|
|
||||||||
1 Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-1114, USA
2 Department of Molecular and Cellular Medicine, Texas A&M University College of Medicine, College Station, Texas 77843-1114, USA
| Abstract |
|---|
|
|
|---|
G) varies with temperature. Here we compare stability curves for many pairs of homologous proteins from thermophilic and mesophilc organisms. Of the basic methods that can be employed to achieve enhanced thermostability, we find that most thermophilic proteins use the simple method that raises the
G at all temperatures as the principal way to increase their Tm. We discuss and compare this thermodynamic method with the possible alternatives. In addition we propose ways that structural alterations and changes to the amino acid sequences might give rise to varied methods used to obtain thermostability. Keywords: protein folding; thermodynamics; protein stability curves; thermophiles; thermostability
| Introduction |
|---|
|
|
|---|
Proteins perform important tasks in all biological systems, and they do so by maintaining a specific globular conformation. This functional state, called the native state, is marginally stabilized in a balancing act of opposing forces. The players in this balancing act have long been identified (Kauzmann 1959), although their relative contributions have been debated (Dill 1990; Creighton 1992; Rose and Wolfenden 1993; Pace et al. 1996; Honig 1999). The major stabilizing forces include the hydrophobic effect and hydrogen bonding while conformational entropy favors the unfolded state. The forces stabilizing the native state outweigh the disruptive forces marginally in a folded protein, in the range of 510 kcal mol1 (Pace 1975). This balance of forces is known as the conformational stability of a protein and is defined thermodynamically as the free energy change,
G, for the native
unfolded state transition. Measurements of and studies on protein stability have remained important over several decades owing to the central role these macromolecules play in maintaining life and their involvement in many diseases affecting humans. Studies on protein stability explore the sequencestructurestability relationship, with stability being the measured thermodynamic quantity, since sequence defines structure, whose interactions afford stability. Sequence is also the variable that organisms alter as they evolve to adapt their proteins to the environments they inhabit. The stability of proteins is usually determined experimentally by perturbing the native state using temperature or denaturing solvent additives (urea, GuHCl) and following this "reaction" by direct (calorimetric) and indirect (spectroscopic) probes (for further details, see Lopez and Makhatadze 2002; Grimsley et al. 2003).
Since this review focuses on thermodynamics of protein stability and protein stability curves in particular, an introduction to these concepts is in order. Becktel and Schellman (1987) introduced protein stability curves, showing plots of free energy of stabilization (
G) as a function of temperature (Fig. 1). Such data are described by a modified version of the GibbsHelmholtz equation, and important thermodynamic parameters can be determined (Equation 1):
![]() |
G(T) is the free energy at a temperature T;
Hm is the change in enthalpy at Tm;
Cp is the change in heat capacity associated with the unfolding of the protein; and Tm is the melting temperature or the temperature at midpoint of transition from native to denatured state. Other parameters of interest that can be calculated using modifications of Equation 1 include TS and
GS, where TS is the temperature of maximum stability or temperature where the change in entropy between native and denatured states is zero and
GS is the conformational stability at this temperature. Protein stability curves also allow the calculation of conformational stability at any temperature, including the habitat temperature of an organism (TE).
|
ASA or change in solvent accessible surface area upon unfolding of a protein. It has been shown that
ASA correlates with thermodynamic quantities like
Cp (Livingstone et al. 1991; Murphy and Freire 1992; Spolar et al. 1992) and the m-value (Myers et al. 1995), a parameter that is used to describe the denaturant-induced unfolding of a protein. Protein structures also emphasize the fact that the native state is held together by a large number of weak noncovalent interactions between constituent amino acids. The fact that proteins are only marginally stable in general makes the ability of thermophilic proteins to function particularly intriguing because, unlike membranes that show heterogeneity in their building block lipids (Russell and Fukunaga 1990), proteins are composed of the same 20 amino acids irrespective of the organism and its habitat.
