The V108M mutation decreases the structural stability of catechol O-methyltransferase.

The human gene for catechol O-methyltransferase has a common single-nucleotide polymorphism that results in substitution of methionine (M) for valine (V) 108 in the soluble form of the enzyme (s-COMT). 108M s-COMT loses enzymatic activity more rapidly than 108V s-COMT at physiological temperature, and the 108M allele has been associated with increased risk of breast cancer and several neuropsychiatric disorders. We used circular dichroism (CD), dynamic light scattering, and fluorescence spectroscopy to examine how the 108V/M polymorphism affects the stability of the purified, recombinant protein to heat and guanidine hydrochloride (GuHCl). COMT contains two tryptophan residues, W143 and W38Y, which are located in loops that border the S-adenosylmethionine (SAM) and catechol binding sites. We therefore also studied the single-tryptophan mutants W38Y and W143Y in order to dissect the contributions of the individual tryptophans to the fluorescence signals. The 108V and 108M proteins differed in the stability of both the tertiary structure surrounding the active site, as probed by the fluorescence yields and emission spectra, and their global secondary structure as reflected by CD. With either probe, the midpoint of the thermal transition of 108M s-COMT was 5 to 7 degrees C lower than that of 108V s-COMT, and the free energy of unfolding at 25 degrees C was smaller by about 0.4 kcal/mol. 108M s-COMT also was more prone to aggregation or partial unfolding to a form with an increased radius of hydration at 37 degrees C. The co-substrate SAM stabilized the secondary structure of both 108V and 108M s-COMT. W143 dominates the tryptophan fluorescence of the folded protein and accounts for most of the decrease in fluorescence that accompanies unfolding by GuHCl. While replacing either tryptophan by tyrosine was mildly destabilizing, the lower stability of the 108M variant was retained in all cases.

Using flexible loop mimetics to extend phi-value analysis to secondary structure interactions.

Chemical synthesis allows the incorporation of nonnatural amino acids into proteins that may provide previously untried probes of their folding pathway and thermodynamic stability. We have used a flexible thioether linker as a loop mimetic in the human yes kinase-associated protein (YAP 65) WW domain, a three-stranded, 44-residue, beta-sheet protein. This linkage avoids problems of incorporating sequences that constrain loops to the extent that they significantly change the nature of the denatured state with concomitant effects on the folding kinetics. An NMR solution structure shows that the thioether linker had little effect on the global fold of the domain, although the loop is apparently more dynamic. The thioether variants are destabilized by up to 1.4 kcal/mol (1 cal = 4.18 J). Preliminary Phi-value analysis showed that the first loop is highly structured in the folding transition state, and the second loop is essentially unstructured. These data are consistent with results from simulated unfolding and detailed protein-engineering studies of structurally homologous WW domains. Previously, Phi-value analysis was limited to studying side-chain interactions. The linkers used here extend the protein engineering method directly to secondary-structure interactions.

Hydrophobic hydration is an important source of elasticity in elastin-based biopolymers.

Molecular dynamics simulations with explicit waters have been employed to investigate the dominant source of elastin's elasticity. An elastin-like peptide, (VPGVG)(18), was pulled and released in molecular dynamics simulations, at 10 and 42 degrees C, lasting several nanoseconds, which is consistent with the experimentally determined dielectric and NMR relaxation time scales. At elastin's physiological temperature and degree of extension, the simulations indicate that the orientational entropy of waters hydrating hydrophobic groups decreases during pulling of the molecule, but it increases upon release. In contrast, the main-chain fluctuations and other measures of mobility suggest that elastin's backbone is more dynamic in the extended than released state. These results and the agreement between the simulations with various experimental observations suggest that hydrophobic hydration is an important source of the entropy-based elasticity of elastin. Moreover, elastin tends to reorder itself to form a hydrophobic globule when it was held in its extended state, indicating that the hydrophobic effect also contributes in the holding process. On the whole, our simulations support the hydrophobic mechanism of elasticity and provide a framework for description of the molecular basis of this phenomenon.

