differences in the dimerization interface relative to other retroviral PRs, such as HIV-1 (human immunodeficiency virus type 1) PR, which appear to be rather stable dimers. Especially the flap region and the N- and C-termini of PRshort are highly flexible. Neglecting these regions, the backbone atom rmsd drops to 0.32 A, highlighting the good definition of the central part of the protein. To exclude that the monomeric state of PRshort is due to cleaving off the RT, we purified the complete PR-RT and performed size exclusion chromatography. Our data show that PR-RT is also monomeric. We thus conclude adoption of a monomeric state of PR-RT to be a regulatory mechanism to inhibit PR activity before virus assembly in order to reduce packaging problems. Dimerization might therefore be triggered by additional viral or cellular factors.

A diverse view of protein dynamics from NMR studies of HIV-1 protease flaps

Internal motion in proteins fulfills a multitude of roles in biological processes. NMR spectroscopy has been applied to elucidate protein dynamics at the atomic level, albeit at a low resolution, and is often complemented by molecular dynamics simulation. However, it is critical to justify the consistency between simulation results and conclusions often drawn from multiple experiments in which uncertainties arising from assumed motional models may not be explicitly evaluated. To understand the role of the flaps of HIV-1 protease dimer in substrate recognition and protease function, many molecular dynamics simulations have been performed. The simulations have resulted in various proposed models of the flap dynamics, some of which are more consistent than others with our working model previously derived from experiments. However, using the working model to discriminate among the simulation results is not straightforward because the working model was derived from a combination of NMR experiments and crystal structure data. In this study, we use the NMR chemical shifts and relaxation data of the protease "monomer" rather than structural data to narrow down the possible conformations of the flaps of the "dimer". For the first time, we show that the tips of the flaps in the unliganded protease dimer interact with each other in solution. Accordingly, we discuss the consistency of the simulations with the model derived from all experimental data.

Solvation influences flap collapse in HIV-1 protease

HIV-1 protease (HIVp) is an important target for the development of therapies to treat AIDS and is one of the classic examples of structure-based drug design. The flap region of HIVp is known to be highly flexible and undergoes a large conformational change upon binding a ligand. Accurately modeling the inherent flexibility of the HIVp system is critical for developing new methods for structure-based drug design. We report several 3-ns molecular dynamics simulations investigating the role of solvation in HIVp flap rearrangement. Using an unliganded crystal structure of HIVp, other groups have observed flap reorganization on the nanosecond timescale. We have also observed rapid, initial flap movement, but we propose that it may be caused by system setup. The initial solvation of the system creates vacuum regions around the protein that may encourage large conformational deformities. By reducing the vacuum space created by the solvation routine, the observed flap collapse is attenuated. Also, a more thorough equilibration procedure preserves a more stable protein conformation over the course of the simulation.

Sampling protein conformations and pathways

Protein flexibility and rigidity can be analyzed using constraint theory, which views proteins as 3D networks of constraints involving covalent bonds and also including hydrophobic interactions and hydrogen bonds. This article describes an algorithm, ROCK (Rigidity Optimized Conformational Kinetics), which generates new conformations for these complex networks with many interlocked rings while maintaining the constraints. These new conformations are tracked for the flexible regions of a protein, while leaving the rigid regions undisturbed. An application to HIV protease demonstrates how large the flap motion can be. The algorithm is also used to generate conformational pathways between two distinct protein conformations. As an example, directed trajectories between the closed and the occluded conformations of the protein dihydrofolate reductase are determined.

Improved prediction of HIV-1 protease-inhibitor binding energies by molecular dynamics simulations

BACKGROUND

The accurate prediction of enzyme-substrate interaction energies is one of the major challenges in computational biology. This study describes the improvement of protein-ligand binding energy prediction by incorporating protein flexibility through the use of molecular dynamics (MD) simulations.

RESULTS

Docking experiments were undertaken using the program AutoDock for twenty-five HIV-1 protease-inhibitor complexes determined by x-ray crystallography. Protein-rigid docking without any dynamics produced a low correlation of 0.38 between the experimental and calculated binding energies. Correlations improved significantly for all time scales of MD simulations of the receptor-ligand complex. The highest correlation coefficient of 0.87 between the experimental and calculated energies was obtained after 0.1 picoseconds of dynamics simulation.

CONCLUSION

Our results indicate that relaxation of protein complexes by MD simulation is useful and necessary to obtain binding energies that are representative of the experimentally determined values.