There have been several studies designed to understand the thermodynamic strategies that proteins from thermophiles use to remain folded at their high habitat temperatures. Proteins from thermophiles alter their sequence such that it optimizes the interactions holding their native conformations together; these optimizations in turn alter key thermodynamic parameters like
Cp,
G, and
H in a way that "tunes" the stability characteristics to the habitat of the organism. As protein chemists, we can measure these cardinal parameters, construct stability curves, and possibly learn about the strategies employed in thermostabilization. Nojima et al. (1977) proposed three different methods of modulating the stability curve of a protein to achieve higher thermostability (greater Tm; Fig. 2). Briefly, a hypothetical mesophilic protein can (I) raise the entire stability curve to higher
G so it now has a higher Tm, (II) broaden its stability curve so it now intersects the abscissa at a higher temperature, or (III) shift the entire stability curve to the right (to higher temperatures). All three methods of achieving higher thermostability have been observed in nature, some independently and others in combination. These methods have underlying thermodynamic mechanisms, for example, increasing the value of
HS (the change in enthalpy measured at TS) without compensating changes in
S will result in a similar stability curve, but with higher
G values at all temperatures (method I). A broadened stability curve (method II) is caused by a reduced
Cp. Lowering the
S or the change in entropy for the folding transition shifts the TS to higher temperatures and has the effect of shifting the stability curve to the right (method III).
|
| Construction of the database |
|---|
|
|
|---|
|
|
The data show that, on average, a thermophilic protein has a Tm 31.5°C higher than its mesophilic homolog, for the 15 cases where data are available. In the case of
G, data were available for 17 of the 26 cases, and the average increase in
G of stabilization for the thermophilic homolog was 8.7 kcal mol1 (for the
G values, the average reported includes
G values listed in column 6 of Table 1
irrespective of the temperature at which they were measured; for both
Tm and 
G, entry 13 was not included). The sequence identity for the protein homologs was also compared where sequences were available. For this purpose, we used the CLUSTALW (Thompson et al. 1994) program as implemented on the EBI server (http://www.ebi.ac.uk/clustalw/) with the default settings. For the 16 cases where alignments were possible, the average sequence identity was 51%. The alignment scores varied from 11% identity (for aspartate aminotransferases from Sulfolobus solfataricus and pig heart cytosol) to 82% (for histone proteins MfA and MfoB). The average value of 51% identity is high considering the diversity of the proteins and the sources from which they are derived.
| Classification of data and example cases |
|---|
|
|
|---|
Stabilization by increased
G and reduced
Cp (methods I and II)
The combination of increased
G and reduced
Cp is the most commonly used way to achieve a higher Tm. Of the 26 sets of proteins, there are eight cases where this combination of stabilizing effects is used to increase the Tm of the thermophilic homolog. The proteins in this group are diverse with a range of sizes from the small (67 residues) nonenzymatic cold shock proteins to the large (398 residues) glycolytic enzyme phosphoglycerate kinase. The range of size and function observed points to broad applicability of this combination of methods to enhance thermostability.
A representative example from this group is the RNase H enzyme (entry 2 in Table 1
) from Thermus thermophilus (Tt) and Escherichia coli (Ec) (Hollien and Marqusee 1999). RNase H is a small enzyme, which cleaves RNA from RNADNA hybrids; the protein from the thermophile (TtRNase H) has 166 residues and shares a 52% sequence identity with its 155-residue mesophilic homolog (EcRNase H). High-resolution structures are available for the two proteins and the structures are very similar (Katayanagi et al. 1992; Ishikawa et al. 1993). To understand the thermodynamic basis of the difference in stability between the two proteins, GuHCl denaturation experiments as a function of temperature were performed to obtain stability curves for these proteins. The data reveal that TtRNase H is indeed more thermostable because of a lowered
Cp and a higher
G over a broad range of temperatures. The
Cp for the thermophilic protein TtRNase H is 0.9 kcal mol K1 lower than that for EcRNase H. The
GS is
5 kcal mol1 higher than the mesophilic homolog; however, the TS are very similar for the two proteins.
