Pressure‐induced structural transition of mature <scp>HIV</scp>‐1 protease from a combined <scp>NMR/MD</scp> simulation approach

Roche, Julien; Louis, John M.; Bax, Ad; Best, Robert B.

doi:10.1002/prot.24931

Cited by 23 publications

(28 citation statements)

References 42 publications

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“…To follow quantitatively the transition of secondary structures of silk fibroin under pressure, a curve-fitting analysis must be employed. Prior to curve fitting, the number of bands under the band profile in the region of 1700-1600 cm 21 were resolved by secondary derivative and Fourier self-deconvolution analyses, as shown in Figures 2 and 3. The bands resolved by these analytical methods were presented in Table 1, and these five bands were used to fit the time-dependent IR spectra in Figure 1.…”

Section: Kinetics Of Conformational Transitions Of Silk Fibroin In mentioning

confidence: 99%

“…In addition to chemical factors, 5,6 physical factors, especially the hydrostatic pressure in silkworm glands may also play an important role. 7 Although a large amount of literature [8][9][10][11][12][13][14][15][16][17][18][19][20][21][22] reported the influence of high hydrostatic pressure on the conformational transitions of many other proteins, no investigation on the effect of pressure on silk fibroin has been found so far.…”

Section: Introductionmentioning

confidence: 99%

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Low pressure‐induced secondary structure transitions of regenerated silk fibroin in its wet film studied by time‐resolved infrared spectroscopy

Liu

Zhou

et al. 2018

Proteins

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The secondary structure transitions of regenerated silk fibroin (RSF) under different external perturbations have been studied extensively, except for pressure. In this work, time-resolved infrared spectroscopy with the attenuated total reflectance (ATR) accessory was employed to follow the secondary structure transitions of RSF in its wet film under low pressure. It has been found that pressure alone is favorable only to the formation of β-sheet structure. Under constant pressure there is an optimum amount of D O in the wet film (D O : film = 2:1) so as to provide the optimal condition for the reorganization of the secondary structure and to have the largest formation of β-sheet structure. Under constant amount of D O and constant pressure, the secondary structure transitions of RSF in its wet film can be divided into three stages along with time. In the first stage, random coil, α-helix, and β-turn were quickly transformed into β-sheet. In the second stage, random coil and β-turn were relatively slowly transformed into β-sheet and α-helix, and the content of α-helix was recovered to the value prior to the application of pressure. In the third and final stage, no measurable changes can be found for each secondary structure. This study may be helpful to understand the secondary structure changes of silk fibroin in silkworm's glands under hydrostatic pressure.

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Section: Kinetics Of Conformational Transitions Of Silk Fibroin In mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Low pressure‐induced secondary structure transitions of regenerated silk fibroin in its wet film studied by time‐resolved infrared spectroscopy

Liu

Zhou

et al. 2018

Proteins

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“…Recent backbone residual dipolar couplings measured for the N-H amide vectors confirmed that PR20 adopts a wide-open flap conformation in solution 17 . Using a combined NMR/MD approach we also showed that pressure perturbation induces the opening of the glycine-rich flaps of the inhibitor-free PR, while no such effect was detected for the inhibitor-free PR20 18 at subdenaturing pressure, therefore confirming that drug-resistance mutations affect the open-closed flap equilibrium of the PR dimer.…”

Section: Introductionmentioning

confidence: 68%

“…These results clearly demonstrate that in contrast to the inhibitor-free PR D25N , PR20 D25N unfolds in a highly cooperative manner, closely approximating an ideal two-state transition. In the absence of inhibitor at atmospheric pressure, PR D25N dimer was shown to adopt a closed conformation with very transient opening of the flaps 42 , while PR20 D25N adopts mostly an open flap conformation in solution 17,18 . Based on the present results, we hypothesize that decreased cooperativity observed for unfolding of the inhibitor-free PR D25N reflects a three-state unfolding transition: closed-flap → open-flap → unfolded, while PR20 D25N undergoes a simple two-state transition: open-flap → unfolded (Fig.…”

Section: Discussionmentioning

confidence: 98%

Evolution under Drug Pressure Remodels the Folding Free-Energy Landscape of Mature HIV-1 Protease