Validation of protein-unfolding transition states identified in molecular dynamics simulations.

Experimental and simulation studies can complement each other nicely in the area of protein folding. Experiment reports on the average properties of a large ensemble (approx. 10(17)-10(19) molecules), typically over time. Molecular dynamics simulations, on the other hand, provide detailed information for a single molecule, a component of the ensemble. By combining these approaches we can obtain not only a more complete picture of folding, but we can also take advantage of the strengths of different methods. For example, experiment cannot provide molecular structures. Molecular dynamics simulations can provide such information, but the simulations are meaningless without a linked experiment. Thus, the interrelated nature of simulation in assessing experimental assumptions and in providing structures to augment energetic descriptions, and experiment in judging whether the simulations are reasonable, provides more confidence in the resulting information about folding. This combination yields tested and testable molecular models of states that evade characterization by conventional methods. Therefore, we have explored the combined use of these methods to map folding/unfolding pathways at atomic resolution, in collaboration with Alan Fersht. Here we focus on chymotrypsin inhibitor 2, a small single-domain, two-state folding protein.

Can non-mechanical proteins withstand force? Stretching barnase by atomic force microscopy and molecular dynamics simulation.

Atomic force microscopy (AFM) experiments have provided intriguing insights into the mechanical unfolding of proteins such as titin I27 from muscle, but will the same be possible for proteins that are not physiologically required to resist force? We report the results of AFM experiments on the forced unfolding of barnase in a chimeric construct with I27. Both modules are independently folded and stable in this construct and have the same thermodynamic and kinetic properties as the isolated proteins. I27 can be identified in the AFM traces based on its previous characterization, and distinct, irregular low-force peaks are observed for barnase. Molecular dynamics simulations of barnase unfolding also show that it unfolds at lower forces than proteins with mechanical function. The unfolding pathway involves the unraveling of the protein from the termini, with much more native-like secondary and tertiary structure being retained in the transition state than is observed in simulations of thermal unfolding or experimentally, using chemical denaturant. Our results suggest that proteins that are not selected for tensile strength may not resist force in the same way as those that are, and that proteins with similar unfolding rates in solution need not have comparable unfolding properties under force.

Interactions within the coiled-coil domain of RetGC-1 guanylyl cyclase are optimized for regulation rather than for high affinity.

RetGC-1, a member of the membrane guanylyl cyclase family of proteins, is regulated in photoreceptor cells by a Ca(2+)-binding protein known as GCAP-1. Proper regulation of RetGC-1 is essential in photoreceptor cells for normal light adaptation and recovery to the dark state. In this study we show that cGMP synthesis by RetGC-1 requires dimerization, because critical functions in the catalytic site must be provided by each of the two polypeptide chains of the dimer. We also show that an intact alpha-helical coiled-coil structure is required to provide dimerization strength for the catalytic domain of RetGC-1. However, the dimerization strength of this domain must be precisely optimized for proper regulation by GCAP-1. We found that Arg(838) within the dimerization domain establishes the Ca(2+) sensitivity of RetGC-1 by determining the strength of the coiled-coil interaction. Arg(838) substitutions dominantly enhance cGMP synthesis even at the highest Ca(2+) concentrations that occur in normal dark-adapted photoreceptor cells. Molecular dynamics simulations suggest that Arg(838) substitutions disrupt a small network of salt bridges to allow an abnormal extension of coiled-coil structure. Substitutions at Arg(838) were first identified by linkage to the retinal degenerative disease, autosomal dominant cone rod dystrophy (adCORD). Consistent with the characteristics of this disease, the Arg(838)-substituted RetGC-1 mutants exhibit a dominant biochemical phenotype. We propose that accelerated cGMP synthesis in humans with adCORD is the primary cause of cone-rod degeneration.

Direct comparison of experimental and calculated folding free energies for hydrophobic deletion mutants of chymotrypsin inhibitor 2: free energy perturbation calculations using transition and denatured states from molecular dynamics simulations of unfolding.