Stabilization by smaller
Cp (method II)
For the set of proteins included in this study, stabilization by reduced
Cp is the second most common method to attain a higher Tm. Five thermophilic proteins have a smaller
Cp compared to their mesophilic homologs, resulting in broader stability curves that allowed them to remain folded over a wider range of temperatures. Proteins in this group show some diversity in terms of their size and function, from the small DNA binding proteins like the 66-residue Sac7d to the large enzyme IPMD, which contains 345 residues. Three of the five proteins in this group are small DNA binding proteins, one is a subdomain of the enzyme phosphoglycerate kinase, and the last protein in this group is IPMD.
As a representative example of this group, consider the Sac7d protein (entry 9 in Table 1
) from Sulfolobus acidocaldarius (McCrary et al. 1996). Sac7d is a small DNA binding protein that is highly basic and whose structure has been solved by NMR spectroscopy (Edmondson et al. 1995). No mesophilic homolog for Sac7d is known; hence, comparisons have been made with a number of proteins of similar size (McCrary et al. 1996). Sac7d is stable over a broad range of pH (010), and DSC experiments have been performed over this pH range to estimate
Cp from a Kirchoff analysis. Solvent denaturation experiments with GuHCl were also performed and a global fit to these data provides a
Cp. This estimate for
Cp was found to be higher than that obtained from the DSC data, and the authors provide an excellent discussion on possible causes for this disparity (McCrary et al. 1996). In any case, either value of
Cp produces stability curves that look very similar to those for other mesophilic proteins of similar size, and the use of either value of
Cp does not cause significant differences in stability at 80°C, the habitat temperature of the organism. Surprisingly, estimates of free energy of at this temperature reveal that the protein is only marginally stable (1.6 kcal mol1).
Stabilization by a higher overall
G (method I)
Stabilization by higher
G is found to be as common a method of stabilization as stabilization by reduced
Cp. In five of the 26 cases, proteins from thermophilic organisms show a higher
G over a broad range of temperatures compared to their mesophilic homologs, thus shifting the stability curve up and achieving a higher Tm in the process. This group contains the three cases of HPr homologs, a pair of small archaeal histones and the enzyme cellulase subdomains. Most proteins in this group are small in size, like the archaeal histones (67 residues) or HPr homologs (88 residues), except for the cellulase catalytic domains, which have
270 amino acids. The composition of this group, with three of the six proteins being HPr homologs, precludes much insight into the diversity of this class in terms of both size and function.
As a representative example from this group, consider the HPr proteins from the thermophile Bacillus staerothermophilus (Bst) and the mesophile Bacillus subtilus (Bs) (entry 14 in Table 1
). HPr or histidine containing protein is involved in the PEP:glycose phosphotransferase system (PTS) in bacteria (Meadow et al. 1990). The BstHPr protein is the same size (88 residues), shows high sequence identity (72%), and has a structure almost identical to that of the mesophilic homolog (Sridharan et al. 2005). The BstHPr protein, however, has a higher Tm (
15°C) and a larger
GS (
3.2 kcal mol1). The complete analyses of stability curves reveal that the
Cp values for the two HPr proteins are very similar at 1.3 kcal mol1K1 (Razvi and Scholtz 2006). The TS values for the two proteins also are similar at 24.1° and 24.8°C (Bs and BstHPr respectively). Therefore, this pair of proteins is a nearly perfect example for stabilization by method I or by a higher overall
G at all temperatures.
The archaeal histone proteins use different methods to gain thermostabilty
We now consider the cases of four archaeal histone homologs: Three of these homologs were derived from hyperthermophilic archaea, and the fourth, from a mesophilic archaeon (Li et al. 1998). The thermophilic histones from Methanothermus fervidus (MfA, MfB) and Pyrococcus strain GB3a (PyA1) (entries 17, 19, and 23, respectively, in Table 1
) were compared to the mesophilic homolog from Methanobacterium formicicum (MfoB). The curious feature of these proteins is that each thermophilic homolog uses a different thermodynamic approach to achieve a higher Tm. The histone MfA, for example (entry 17 in Table 1
), belongs to the group of proteins that utilize a higher
G at all temperatures (method I). The other two homologs increase their Tm by a combination of all three methods (MfB) or by combining a higher overall
G with a higher TS (PyA1).
