Acid and Thermal Denaturation of Barnase Investigated by Molecular Dynamics Simulations

Caflisch, Amedeo; Karplus, Martin

doi:10.1006/jmbi.1995.0528

Cited by 171 publications

(143 citation statements)

References 77 publications

(73 reference statements)

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“…Broken protein-protein hydrogen bonds are replaced by protein-water hydrogen bonds. The observed behavior is consistent with the findings in unfolding simulations of barnase (Caflisch & Karplus, 1995).…”

Section: K Simulations Setsupporting

confidence: 89%

Dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin

1997

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Molecular dynamics simulations in solution are performed for a rubredoxin from the hyperthermophilic archaeon Pymcoccus furiosus (RdPf) and one from the mesophilic organism Desulfovibrio vulgaris (RdDv). The two proteins are simulated at four temperatures: 300 K, 373 K, 473 K (two sets), and 500 K; the various simulations extended from 200 ps to 1,020 ps. At room temperature, the two proteins are stable, remain close to the crystal structure, and exhibit similar dynamic behavior; the RMS residue fluctuations are slightly smaller in the hyperthermophilic protein. An analysis of the average energy contributions in the two proteins is made; the results suggest that the intraprotein energy stabilizes RdPf relative to RdDv. At 373 K, the mesophilic protein unfolds rapidly (it begins to unfold at 300 ps), whereas the hyperthermophilic does not unfold over the simulation of 600 ps. This is in accord with the expected stability of the two proteins. At 473 K, where both proteins are expected to be unstable, unfolding behavior is observed within 200 ps and the mesophilic protein unfolds faster than the hyperthermophilic one. At 500 K, both proteins unfold; the hyperthermophilic protein does so faster than the mesophilic protein. The unfolding behavior for the two proteins is found to be very similar. Although the exact order of events differs from one trajectory to another, both proteins unfold first by opening of the loop region to expose the hydrophobic core. This is followed by unzipping of the @-sheet. The results obtained in the simulation are discussed in terms of the factors involved in flexibility and thermostability.

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Section: K Simulations Setsupporting

confidence: 89%

Dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin

1997

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“…Assuming that the REMD boundary line approximately delimits the highest barriers, we conclude that the last step to folding, the water expulsion transition, is indeed the rate-limiting step in both Trp-cage folding routes. In an early simulation study of barnase in explicit solvent, Caflisch and Karplus (44) showed that water entrance is a key step in unfolding. A water-expulsion transition occurring during the packing of the hydrophobic core was also observed in other computational studies (44)(45)(46).…”

Section: Ts Calculationmentioning

confidence: 99%

Sampling the multiple folding mechanisms of Trp-cage in explicit solvent

Juraszek

Bolhuis

2006

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

235

336

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We investigate the kinetic pathways of folding and unfolding of the designed miniprotein Trp-cage in explicit solvent. Straightforward molecular dynamics and replica exchange methods both have severe convergence problems, whereas transition path sampling allows us to sample unbiased dynamical pathways between folded and unfolded states and leads to deeper understanding of the mechanisms of (un)folding. In contrast to previous predictions employing an implicit solvent, we find that Trp-cage folds primarily (80% of the paths) via a pathway forming the tertiary contacts and the salt bridge, before helix formation. The remaining 20% of the paths occur in the opposite order, by first forming the helix. The transition states of the rate-limiting steps are solvated native-like structures. Water expulsion is found to be the last step upon folding for each route. Committor analysis suggests that the dynamics of the solvent is not part of the reaction coordinate. Nevertheless, during the transition, specific water molecules are strongly bound and can play a structural role in the folding.protein folding ͉ reaction coordinate ͉ transition path sampling ͉ replica exchange ͉ transition state ensemble E lucidating the mechanism by which proteins fold into their native state remains a central issue in molecular biology. For single domain two-state folding proteins, several decades of experimental, theoretical, and simulation studies have revealed two major qualitative folding mechanisms. In the diffusion-collision mechanism (1), proteins first form secondary structure elements followed by a diffusive search toward the tertiary native state structure. In the nucleation-condensation mechanism (2), a nucleus of crucial tertiary contacts is made, around which the native structure condensates. In recent years, these two mechanisms were combined in a unified view (3).By bridging the gap between experiments and computer simulation, the discovery of small and fast folding proteins has contributed much to the understanding of generic folding mechanisms. The fastest of those is the designed 20-residue miniprotein Trp-cage (NLYIQ WLKDG GPSSG RPPPS) (4), which folds in 4 s to a native state with an ␣-helix, a salt bridge, and a polyproline II helix shielding the central tryptophan from solvent. Laser temperaturejump spectroscopy experiments by Qiu et al. (5) indicated two-state folding. Subsequently, fluorescent correlation spectroscopy by Neuweiler et al. (6) revealed that the protein (un)folds in a more complicated manner via an intermediate molten globule-like state, characterized by exposure of the tryptophan to the solvent. It remains unclear at what stage of folding the helix is being formed. Recent UV-resonance Raman spectroscopy measurements show some evidence of a helical structure in the denaturated state of Trp-cage, and thus suggest that an early formation of the helix is possible (7). Many molecular dynamics (MD) simulations were performed to investigate thermodynamic stability of the protein and elucidate possible folding p...