Previous molecular dynamics (MD) simulations of thermal denaturation of chymotrypsin inhibitor 2 (CI2) have provided transition-state models in good agreement with experiment. Unfortunately, however, the comparisons have been necessarily indirect. The simulations have provided detailed structural information but not energetics, while from experiment, structure is inferred from a ratio of free energy changes upon mutation (Phi values). Here, direct comparison with experimental free energies is obtained by performing free energy perturbation calculations of hydrophobic deletion mutants of CI2 using transition- and denatured-state structures from various denaturation MD simulations. The agreement between the calculated and experimental DeltaDeltaG and Phi values is quite good (R = 0.8-0.9). In addition, given the availability of realistic atomic models for the denatured protein, the common approach of using small peptides to represent the denatured state in stability calculations can now be evaluated. To this end, two different extended tripeptide models were used: one using the sequence from the protein with the residue to be mutated in the center and the other with this residue surrounded by Ala residues. The results for the two peptides agree neither with one another nor with the different full-length denatured-state models, which do provide results in good agreement with experiment. This finding is noteworthy because the denatured state of CI2 is very disrupted with little residual structure, such that the peptides might have been expected to serve as reasonable models. Overall the calculations presented here validate our previous MD-generated transition- and denatured-state models and therefore the simulated unfolding pathways and their relevance to refolding.

Protein folding from a highly disordered denatured state: the folding pathway of chymotrypsin inhibitor 2 at atomic resolution.

Previous experimental and theoretical studies have produced high-resolution descriptions of the native and folding transition states of chymotrypsin inhibitor 2 (CI2). In similar fashion, here we use a combination of NMR experiments and molecular dynamics simulations to examine the conformations populated by CI2 in the denatured state. The denatured state is highly unfolded, but there is some residual native helical structure along with hydrophobic clustering in the center of the chain. The lack of persistent nonnative structure in the denatured state reduces barriers that must be overcome, leading to fast folding through a nucleation-condensation mechanism. With the characterization of the denatured state, we have now completed our description of the folding/unfolding pathway of CI2 at atomic resolution.

Mapping the early steps in the pH-induced conformational conversion of the prion protein.

Under certain conditions, the prion protein (PrP) undergoes a conformational change from the normal cellular isoform, PrP(C), to PrP(Sc), an infectious isoform capable of causing neurodegenerative diseases in many mammals. Conversion can be triggered by low pH, and in vivo this appears to take place in an endocytic pathway and/or caveolae-like domains. It has thus far been impossible to characterize the conformational change at high resolution by experimental methods. Therefore, to investigate the effect of acidic pH on PrP conformation, we have performed 10-ns molecular dynamics simulations of PrP(C) in water at neutral and low pH. The core of the protein is well maintained at neutral pH. At low pH, however, the protein is more dynamic, and the sheet-like structure increases both by lengthening of the native beta-sheet and by addition of a portion of the N terminus to widen the sheet by another two strands. The side chain of Met-129, a polymorphic codon in humans associated with variant Creutzfeldt-Jakob disease, pulls the N terminus into the sheet. Neutralization of Asp-178 at low pH removes interactions that inhibit conversion, which is consistent with the Asp-178-Asn mutation causing human prion diseases.

The molecular basis for the inverse temperature transition of elastin.