Stabilization by increased
G, smaller
Cp, and higher TS (methods I, II, and III)
This group of thermophilic proteins achieves higher Tm by a combination of all three methods, and the archaeal histone MfB is representative of this class. This histone attains a higher Tm by combining a reduced
Cp with higher TS and
G (methods I, II, and III). Three other thermophilic proteins were found to use this approach to increase their Tm; two of them are metal-cluster-containing proteins ferridoxin and rubredoxin. The third is the MGMT enzyme, which is also the largest protein in this group (174 residues).
MfB (entry 19 in Table 1
) shares 80% sequence identity with MfoB, the mesophilic histone homolog, and both proteins, like other histones studied here, are dimers in solution and unfold in a two-state manner to monomers (Li et al. 1998). DSC and thermal denaturation experiments monitored by CD have been used to construct stability curves for these proteins and the
Cp estimates are in good agreement. Also, theoretical estimates (Murphy and Freire 1992; Spolar et al. 1992; Myers et al. 1995) for the thermophilic homolog for which a structure is available are in good agreement with experimental values. The
Cp for histone MfB, the thermophilic homolog, is 1.9 kcal mol1K1, which is lower than that for MfoB (2.6 kcal mol1K1). The
GS for the thermophilic MfB is 14.6 kcal mol1, which is more than twice that for MfoB. The TS for MfB (40°C) is significantly greater than that for MfoB (32°C). Together these thermodynamic features of the MfB protein cause the Tm to be 113°C, significantly higher than that for MfoB (74.8°C).
Stabilization by increased
G and higher TS (methods I and III)
The third thermophilic histone homolog PyA1 represents a small group of proteins that achieve high Tm by combining a higher overall
G with a higher TS (methods I and III). Two other thermophilic proteins use this approach to achieve higher Tm: DHFR and cytochrome c-552 from Thermotoga maritima. PyA1 (entry 23 in Table 1
) is the same size as the mesophilic homolog, MfoB (67 residues), and they share 57% sequence identity (Li et al. 1998). Analyses of DSC and CD monitored unfolding experiments provided nearly identical
Cp estimates for the two proteins. The
Cp for PyA1 is 2.4 kcal mol1K1 and for MfoB it is 2.6 kcal mol1K1. The
GS for PyA1 is, however, larger than for MfoB (17.2 kcal mol1 vs. 7.2 kcal mol1). The TS for PyA1 is 44°C, which is significantly higher than that for MfoB (32°C). The high
GS and TS for PyA1, in comparison with the mesophilic homolog MfoB, make this protein a good example for thermostabilization by a combination of methods I and III.
Stabilization by reduced
Cp and higher TS (methods II and III)
The only case we found of a thermophilic protein using a combination of a reduced
Cp and higher TS to achieve a higher Tm is farnesyl diphosphate/geranylgeranyl diphosphate synthase. This is a dimeric enzyme from Thermococcus kodakiensis that has 343 residues (Fujiwara et al. 2004). GuHCl denaturation experiments performed at different temperatures were combined to construct a stability curve for this enzyme. Other thermodynamic parameters, like Tm (91°C),
Cp (2 kcal mol1 K1),
GS (3.8 kcal mol1), and TS (60°C), were estimated from the stability curve. From comparisons with other thermostable proteins, the investigators concluded that their enzyme achieved a higher Tm by a combination of lower
Cp with higher TS. No details of this comparison were provided.
| General observations on enhanced thermostability |
|---|
|
|
|---|
We find that the most common way to attain a higher Tm in proteins from thermophiles is to raise the stability curve to higher values of
G (higher intrinsic stability) at all temperatures; 77% of the thermophilic proteins in this study use higher
G independently or in combination with other stabilizing effects to increase Tm. The next most popular method used to attain a higher Tm is to lower
Cp (70% of thermophilic proteins in this study). Finally, the least number of occurrences (31% of the thermophilic proteins in this study) are reported for cases where the thermophilic protein exhibits a higher TS compared to the mesophilic homolog. However, it is pertinent to rationalize these observations based on how it might be easier to adopt one strategy rather than the other in terms of sequence changes because changes in
G,
Cp, or TS are effects of sequence alterations manifested through changes in structure.