Correlation between normal modes in the 20-200 cm-1 frequency range and localized torsion motions related to certain collective motions in proteins

In certain biologically relevant collective motions, such as protein domain motions and sub-domain motions, large amplitude movements are localized in one or a few flexible regions consisting of a small number of residues. This paper explores the possible use of normal mode analysis in probing localized vibrational torsion motions in these flexible regions that may be related to certain collective motions. The normal modes of 10 structures of five proteins in different conformation (TRP repressor, calmodulin, calbindin D(9k), HIV-1 protease and troponin C), known to have shear or hinge domain or sub-domain motion, respectively, are analyzed. Our study identifies, for each structure, unique normal modes in the 20-200 cm-1 frequency range, whose corresponding motions are primarily concentrated in the region where large amplitude torsion movements of a known domain or sub-domain motion occur. This suggests possible correlation between normal modes at 20-200 cm-1 frequency range and initial fluctuational motions leading to localized collective motions in proteins, and thus the potential application of normal mode analysis in facilitating the study of biologically important localized motions in biomolecules.

Molecular dynamics simulations of wild-type and point mutation human prion protein at normal and elevated temperature

This paper describes molecular dynamics simulations of prion protein at 300 and 500 K. This was undertaken to gain insight into the factors involved in the stability of prion protein. Simulations were done using the Particle Mesh Ewald (PME) method using a homology model of the C-terminal fragment of human prion protein and the NMR structure of the human prion protein. The simulations at both 300 and 500 K were stable. Simulations were also undertaken with a mutant known to be associated with prion disease: Asp178Asn. The Asp178Asn simulation trajectory was observed to be much less stable than for the wild-type protein trajectory. Significant breakdown in secondary structure was observed for Asp178Asn at 500 K.

Role of conformational fluctuations in the enzymatic reaction of HIV-1 protease

The emergence of compensatory drug-resistant mutations in HIV-1 protease challenges the common view of the reaction mechanism of this enzyme. Here, we address this issue by performing classical and ab initio molecular dynamics simulations (MD) on a complex between the enzyme and a peptide substrate. The classical MD calculation reveals large-scale protein motions involving the flaps and the cantilever. These motions modulate the conformational properties of the substrate at the cleavage site. The ab initio calculations show in turn that substrate motion modulates the activation free energy barrier of the enzymatic reaction dramatically. Thus, the catalytic power of the enzyme does not arise from the presence of a pre-organized active site but from the protein mechanical fluctuations. The implications of this finding for the emergence of drug-resistance are discussed.

Rapid structural fluctuations of the free HIV protease flaps in solution: relationship to crystal structures and comparison with predictions of dynamics calculations

Crystal structures have shown that the HIV-1 protease flaps, domains that control access to the active site, are closed when the active site is occupied by a ligand. Although flap structures ranging from closed to semi-open are observed in the free protease, crystal structures reveal that even the semi-open flaps block access to the active site, indicating that the flaps are mobile in solution. The goals of this paper are to characterize the secondary structure and fast (sub-ns) dynamics of the flaps of the free protease in solution, to relate these results to X-ray structures and to compare them with predictions of dynamics calculations. To this end we have obtained nearly complete backbone and many sidechain signal assignments of a fully active free-protease construct that is stabilized against autoproteolysis by three point mutations. The secondary structure of this protein was characterized using the chemical shift index, measurements of (3h)J(NC') couplings across hydrogen bonds, and NOESY connectivities. Analysis of these measurements indicates that the protease secondary structure becomes irregular near the flap tips, residues 49-53. Model-free analysis of (15)N relaxation parameters, T(1), T(2) (T(1rho)) and (15)N-[(1)H] NOE, shows that residues in the flap tips are flexible on the sub-ns time scale, in contrast with previous observations on the inhibitor-bound protease. These results are compared with theoretical predictions of flap dynamics and the possible biological significance of the sub-ns time scale dynamics of the flap tips is discussed.

