| 1. |
- Adams, Christopher, et al.
(författare)
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Probing Solution-Phase and Gas-Phase Structures of Trp-cage Cations by Chiral Substitution and Spectroscopic Techniques
- 2006
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Ingår i: International Journal of Mass Spectrometry. - : Elsevier BV. - 1387-3806 .- 1873-2798. ; 253:3, s. 263-273
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Tidskriftsartikel (refereegranskat)abstract
- The relevance of gas-phase protein structure to its solution structure is of the utmost importance in studying biomolecules by mass spectrometry. D-Amino acid substitutions within a minimal protein. Trp-cage. were used to correlate solution-phase properties as measured by circular dichroism with solution/gas-phase conformational features of protein cations probed via charge state distribution (CSD) in electrospray ionization. and gas-phase features revealed by tandem mass spectrometry (MS/MS). The gas-phase features were additionally supported by force-field molecular dynamics simulations. CD data showed that almost any single-residue D-substitution destroys the most prominent CD feature of the "native" all-L isomer, alpha-helicity. CSD was able to qualitatively assess the degree of compactness of solution-phase molecular structures. CSD results were consistent with the all-L form being the most compact in solution among all studied stereoisomers except for the D-Asn(1) isomer. D-substitutions of the aromatic Y(3), W(6) and Q(5) residues generated the largest deviations in CSD data among single amino acid substitutions. consistent with the critical role of these residues in Trp-cage stability. Electron capture dissociation of the stereoisomer dications gave an indication that some gas-phase structural features of Trp-cage are similar to those in solution. This result is supported by MDS data oil five of the studied stereoisomer dications in the gas-phase. The MDS-derived minimum-energy structures possessed more extensive hydrogen bonding than the solution-phase structure of the native form, deviating from the latter by 3-4 angstrom and were not 'inside-out' compared to native structures. MDS data could be correlated with CD data and even with ECD results. which aided in providing a long-range structural constraint for MDS. The overall conclusion is the general resemblance, despite the difference on the detailed level, of the preferred structures in both phases for the mini protein Trp-cage.
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| 2. |
- Iavarone, A. T, et al.
(författare)
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Fluorescence probe of Trp-cage protein conformation in solution and in gas phase
- 2007
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 129:21, s. 6726-6735
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Tidskriftsartikel (refereegranskat)abstract
- Measurements of protein unfolding in the absence of solvent, when combined with unfolding studies in solution, offer a unique opportunity to measure the effects of solvent on protein structure and dynamics. The experiments presented here rely on the fluorescence of an attached dye to probe the local conformational dynamics through interactions with a Trp residue and fields originating on charge sites. We present fluorescence measurements of thermal fluctuations accompanying conformational change of a miniprotein, Trp-cage, in solution and in gas phase. Molecular dynamics (MD) simulations are performed as a function of temperature, charge state, and charge location to elucidate the dye-protein conformational dynamics leading to the changes in measured fluorescence. The results indicate that the stability of the unsolvated protein is dominated by hydrogen bonds. Substituting asparagine for aspartic acid at position 9 results in a dramatic alteration of the solution unfolding curve, indicating that the salt bridge involving Lys8, Asp9, and Arg16 (+ - +) is essential for Trp-cage stability in solution. In contrast, this substitution results in minor changes in the unfolding curve of the unsolvated protein, showing that hydrogen bonds are the major contributor to the stability of Trp-cage in gas phase. Consistent with this hypothesis, the decrease in the number of hydrogen bonds with increasing temperature indicated by MD simulations agrees reasonably well with the experimentally derived enthalpies of conformational change. The simulation results display relatively compact conformations compared with NMR structures that are generally consistent with experimental results. The measured unfolding curves of unsolvated Trp-cage ions are invariant with the acetonitrile content of the solution from which they are formed, possibly as a result of conformational relaxation during or after desolvation. This work demonstrates the power of combined solution and gas-phase studies and of single-point mutations to identify specific noncovalent interactions which contribute to protein-fold stability. The combination of experiment and simulation is particularly useful because these approaches yield complementary information which can be used to deduce the details of structural changes of proteins in the gas phase.
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| 3. |
- Marklund, Erik G., et al.
(författare)
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Structural stability of electrosprayed proteins : temperature and hydration effects
- 2009
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 11:36, s. 8069-8078
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Tidskriftsartikel (refereegranskat)abstract
- Electrospray ionization is a gentle method for sample delivery, routinely used in gas-phase studies of proteins. It is crucial for structural investigations that the protein structure is preserved, and a good understanding of how structure is affected by the transition to the gas phase is needed for the tuning of experiments to meet that requirement. Small amounts of residual solvent have been shown to protect the protein, but temperature is important too, although it is not well understood how the latter affects structural details. Using molecular dynamics we have simulated four sparingly hydrated globular proteins (Trp-cage; Ctf, a C-terminal fragment of a bacterial ribosomal protein; ubiquitin; and lysozyme) in vacuum starting at temperatures ranging from 225 K to 425 K. For three of the proteins, our simulations show that a water layer corresponding to 3 angstrom preserves the protein structure in vacuum, up to starting temperatures of 425 K. Only Ctf shows minor secondary structural changes at lower starting temperatures. The structural conservation stems mainly from interactions with the surrounding water. Temperature scales in simulations are not directly translatable into experiments, but the wide temperature range in which we find the proteins to be stable is reassuring for the success of future single particle imaging experiments. The water molecules aggregate in clusters and form patterns on the protein surface, maintaining a reproducible hydrogen bonding network. The simulations were performed mainly using OPLS-AA/L, with cross checks using AMBER03 and GROMOS96 53a6. Only minor differences between the results from the three different force fields were observed.