To increase the
G of a protein at all temperatures, many options are available at the sequence level since any number of interactions like salt bridges, hydrogen bonds, or hydrophobic interactions may be added by single amino acid changes (for example, Pace 2000; Perl et al. 2000)). Similarly, to attain a lower
Cp, the sequence can be altered in many ways to provide for tighter core packing or by simply promoting structured clusters that persist in the denatured state, since
Cp is strongly correlated with
ASA for protein unfolding (Murphy and Freire 1992; Spolar et al. 1992; Myers et al. 1995). For example, it was suggested that a structured cluster in denatured TtRNase H caused the reduced
Cp for this protein, and this effect could be reversed by a single amino acid change (Guzman-Casado et al. 2003; Robic et al. 2003).
Stabilization by shifting the stability curve to higher temperatures (higher TS) is the least common method in our data set. This might be because very specific changes to the sequence would be required to reduce
S or the change in entropy between the folded and the unfolded states. Since this requires that either the entropy of the denatured state be reduced relative to the folded state or the entropy of the folded state be enhanced to more closely match that of the denatured state, it will require rather precise changes in the sequence that affect one of the two states differentially. For example, constraining a certain loop in the denatured state by introduction of proline residues or introduction of glycine residues in structured regions of a protein can reduce
S, by decreasing the configurational entropy of the denatured state or increasing it for the native state, respectively. Specialized mutations like these will reduce the
S of folding, resulting in higher TS. A curious feature of proteins in this class is that a majority of them are not enzymes. This could be because nonenzymatic proteins are tolerant of more stable conformations (thus more "rigid" conformations as discussed by Jaenicke 2000) afforded by enhanced TS. Unlike a lowered
Cp, which makes for a shallow stability curve, a high TS (method III) or high
G (method I) both provide for higher
G at high temperatures.
At the molecular level, however, each of the methods of stabilization are results of features like an increased number of hydrogen bonds, salt bridges, improved core packing, shorter and/or tighter surface loops, enhanced secondary structure propensities, or oligomerization. There have been many studies (Matthews 1993; Vogt and Argos 1997; Vogt et al. 1997; Szilagyi and Zavodszky 2000) that compare homologous proteins with known three-dimensional structures in which the number of stabilizing interactions have been compared with the aim of developing a "unifying set of rules" for thermostabilization (Petsko 2001). Although such a set of rules remains elusive, the results have been used to rationally design variants of proteins with desired properties (Bryan 2000; Eijsink et al. 2004). Computational methods have also been used with some success to rationally design proteins with enhanced thermostability (Dahiyat et al. 1997; Malakauskas and Mayo 1998; Korkegian et al. 2005). Directed evolution is another novel technique used to design protein variants with desired properties, which requires no a priori knowledge of stabilizing/destabilizing interactions like the rational design methodology. This technique has been applied to a large number of proteins with a good measure of success (Sieber et al. 1998; Wintrode and Arnold 2000; Arnold et al. 2001; Eijsink et al. 2005). It remains to be determined which thermodynamic methods have been used to achieve higher thermostability in the proteins designed by these methods. It should be especially enlightening to see the results for proteins designed by directed evolution, since this method is least constrained in terms of the sequence space explored and types of interactions that might be altered.
In conclusion, it appears that molecular studies, as well as those that characterize the thermodynamics, both fail to reveal a single cause (molecular) or effect (thermodynamic) that completely explains the ability of thermophilic proteins to survive and function at their high habitat temperatures. Instead, proteins appear to rely on combinations of stabilizing effects that manifest themselves in alterations of different thermodynamic parameters. Thus, as proteins have taught us time and time again, they are extremely adaptable and there is no single mechanism they use to maintain structure and function at high temperatures.
| Footnotes |
|---|
Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.062130306.