Elastin undergoes an "inverse temperature transition" such that it becomes more ordered as the temperature increases. To investigate the molecular basis for this behavior, molecular dynamics simulations were conducted above and below the transition temperature. Simulations of a 90-residue elastin peptide, (VPGVG)(18), with explicit water molecules were performed at seven different temperatures between 7 and 42 degrees C, for a total of 80 ns. Beginning from an idealized beta-spiral structure, hydrophobic collapse was observed over a narrow temperature range in the simulations. Moreover, simulations above and below elastin's transition temperature indicate that elastin has more turns and distorted beta-structure at higher temperatures. Water was critical to the inverse temperature transition and elastin-associated water molecules can be divided into three categories: those closely associated with beta II turns; those that form hydrogen bonds with the main-chain groups; and those hydrating the hydrophobic side-chains. Water-swollen, monomeric elastin above the transition temperature is best described as a compact amorphous structure with distorted beta-strands, fluctuating turns, buried hydrophobic residues, and main-chain polar atoms that participate in hydrogen bonds with water. Below the transition temperature, elastin is expanded with approximately 40 % local beta-spiral structure. Overall the simulations are in agreement with experiment and therefore appear to provide an atomic-level description of the conformational properties of elastin monomers and the basis for their elastomeric properties.

A comparison of experimental and computational methods for mapping the interactions present in the transition state for folding of FKBP12.

The folding pathway of FKBP12, a 107 residue α/ß protein, has been characterised in detail using a combination of experimental and computational techniques. FKBP12 follows a two-state model of folding in which only the denatured and native states are significantly populated; no intermediate states are detected. The refolding rate constant in water is 4 s(-1) at 25 °C. Two different experimental strategies were employed for studying the transition state for folding. In the first case, a non-mutagenic approach was used and the unfolding and refolding of the wild-type protein measured as a function of experimental conditions such as temperature, denaturant, ligand and trifluoroethanol (TFE) concentration. These data suggest a compact transition state relative to the unfolded state with some 70% of the surface area buried. The ligand-binding site, whichis mainly formed by two long loops, is largely unstructured in the transition state. TFE experiments suggest that the α-helix may be formed in the transition state. The second experimental approach involved using protein engineering techniques with φ-value analysis. Residue-specific information on the structure and energetics of the transition state can be obtained by this method. 34 mutations were made at sites throughout the protein to probe the extent of secondary and tertiary structure in the transition state. In contrast to some other proteins of this size, no element of structure is fully formed in the transition state, instead, the transition state is similar to that found for smaller, single-domain proteins, such as chymotrypsin inhibitor 2 and the SH3 domainfrom α-spectrin. For FKBP12, the central three strands of the ß-sheet (2, 4 and 5), comprise the most structured region of the transition state. In particular Val 101, which is one of the most highly buried residues and located in the middle of the central ß-strand,makes approximately 60% of its native interactions. The outer ß-strands, and the ends of the central ß-strands are formed to a lesser degree. The short α-helix is largely unstructured in the transition state as are the loops. The data are consistent with a nucleation-condensation model of folding, the nucleus of which is formed by side chains within ß-strands 2, 4 and 5 and the C-terminus of the α-helix. These residues are distant in the primary sequence, demonstrating the importance of tertiary interactions in the transition state. High-temperature molecular dynamic simulations on the unfoldingpathway of FKBP12 are in good agreement with the experimental results.

NMR studies of the association of cytochrome b5 with cytochrome c.

In an effort to gain greater insight into the molecular mechanism of the electron-transfer reactions of cytochrome b(5), the bovine cytochrome b(5)-horse cytochrome c complex has been investigated by high-resolution multidimensional NMR spectroscopy using (13)C, (15)N-labeled cytochrome b(5) expressed from a synthetic gene. Chemical shifts of the backbone (15)N, (1)H, and (13)C resonances for 81 of the 82 residues of [U-90% (13)C,U-90% (15)N]-ferrous cytochrome b(5) in a 1:1 complex with ferrous cytochrome c were compared with those of ferrous cytochrome b(5) in the absence of cytochrome c. A total of 51% of these residues showed small, but significant, changes in chemical shifts (the largest shifts were 0.1 ppm for the amide (1)H, 1.15 for (13)C(alpha), 1.03 ppm for the amide (15)N, and 0.15 ppm for the (1)H(alpha) resonances). Some of the residues exhibiting chemical shift changes are located in a region that has been implicated as the binding surface to cyt c [Salemme, F. R. (1976) J. Mol. Biol. 10, 563-568]. Surprisingly, many of the residues with changes are not located on this surface. Instead, they are located within and around a cleft observed to form in a molecular dynamics study of cytochrome b(5) [Storch, E. M., and Daggett, V. (1995) Biochemistry 34, 9682-9693](.) The rim of this cleft can readily accommodate cytochrome c. Molecular dynamics simulations of the Salemme and cleft complexes were performed for 2 ns and both complexes were stable.

Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation.

The Engrailed Homeodomain protein has the highest refolding and unfolding rate constants directly observed to date. Temperature jump relaxation measurements gave a refolding rate constant of 37,500 s(-1) in water at 25 degrees C, rising to 51,000 s(-1) around 42 degrees C. The unfolding rate constant was 1,100 s(-1) in water at 25 degrees C and 205,000 s(-1) at 63 degrees C. The unfolding half-life is extrapolated to be approximately 7.5 ns at 100 degrees C, which allows real-time molecular dynamics unfolding simulations to be tested on this system at a realistic temperature. Preliminary simulations did indeed conform to unfolding on this time scale. Further, similar transition states were observed in simulations at 100 degrees C and 225 degrees C, suggesting that high-temperature simulations provide results applicable to lower temperatures.

Long timescale simulations.

Computers are becoming increasingly fast, making it possible to perform simulations of macromolecules on timescales that were previously inaccessible. Questions have arisen concerning how well we are keeping up with computer power and the state of the art with respect to long molecular dynamics simulations in solvent. More importantly, however, simulations of macromolecules are performed to aid the understanding of biochemical phenomena. So, what are we learning from longer simulations and are they providing reliable insight into protein dynamics, conformational behavior and function?

Towards a complete description of the structural and dynamic properties of the denatured state of barnase and the role of residual structure in folding.

The detailed characterization of denatured proteins remains elusive due to their mobility and conformational heterogeneity. NMR studies are beginning to provide clues regarding residual structure in the denatured state but the resulting data are too sparse to be transformed into molecular models using conventional techniques. Molecular dynamics simulations can complement NMR by providing detailed structural information for components of the denatured ensemble. Here, we describe three independent 4 ns high-temperature molecular dynamics simulations of barnase in water. The simulated denatured state was conformationally heterogeneous with respect to the conformations populated both within a single simulation and between simulations. Nonetheless, there were some persistent interactions that occurred to varying degrees in all simulations and primarily involved the formation of fluid hydrophobic clusters with participating residues changing over time. The region of the beta(3-4) hairpin contained a particularly high degree of such side-chain interactions but it lacked beta-structure in two of the three denatured ensembles: beta(3-4) was the only portion of the beta-structure to contain significant residual structure in the denatured state. The two principal alpha-helices (alpha1 and alpha2) adopted dynamic helical structure. In addition, there were persistent contacts that pinched off core 2 from the body of the protein. The rest of the protein was unstructured, aside from transient and mostly local side-chain interactions. Overall, the simulated denatured state contains residual structure in the form of dynamic, fluctuating secondary structure in alpha1 and alpha2, as well as fluctuating tertiary contacts in the beta(3-4) region, and between alpha1 and beta(3-4), in agreement with previous NMR studies. Here, we also show that these regions containing residual structure display impaired mobility by both molecular dynamics and NMR relaxation experiments. The residual structure was important in decreasing the conformational states available to the chain and in repairing disrupted regions. For example, tertiary contacts between beta(3-4) and alpha1 assisted in the refolding of alpha1. This contact-assisted helix formation was confirmed in fragment simulations of beta(3-4) and alpha1 alone and complexed, and, as such, alpha1 and beta(3-4) appear to be folding initiation sites. The role of these sites in folding was investigated by working backwards and considering the simulation in reverse, noting that earlier time-points from the simulations provide models of the major intermediate and transition states in quantitative agreement with data from both unfolding and refolding experiments. Both beta(3-4) and alpha1 are dynamic in the denatured state but when they collide and make enough contacts, they provide a loose structural scaffold onto which further beta-strands pack. The beta-structure condenses about beta(3-4), while alpha1 aids in stabilizing beta(3-4) and maintaining its orientation. The resulting beta-structure is relatively planar and loose in the major intermediate. Further packing ensues, and as a result the beta-sheet twists, leading to the major transition state. The structure is still expanded and loops are not well formed at this point. Fine-tuning of the packing interactions and the final condensation of the structure then occurs to yield the native state.