Louis

Roche

2016

Journal of Molecular Biology

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Using high-pressure NMR spectroscopy and differential scanning calorimetry, we investigate the folding landscape of the mature HIV-1 protease homodimer. The cooperativity of unfolding was measured in the absence or presence of an active site inhibitor DMP323, for the active protease (PR), its inactive variant PRD25N and an extremely multi-drug resistant mutant, PR20. The individual fit of the pressure denaturation profiles gives rise to first order, ΔGNMR, and second order, ΔVNMR (the derivative of ΔGNMR with pressure) apparent thermodynamic parameters for each amide proton considered. Heterogeneity in the apparent ΔVNMR values reflects departure from an ideal cooperative unfolding transition. The narrow to broad distribution of ΔVNMR spanning the extremes from inhibitor-free PR20D25N to PR-DMP323 complex, and distinctively for PRD25N-DMP323 complex, indicated large variations in folding cooperativity. Consistent with this data, the shape of thermal unfolding transitions varies from asymmetric for PR to nearly symmetric for PR20, as dimer-inhibitor ternary complexes. Lack of structural cooperativity was observed between regions located close to the active site, including the hinge and tip of the glycine-rich flaps, and the rest of the protein. These results strongly suggest that inhibitor binding drastically decreases the cooperativity of unfolding by trapping the closed flap conformation in a deep energy minimum. To evade this conformational trap, PR20 evolves exhibiting a smoother folding landscape with nearly an ideal two-state (cooperative) unfolding transition. This study highlights the malleability of retroviral protease folding pathways by illustrating how the selection of mutations under drug pressure remodels the free-energy landscape as a primary mechanism.

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“…Amber 99SB and general amber force field (GAFF) [39–41] were used for CDK8/CycC and the nine ligands, respectively. Single protonation states were used for all histidine residues according to predictions from comparing results for MCCE [42, 43], ProPKa [44, 45], and DelPhiPKa [46, 47]. Six Cl − ions were placed to maintain a neutral system.…”

Section: Methodsmentioning

confidence: 99%

A molecular dynamics investigation of CDK8/CycC and ligand binding: conformational flexibility and implication in drug discovery

Cholko

Chen

Tang

et al. 2018

J Comput Aided Mol Des

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Abnormal activity of cyclin-dependent kinase 8 (CDK8) along with its partner protein cyclin C (CycC) is a common feature of many diseases including colorectal cancer. Using molecular dynamics (MD) simulations, this study determined the dynamics of the CDK8-CycC system and we obtained detailed breakdowns of binding energy contributions for four type-I and five type-II CDK8 inhibitors. We revealed system motions and conformational changes that will affect ligand binding, confirmed the essentialness of CycC for inclusion in future computational studies, and provide guidance in development of CDK8 binders. We employed unbiased all-atom MD simulations for 500 ns on twelve CDK8-CycC systems, including apoproteins and protein-ligand complexes, then performed principal component analysis (PCA) and measured the RMSF of key regions to identify protein dynamics. Binding pocket volume analysis identified conformational changes that accompany ligand binding. Next, H-bond analysis, residue-wise interaction calculations, and MM/PBSA were performed to characterize protein-ligand interactions and find the binding energy. We discovered that CycC is vital for maintaining a proper conformation of CDK8 to facilitate ligand binding and that the system exhibits motion that should be carefully considered in future computational work. Surprisingly, we found that motion of the activation loop did not affect ligand binding. Type-I and type-II ligand binding is driven by van der Waals interactions, but electrostatic energy and entropic penalties affect type-II binding as well. Binding of both ligand types affects protein flexibility. Based on this we provide suggestions for development of tighter-binding CDK8 inhibitors and offer insight that can aid future computational studies.

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Pressure‐induced structural transition of mature HIV‐1 protease from a combined NMR/MD simulation approach

Cited by 23 publications

References 42 publications

Low pressure‐induced secondary structure transitions of regenerated silk fibroin in its wet film studied by time‐resolved infrared spectroscopy

Low pressure‐induced secondary structure transitions of regenerated silk fibroin in its wet film studied by time‐resolved infrared spectroscopy

Evolution under Drug Pressure Remodels the Folding Free-Energy Landscape of Mature HIV-1 Protease

A molecular dynamics investigation of CDK8/CycC and ligand binding: conformational flexibility and implication in drug discovery

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