Abbreviations: Tm, melting temperature or temperature at midpoint of transition from native to denatured state in a thermal denaturation;
GT, free energy of stabilization at a temperature T;
Cp, change in heat capacity associated with protein unfolding;
H, change in enthalpy;
S, change in entropy; TS, temperature of maximal stability or temperature where change in entropy between native and denatured states is zero;
GS, free energy of stabilization at TS; TE, environment or habitat temperature of an organism;
ASA, change in solvent accessible surface area upon protein unfolding; GuHCl, guanidine hydrochloride; CspB, cold shock protein B; CheY, chemotactic protein Y; HPr, histidine containing phospho-carrier protein; MfA, archaeal histone A from hyperthermophile Methanothermus fervidus; MfB, archaeal histone B from hyperthermophile Methanothermus fervidus; PyA1, archaeal histone from hyperthermophile Pyrococcus strain GB3a; MfoB; archaeal histone B from mesophile Methanobacterium formicicum; IPMD, isopropyl malate dehydrogenase; MGMT, O6Methyl guanine DNA methyl transferase; DHFR, dihydrofolate reductase.
| Acknowledgments |
|---|
| References |
|---|
|
|
|---|
Arnold F.H., Wintrode P.L., Miyazaki K., Gershenson A. 2001. How enzymes adapt: Lessons from directed evolution. Trends Biochem. Sci. 26: 100106.[CrossRef][Medline]
Arnone M.I., Birolo L., Pascarella S., Cubellis M.V., Bossa F., Sannia G., Marino G. 1997. Stability of aspartate aminotransferase from Sulfolobus solfataricus. Protein Eng. 10: 237248.
Bava K.A., Gromiha M.M., Uedaira H., Kitajima K., Sarai A. 2004. ProTherm, version 4.0: Thermodynamic database for proteins and mutants. Nucleic Acids Res. 32: D120D121.
Beadle B.M., Baase W.A., Wilson D.B., Gilkes N.R., Shoichet B.K. 1999. Comparing the thermodynamic stabilities of a related thermophilic and mesophilic enzyme. Biochemistry 38: 25702576.[CrossRef][Medline]
Becktel W.J. and Schellman J.A. 1987. Protein stability curves. Biopolymers 26: 18591877.[CrossRef][Medline]
Bryan P.N. 2000. Protein engineering of Subtilisin. Biochim. Biophys. Acta 1543: 203222.[CrossRef][Medline]
Consalvi V., Chiaraluce R., Giangiacomo L., Scandurra R., Christova P., Karshikoff A., Knapp S., Ladenstein R. 2000. Thermal unfolding and conformational stability of the recombinant domain II of glutamate dehydrogenase from the hyperthermophile Thermotoga maritima. Protein Eng. 13: 501507.
Creighton T.E. 1992. Folding and binding. Curr. Opin. Struct. Biol. 2: 15.[Medline]
Dahiyat B.I., Sarisky C.A., Mayo S.L. 1997. De novo protein design: Towards fully automated sequence selection. J. Mol. Biol. 273: 789796.[CrossRef][Medline]
Dams T. and Jaenicke R. 1999. Stability and folding of dihydrofolate reductase from the hyperthermophilic bacterium Thermotoga maritima. Biochemistry 38: 91699178.[CrossRef][Medline]
Deutschman W.A. and Dahlquist F.W. 2001. Thermodynamic basis for the increased thermostability of CheY from the hyperthermophile Thermotoga maritima. Biochemistry 40: 1310713113.[CrossRef][Medline]
Dill K.A. 1990. Dominant forces in protein folding. Biochemistry 29: 71337155.[CrossRef][Medline]
Edmondson S.P., Qiu L., Shriver J.W. 1995. Solution structure of the DNA-binding protein Sac7d from the hyperthermophile Sulfolobus acidocaldarius. Biochemistry 34: 1328913304.[CrossRef][Medline]