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| 4. |
- Patriksson, Alexandra, et al.
(författare)
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A direct comparison of protein structure in the gas and solution phase - the Trp-cage
- 2007
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 111:46, s. 13147-13150
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Tidskriftsartikel (refereegranskat)abstract
- Molecular dynamics simulations of zwitterions of the Trp-cage protein in the gas phase show that the most stable ion in vacuo has preserved the charge locations acquired in solution. A direct comparison of the gas and solution-phase structures reveals that, despite the similarity in charge location, there is significant difference in the structures, with a substantial increase in hydrogen bonds and exposure of hydrophobic parts in the gas phase. The structure of the salt bridge in the gas phase is also much more stable than in the (experimental) solution structure.
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| 5. |
- Patriksson, Alexandra, et al.
(författare)
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A temperature predictor for parallel tempering simulations
- 2008
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 10:15, s. 2073-2077
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Tidskriftsartikel (populärvet., debatt m.m.)abstract
- An algorithm is proposed that generates a set of temperatures for use in parallel tempering simulations ( also known as temperature- replica exchange molecular dynamics simulations) of proteins to obtain a desired exchange probability P-des. The input consists of the number of protein atoms and water molecules in the system, information about the use of constraints and virtual sites and the lower temperature limits. The temperatures generated yield probabilities which are very close to Pdes ( correlation 97%), independent of force. field and over a wide temperature range.
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| 6. |
- Patriksson, Alexandra, 1977-
(författare)
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From Solution into Vacuum - Structural Transitions in Proteins
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Information about protein structures is important in many areas of life sciences, including structure-based drug design. Gas phase methods, like electrospray ionization and mass spectrometry are powerful tools for the analysis of molecular interactions and conformational changes which complement existing solution phase methods. Novel techniques such as single particle imaging with X-ray free electron lasers are emerging as well. A requirement for using gas phase methods is that we understand what happens to proteins when injected into vacuum, and what is the relationship between the vacuum structure and the solution structure.Molecular dynamics simulations in combination with experiments show that protein structures in the gas phase can be similar to solution structures, and that hydrogen bonding networks and secondary structure elements can be retained. Structural changes near the surface of the protein happen quickly (ns-µs) during transition from solution into vacuum. The native solution structure results in a reasonably well defined gas phase structure, which has high structural similarity to the solution structure.Native charge locations are in some cases also preserved, and structural changes, due to point mutations in solution, can also be observed in vacuo. Proteins do not refold in vacuo: when a denatured protein is injected into vacuum, the resulting gas phase structure is different from the native structure.Native structures can be protected in the gas phase by adjusting electrospray conditions to avoid complete evaporation of water. A water layer with a thickness of less than two water molecules seems enough to preserve native conditions.The results presented in this thesis give confidence in the continued use of gas phase methods for analysis of charge locations, conformational changes and non-covalent interactions, and provide a means to relate gas phase structures and solution structures.
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| 7. |
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| 8. |
- Patriksson, Alexandra, et al.
(författare)
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Proteins structures under electrospray conditions
- 2007
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Ingår i: Biochemistry. - : American Chemical Society (ACS). - 0006-2960 .- 1520-4995. ; 46:4, s. 933-945
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Tidskriftsartikel (refereegranskat)abstract
- During electrospray ionization (ESI), proteins are transferred from solution into vacuum, a process that influences the conformation of the protein. Exactly how much the conformation changes due to the dehydration process, and in what way, is difficult to determine experimentally. The aim of this study is therefore to monitor what happens to protein structures as the surrounding waters gradually evaporate, using computer simulations of the transition of proteins from water to vacuum. Five different proteins have been simulated with water shells of varying thickness, enabling us to mimic the entire dehydration process. We find that all protein structures are affected, at least to some extent, by the transfer but that the major features are preserved. A water shell with a thickness of roughly two molecules is enough to emulate bulk water and to largely maintain the solution phase structure. The conformations obtained in vacuum are quite similar and make up an ensemble which differs from the structure obtained by experimental means, and from the solution phase structure as found in simulations. Dehydration forces the protein to make more intramolecular hydrogen bonds, at the expense of exposing more hydrophobic area (to vacuum). Native hydrogen bonds usually persist in vacuum, yielding an easy route to refolding upon rehydration. The findings presented here are promising for future bio-imaging experiments with X-ray free electron lasers, and they strongly support the validity of mass spectrometry experiments for studies of intra- and intermolecular interactions.
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| 9. |
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| 10. |
- Van Der Spoel, David, et al.
(författare)
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Protein Folding Properties from Molecular Dynamics Simulations
- 2007
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Ingår i: Applied Parallel Computing. - 9783540757542 ; , s. 109-115
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Konferensbidrag (refereegranskat)abstract
- Protein folding simulations have contributed significantly to our understanding of the problem, since it is difficult to study individual molecules during the folding process. We have recently performed folding simulations of Chignolin, a decapeptide (Seibert et al., J. Mol. Biol. 354 (2006) p. 173) and introduced a new algorithm for deriving kinetics information as well as thermodynamics from the trajectories (Van der Spoel & Seibert, Phys. Rev. Lett. 96 (2006), p. 238102). Here we investigate the algorithm further and show that the folding reaction for Chignolin is a two-state folding reaction, in accord with experimental data.
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