The investigation of the effects of counterions in protein dynamics simulations

Molecular simulations able to exactly represent solvated charged proteins are helpful in understanding protein dynamics, structure and function. In the present study we have used two different starting structures of papain (a typical, stable, globular protein of intermediate net charge) and different modeling procedures to evaluate some effects of counterions in simulations. A number of configurations have been generated and relaxed for each system by various combinations of constrained simulated annealing and molecular dynamics procedures, using the AMBER force field. The analysis of trajectories shows that the simulations of solvated proteins are moderately sensitive to the presence of counterions. However, this sensitivity is highly dependent on the starting model and different procedures of equilibration used. The neutralized systems tend to evince smaller root mean square deviations regardless of the system investigated and the simulation procedure used. The results of parameterized fitting of the simulated structures to the crystallographic data, giving quantitative measure of the total charge influence on the stability of various elements of the secondary structure, revealed a clear scatter of different reactions of various systems' secondary structures to counterions addition: some systems apparently were stabilized when neutralized, while the others were not. Thus, one cannot unequivocally state, despite consideration of specific simulation conditions, whether protein secondary structures are more stable when they have neutralized charges. This suggests that caution should be taken when claiming the stabilizing effect of counterions in simulations other than those involving small, unstable polypeptides or highly charged proteins.

1.9 A x-ray study shows closed flap conformation in crystals of tethered HIV-1 PR

Three-dimensional structure of an asymmetrically mutated (C95M) tethered human immunodeficiency virus type 1 protease enzyme (HIV-1 PR) has been determined in an unliganded form using X-ray diffraction data to 1.9 A resolution. The structure, refined using X-PLOR to an R factor of 19.5%, is unexpectedly similar to the ligand-bound native enzyme, rather than to the ligand-free native enzyme. In particular, the two flaps in the tethered dimer are in a closed configuration. The environments around M95 and C1095 are identical, showing no structural effect of this asymmetric mutation at position 95. Oxidation of Cys1095 has been observed for the first time. There is one well-defined water molecule that hydrogen bonds to both carboxyl groups of the essential aspartic acids in the active site. Proteins 2001;43:57-64.

Trp42 rotamers report reduced flexibility when the inhibitor acetyl-pepstatin is bound to HIV-1 protease

The Q7K/L331/L631 HIV-1 protease mutant was expressed in Escherichia coli and the effect of binding a substrate-analog inhibitor, acetyl-pepstatin, was investigated by fluorescence spectroscopy and molecular dynamics. The dimeric enzyme has four intrinsic tryptophans, located at positions 6 and 42 in each monomer. Fluorescence spectra and acrylamide quenching experiments show two differently accessible Trp populations in the apoenzyme with k(q1) = 6.85 x 10(9) M(-1) s(-1) and k(q2) = 1.88 x 10(9) M(-1) s(-1), that merge into one in the complex with k(q) = 1.78 x 10(9) M(-1) s(-1). 500 ps trajectory analysis of Trp X1/X2 rotameric interconversions suggest a model to account for the observed Trp fluorescence. In the simulations, Trp6/Trp6B rotameric interconversions do not occur on this timescale for both HIV forms. In the apoenzyme simulations, however, both Trp42s and Trp42Bs are flipping between X1/X2 states; in the complexed form, no such interconverions occur. A detailed investigation of the local Trp environments sampled during the molecular dynamics simulation suggests that one of the apoenzyme Trp42B rotameric interconversions would allow indole-quencher contact, such as with nearby Tyr59. This could account for the short lifetime component. The model thus interprets the experimental data on the basis of the conformational fluctuations of Trp42s alone. It suggests that the rotameric interconversions of these Trps, located relatively far from the active site and at the very start of the flap region, becomes restrained when the apoenzyme binds the inhibitor. The model is thus consistent with associating components of the fluorescence decay in HIV-1 protease to ground state conformational heterogeneity.

Conformational flexibility of the catalytic Asp dyad in HIV-1 protease: An ab initio study on the free enzyme

The enzyme protease from the human immunodeficiency virus type 1 (HIV-1 PR) is one of the main targets for therapeutic intervention in AIDS. Computer modeling is useful for probing the binding of novel ligands, yet empirical force field-based methods have encountered problems in adequately describing interactions of the catalytic aspartyl pair. In this work we use ab initio dynamic methods to study the molecular interactions and the conformational flexibility of the Asp dyad in the free enzyme. Calculations are performed on model complexes that include, besides the Asp dyad, the conserved Thr26 and Gly27 residues and water molecules present in the active site channel. Our calculations provide proton location and binding mode of the active-site water molecule, which turn out to be different from those of the eukariotic isoenzyme. Furthermore, the calculations reproduce well the structural features of the aspartyl dyad in the protein. Finally, they allow the identification of both dipole/charge interactions and a low-barrier hydrogen bond as important stabilizing factors for the peculiar conformation of the active site. These findings are consistent with site-directed mutagenesis experiments on the 27, 27; positions (Bagossi et al., Protein Eng 1996;9:997-1003). The electric field of the protein frame (included in some of the calculations) does not affect significantly the chemical bonding at the cleavage site. Proteins 2000;39:26-36.