Eijsink V.G., Bjork A., Gaseidnes S., Sirevag R., Synstad B., van den Burg B., Vriend G. 2004. Rational engineering of enzyme stability. J. Biotechnol. 113: 105120.[CrossRef][Medline]
Eijsink V.G., Gaseidnes S., Borchert T.V., van den Burg B. 2005. Directed evolution of enzyme stability. Biomol. Eng. 22: 2130.[CrossRef][Medline]
Fujiwara S., Yamanaka A., Hirooka K., Kobayashi A., Imanaka T., Fukusaki E. 2004. Temperature-dependent modulation of farnesyl diphosphate/geranylgeranyl diphosphate synthase from hyperthermophilic archaea. Biochem. Biophys. Res. Commun. 325: 10661074.[CrossRef][Medline]
Grattinger M., Dankesreiter A., Schurig H., Jaenicke R. 1998. Recombinant phosphoglycerate kinase from the hyperthermophilic bacterium Thermotoga maritima: Catalytic, spectral and thermodynamic properties. J. Mol. Biol. 280: 525533.[CrossRef][Medline]
Grimsley G.R., Huyghues-Despointes B.M.P., Pace C.N., Scholtz J.M. 2003. Measuring the conformational stability of a protein. In Purifying proteins for proteomics: A laboratory manual (ed. Simpson R.J.) . pp. 535566. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
Guzman-Casado M., Parody-Morreale A., Robic S., Marqusee S., Sanchez-Ruiz J.M. 2003. Energetic evidence for formation of a pH-dependent hydrophobic cluster in the denatured state of Thermus thermophilus ribonuclease H. J. Mol. Biol. 329: 731743.[CrossRef][Medline]
Hernandez G. and LeMaster D.M. 2001. Reduced temperature dependence of collective conformational opening in a hyperthermophile rubredoxin. Biochemistry 40: 1438414391.[CrossRef][Medline]
Hiller R., Zhou Z.H., Adams M.W., Englander S.W. 1997. Stability and dynamics in a hyperthermophilic protein with melting temperature close to 200°C. Proc. Natl. Acad. Sci. 94: 1132911332.
Hollien J. and Marqusee S. 1999. A thermodynamic comparison of mesophilic and thermophilic ribonucleases H. Biochemistry 38: 38313836.[CrossRef][Medline]
Honig B. 1999. Protein folding: From the Levinthal paradox to structure prediction. J. Mol. Biol. 293: 283293.[CrossRef][Medline]
Hu C.Q. and Sturtevant J.M. 1989. A differential scanning calorimetric study of the binding of sulfate ion and of Cibacron blue F3GA to yeast phosphoglycerate kinase. Biochemistry 28: 813818.[CrossRef][Medline]
Ionescu R.M., Smith V.F., O'Neill Jr. J.C., Matthews C.R. 2000. Multistate equilibrium unfolding of Escherichia coli dihydrofolate reductase: Thermodynamic and spectroscopic description of the native, intermediate, and unfolded ensembles. Biochemistry 39: 95409550.[CrossRef][Medline]
Ishikawa K., Okumura M., Katayanagi K., Kimura S., Kanaya S., Nakamura H., Morikawa K. 1993. Crystal structure of ribonuclease H from Thermus thermophilus HB8 refined at 2.8 Å resolution. J. Mol. Biol. 230: 529542.[CrossRef][Medline]
Jacob M., Holtermann G., Perl D., Reinstein J., Schindler T., Geeves M.A., Schmid F.X. 1999. Microsecond folding of the cold shock protein measured by a pressure-jump technique. Biochemistry 38: 28822891.[CrossRef][Medline]
Jaenicke R. 1991. Protein stability and molecular adaptation to extreme conditions. Eur. J. Biochem. 202: 715728.[Medline]
Jaenicke R. 1998. What ultrastable globular proteins teach us about protein stabilization. Biochemistry (Mosc.) 63: 312321.[Medline]
Jaenicke R. 2000. Do ultrastable proteins from hyperthermophiles have high or low conformational rigidity? Proc. Natl. Acad. Sci. 97: 29622964.