Characterization of the unfolding pathway of the cell-cycle protein p13suc1 by molecular dynamics simulations: implications for domain swapping.

BACKGROUND: The p13suc1 gene product is a member of the cks (cyclin-dependent protein kinase subunit) protein family and has been implicated in regulation of the cell cycle. Various crystal structures of suc1 are available, including a globular, monomeric form and a beta-strand exchanged dimer. It has been suggested that conversions between these forms, and perhaps others, may be important in the regulation of the cell cycle. RESULTS: We have undertaken molecular dynamics simulations of protein unfolding to investigate the conformational properties of suc1. Unfolding transition states were identified for each of four simulations. These states contain some native secondary structure, primarily helix alpha1 and the core of the beta sheet. The hydrophobic core is loosely packed. Further unfolding leads to an intermediate state that is slightly more expanded than the transition state, but with considerably fewer nonlocal, tertiary packing contacts and less secondary structure. The helices are fluctuating but partially formed in the denatured state and beta2 and beta4 remain associated. CONCLUSIONS: It appears that suc1 folds by a nucleation-condensation mechanism, similar to that observed for two-state folding proteins. However, suc1 forms an intermediate during unfolding and contains considerable residual structure in the denatured state. The stability of the beta2-beta4 residual structure is surprising, because beta4 is the strand involved in domain swapping. This stability suggests that the domain-swapping event, if physiologically relevant, may require the assistance of additional factors in vivo or occur early in the folding process.

Staphylococcal protein A: unfolding pathways, unfolded states, and differences between the B and E domains.

We present multiple native and denaturation simulations of the B and E domains of the three-helix bundle protein A, totaling 60 ns. The C-terminal helix (H3) consistently denatures later than either of the other two helices and contains residual helical structure in the denatured state. These results are consistent with experiments suggesting that the isolated H3 fragment is more stable than H1 and H2 and that H3 forms early in folding. Interestingly, the denatured state of the B domain is much more compact than that of the E domain. This sequence-dependent effect on the dimensions of the denatured state and the lack of correlation with structure suggest that the radius of gyration can be a misleading reaction coordinate for unfolding/folding. Various unfolding and refolding events are observed in the denaturation simulations. In some cases, the transitions are facilitated through interactions with other portions of the protein-contact-assisted helix formation. In the native simulations, the E domain is very stable: after 6 ns, the C(alpha) root-mean-square deviation from the starting structure is less than 1.4 A. In contrast, the native state of the B domain deviates more and its inter-helical angles fluctuate. In apparent contrast, we note that the B domain is thermodynamically more stable than the E domain. The simulations suggest that the increased stability of the B domain may be due to heightened mobility, and therefore entropy, in the native state and decreased mobility/entropy in the more compact denatured state.

The effects of disulfide bonds on the denatured state of barnase.

The effects of engineered disulfide bonds on protein stability are poorly understood because they can influence the structure, dynamics, and energetics of both the native and denatured states. To explore the effects of two engineered disulfide bonds on the stability of barnase, we have conducted a combined molecular dynamics and NMR study of the denatured state of the two mutants. As expected, the disulfide bonds constrain the denatured state. However, specific extended beta-sheet structure can also be detected in one of the mutant proteins. This mutant is also more stable than would be predicted. Our study suggests a possible cause of the very high stability conferred by this disulfide bond: the wild-type denatured ensemble is stabilized by a nonnative hydrophobic cluster, which is constrained from occurring in the mutant due to the formation of secondary structure.