Flap opening and dimer-interface flexibility in the free and inhibitor-bound HIV protease, and their implications for function

BACKGROUND

(1)H and (15)N transverse relaxation measurements on perdeuterated proteins are ideally suited for detecting backbone conformational fluctuations on the millisecond-microsecond timescale. The identification of conformational exchange on this timescale by measuring the relaxation of both (1)H and (15)N holds great promise for the elucidation of functionally relevant conformational changes in proteins.

RESULTS

We measured the transverse (1)H and (15)N relaxation rates of backbone amides of HIV-1 protease in its free and inhibitor-bound forms. An analysis of these rates, obtained as a function of the effective rotating frame field, provided information about the timescale of structural fluctuations in several regions of the protein. The flaps that cover the active site of the inhibitor-bound protein undergo significant changes of backbone (φ,psi) angles, on the 100 micros timescale, in the free protein. In addition, the intermonomer beta-sheet interface of the bound form, which from protease structure studies appears to be rigid, was found to fluctuate on the millisecond timescale.

CONCLUSIONS

We present a working model of the flap-opening mechanism in free HIV-1 protease which involves a transition from a semi-open to an open conformation that is facilitated by interaction of the Phe53 ring with the substrate. We also identify a surprising fluctuation of the beta-sheet intermonomer interface that suggests a structural requirement for maturation of the protease. Thus, slow conformational fluctuations identified by (1)H and (15)N transverse relaxation measurements can be related to the biological functions of proteins.

Reaction path and free energy calculations of the transition between alternate conformations of HIV-1 protease

Two different structures of ligand-free HIV protease have been determined by X-ray crystallography. These structures differ in the position of two 12 residue, beta-hairpin regions (or "flaps") which cap the active site. The movements of the flaps must be involved in the binding of substrates since, in either conformation, the flaps block the binding site. One of these structures is similar to structures of the ligand-bound enzyme; however, the importance of both structures to enzyme function is unclear. This transformation takes place on a time scale too long for conventional molecular dynamics simulations, so the process was studied by first identifying a reaction path between the two structures and then calculating the free energy along this path using umbrella sampling. For the ligand-free enzyme, it is found that the two structures are nearly equally stable, with the ligand-bound-type structure being less stable, consistent with X-ray crystallography data. The more stable open structure does not have a lower potential energy, but is stabilized by entropy. The transition occurs through a collapse and reformation of the beta-sheet structure of the conformationally flexible, glycine-rich flap ends. Additionally, some problems in studying conformational changes in proteins through the use of a single reaction path are addressed.

Importance of explicit salt ions for protein stability in molecular dynamics simulation

The accurate and efficient treatment of electrostatic interactions is one of the challenging problems of molecular dynamics simulation. Truncation procedures such as switching or shifting energies or forces lead to artifacts and significantly reduced accuracy. The particle mesh Ewald (PME) method is one approach to overcome these problems by providing a computationally efficient means of calculating all long-range electrostatic interactions in a periodic simulation box by use of fast Fourier transformation techniques. For the application of the PME method to the simulation of a protein with a net charge in aqueous solution, counterions are added to neutralize the system. The usual procedure is to add charge-balancing counterions close to charged residues to neutralize the protein surface. In the present article, we show that for MD simulation of a small protein of marginal stability, the YAP-WW domain, explicit modeling of 0.2 M ionic strength (in addition to the charge-balancing counterions) is necessary to maintain a stable protein structure. Without explicit ions throughout the periodic simulation box, the charge-balancing counterions on the protein surface diffuse away from the protein, resulting in destruction of the beta-sheet secondary structure of the WW domain.

A further implementation of the rotational symmetry boundary conditions for calculations of P4(3)2(1)2 symmetry crystals

One of the most accurate styles of protein simulation is to calculate proteins in crystalline environment without neglect of long-range interactions. The long-range interactions can be accelerated by various methods. However, as a unit cell of a protein crystal is a large molecular assembly, its simulation is still unpractical without high-speed computers. Thus this article is addressed to the reduction of calculational volumes for protein crystal simulation by a further implementation of the rotational symmetry boundary condition method. For protein crystals in P4(3)2(1)2 symmetry, a computational cell and related tables were developed. A 120-ps molecular dynamics simulation was performed for a P4(3)2(1)2 symmetry crystal of glycogen phosphorylase b under rotational symmetry boundary conditions. The computational cell was one-eighth of the unit cell in volume, and less than about one-fourth of the conventional periodic boundary box. Generation of neighbor atom pair lists was greatly accelerated, and thus the simulation was practical even with a personal computer.