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“…The use of high temperature simulations to overcome the conformation sampling problem is well documented. [23][24][25][26][27] The additional kinetic energy introduced in the simulation allows crossing of high energy barriers, ensuring a broad sampling of the conformational space, and simultaneously promoting the thermal unfolding of the proteins under study. Moreover, if reasonable comparisons with experimental denaturation studies are to be made, performing multiple simulations becomes critical to probe the multitude of conformations accessible to the protein between the native and the unfolded states.…”

Section: General Considerationsmentioning

confidence: 99%

“…[18][19][20][21][22] Although some groups have proposed promising strategies to track the protein folding pathways by computer simulations, computer limitations have made protein unfolding more tractable than protein folding. [23][24][25][26][27] In fact, simulation protocols making use of high temperature do increase the rate of these processes and in addition provide unfolding conditions. As pointed out by Finkelstein,28 though, care must be taken while extrapolating MD results obtained at extreme unfolding conditions to the protein folding problem.…”

Section: Introductionmentioning

confidence: 99%

Potentially amyloidogenic conformational intermediates populate the unfolding landscape of transthyretin: Insights from molecular dynamics simulations

et al. 2010

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Protein aggregation into insoluble fibrillar structures known as amyloid characterizes several neurodegenerative diseases, including Alzheimer's, Huntington's and Creutzfeldt-Jakob. Transthyretin (TTR), a homotetrameric plasma protein, is known to be the causative agent of amyloid pathologies such as FAP (familial amyloid polyneuropathy), FAC (familial amyloid cardiomiopathy) and SSA (senile systemic amyloidosis). It is generally accepted that TTR tetramer dissociation and monomer partial unfolding precedes amyloid fibril formation. To explore the TTR unfolding landscape and to identify potential intermediate conformations with high tendency for amyloid formation, we have performed molecular dynamics unfolding simulations of WT-TTR and L55P-TTR, a highly amyloidogenic TTR variant. Our simulations in explicit water allow the identification of events that clearly discriminate the unfolding behavior of WT and L55P-TTR. Analysis of the simulation trajectories show that (i) the L55P monomers unfold earlier and to a larger extent than the WT; (ii) the single a-helix in the TTR monomer completely unfolds in most of the L55P simulations while remain folded in WT simulations; (iii) L55P forms, early in the simulations, aggregation-prone conformations characterized by full displacement of strands C and D from the main b-sandwich core of the monomer; (iv) L55P shows, late in the simulations, severe loss of the H-bond network and consequent destabilization of the CBEF b-sheet of the b-sandwich; (v) WT forms aggregationcompatible conformations only late in the simulations and upon extensive unfolding of the monomer. These results clearly show that, in comparison with WT, L55P-TTR does present a much higher probability of forming transient conformations compatible with aggregation and amyloid formation.

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Acid and Thermal Denaturation of Barnase Investigated by Molecular Dynamics Simulations

Cited by 171 publications

References 77 publications

Dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin

Dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin

Sampling the multiple folding mechanisms of Trp-cage in explicit solvent

Potentially amyloidogenic conformational intermediates populate the unfolding landscape of transthyretin: Insights from molecular dynamics simulations

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