Analysis of the structure of chemically synthesized HIV-1 protease complexed with a hexapeptide inhibitor. Part I: Crystallographic refinement of 2 A data

The structure of a complex between a hexapeptide-based inhibitor, MVT-101, and the chemically synthesized (Aba 67,95,167,195; Aba: L-alpha-amino-n-butyric acid) protease from the human immunodeficiency virus (HIV-1), reported previously at 2.3 A has now been refined to a crystallographic R factor of 15.4% at 2.0 A resolution. Root mean square deviations from ideality are 0.18 A for bond lengths and 2.4 degrees for the angles. The inhibitor can be fitted to the difference electron density map in two alternative orientations. Drastic differences are observed for positions and interactions at P3/S3 and P3'/S3' subsites of the two orientations due to different crystallographic environments.

A pseudo-particle approach for studying protein-ligand models truncated to their active sites

A molecular dynamics method has been developed to describe the structural and dynamic properties of protein-ligand complexes that are truncated to their active sites. The active site is comprised of the ligand and discontinuous, positionally unrestrained peptide chains. This truncated active-site complex is surrounded by big unspecific pseudo-particles representing the complete protein and the solvent. Thus, knowledge of the folding of the outer parts of the protein is not required, and the method can be applied to protein models, derived from homology modeling. The method has been tested using ligand complexes of adenylate kinase, retinol binding protein, HIV-1 protease, and human leucocyte antigen. Comparisons with their crystal structures and with results from time-demanding simulations of the whole complexes in explicit water solvent show that the ligand binding properties are conserved. Most of the hydrogen bonds between the ligand and the active-site residues are reproduced and, furthermore, the simulation time is reduced.

Resistance of HIV type 1 to proteinase inhibitor Ro 31-8959

During replication of human immunodeficiency virus type 1 (HIV-1), proteolytic cleavage of Gag and Gag-Pol precursor proteins into different functional protein subunits is catalyzed by the viral proteinase, and this enzyme is the target of the antiviral proteinase inhibitor, Ro 31-8959. We investigated in vitro which HIV mutants with reduced sensitivity to Ro 31-8959 emerged during proteinase inhibition treatment; from three different HIV-1 strains, comparable progeny virus resistant to proteinase inhibitor were found, whereas the same experimental protocol detected no resistant HIV-2 mutants. Molecular analysis of the mutations underlying resistance revealed a multistep mechanism in which an amino acid exchange was common to all resistant isolates, and in all experiments preceded further exchanges at position 90 (leucine to methionine) and/or at position 54 (isoleucine to valine). For wild-type strains the 90% inhibitory concentrations of Ro 31-8959 were close to 20 nM, whereas HIV-1 mutants with all 3 amino acid exchanges had more than 50-fold increased 90% inhibitory concentrations (above 1000 nM). The primary event (Gly-48 to valine) occurs at the hinge of the flaps of the proteinase, thus hampering entry of the inhibitor to the active center and suggesting steric hindrance. Detailed knowledge of this stereotypic process could open inhibitor design, thus preventing conceivable escape of resistant virus on proteinase inhibitor action.

Flap opening in HIV-1 protease simulated by 'activated' molecular dynamics

We have used an 'activated' molecular dynamics approach to simulate flap opening in HIV-1 protease. An initial impulse for flap opening was provided by applying harmonic constraints to non-flap residues. After an initial 'melting' phase, the two beta-hairpin structures that constitute the flaps opened to a 25 A gap within 200 ps of simulation. Analysis of backbone torsion angles suggests that flap opening is related to conformational changes at Lys 45, Met 46, Gly 52 and Phe 53. In contrast, similar molecular dynamics simulations on the M46I mutant, which is associated with drug resistance, indicates that this mutation stabilizes the flaps in a closed conformation.

Methodological advances in molecular dynamics simulations of biological systems

New advances in the techniques used to simulate specific statistical ensembles provide molecular dynamics algorithms that permit rigorous connections to be made between thermodynamic observables and calculated quantities in simulations of biological molecules. The complete inclusion of electrostatic forces in simulations also improves the comparison between calculations of simple structural measures in crystals and X-ray crystallographic results. These advances coupled with the ongoing development of more accurate inter/intramolecular forcefields with enhanced accuracy provide guidelines and benchmarks for comparison as we move to study more complicated biological problems.