Jaenicke R. and Bohm G. 2001. Thermostability of proteins from Thermotoga maritima. Methods Enzymol. 334: 438469.[Medline]
Jaenicke R. and Zavodszky P. 1990. Proteins under extreme physical conditions. FEBS Lett. 268: 344349.[CrossRef][Medline]
Kanaya S. and Itaya M. 1992. Expression, purification, and characterization of a recombinant ribonuclease H from Thermus thermophilus HB8. J. Biol. Chem. 267: 1018410192.
Katayanagi K., Miyagawa M., Matsushima M., Ishikawa M., Kanaya S., Nakamura H., Ikehara M., Matsuzaki T., Morikawa K. 1992. Structural details of ribonuclease H from Escherichia coli as refined to an atomic resolution. J. Mol. Biol. 223: 10291052.[CrossRef][Medline]
Kauzmann W. 1959. Some factors in the interpretation of protein denaturation. Adv. Protein Chem. 14: 163.[Medline]
Knapp S., Karshikoff A., Berndt K.D., Christova P., Atanasov B., Ladenstein R. 1996. Thermal unfolding of the DNA-binding protein Sso7d from the hyperthermophile Sulfolobus solfataricus. J. Mol. Biol. 264: 11321144.[CrossRef][Medline]
Knapp S., Mattson P.T., Christova P., Berndt K.D., Karshikoff A., Vihinen M., Smith C.I., Ladenstein R. 1998. Thermal unfolding of small proteins with SH3 domain folding pattern. Proteins 31: 309319.[CrossRef][Medline]
Korkegian A., Black M.E., Baker D., Stoddard B.L. 2005. Computational thermostabilization of an enzyme. Science 308: 857860.
Lee C.F., Allen M.D., Bycroft M., Wong K.B. 2005. Electrostatic interactions contribute to reduced heat capacity change of unfolding in a thermophilic ribosomal protein l30e. J. Mol. Biol. 348: 419431.[CrossRef][Medline]
Li W.T., Grayling R.A., Sandman K., Edmondson S., Shriver J.W., Reeve J.N. 1998. Thermodynamic stability of archaeal histones. Biochemistry 37: 1056310572.[CrossRef][Medline]
Livingstone J.R., Spolar R.S., Record Jr. M.T. 1991. Contribution to the thermodynamics of protein folding from the reduction in water-accessible nonpolar surface area. Biochemistry 30: 42374244.[CrossRef][Medline]
Lopez M.M. and Makhatadze G.I. 2002. Differential scanning calorimetry. Methods Mol. Biol. 173: 113119.[Medline]
Malakauskas S.M. and Mayo S.L. 1998. Design, structure and stability of a hyperthermophilic protein variant. Nat. Struct. Biol. 5: 470475.[CrossRef][Medline]
Matthews B.W. 1993. Structural and genetic analysis of protein stability. Annu. Rev. Biochem. 62: 139160.[CrossRef][Medline]
McCrary B.S., Edmondson S.P., Shriver J.W. 1996. Hyperthermophile protein folding thermodynamics: Differential scanning calorimetry and chemical denaturation of Sac7d. J. Mol. Biol. 264: 784805.[CrossRef][Medline]
Meadow N.D., Fox D.K., Roseman S. 1990. The bacterial phosphoenolpyruvate: Glycose phosphotransferase system. Annu. Rev. Biochem. 59: 497542.[CrossRef][Medline]
Milla M.E., Brown B.M., Sauer R.T. 1994. Protein stability effects of a complete set of alanine substitutions in Arc repressor. Nat. Struct. Biol. 1: 518523.[CrossRef][Medline]
Motono C., Oshima T., Yamagishi A. 2001. High thermal stability of 3-isopropylmalate dehydrogenase from Thermus thermophilus resulting from low
Cp of unfolding. Protein Eng. 14: 961966.
Murphy K.P. and Freire E. 1992. Thermodynamics of structural stability and cooperative folding behavior in proteins. Adv. Protein Chem. 43: 313361.[Medline]
Myers J.K., Pace C.N., Scholtz J.M. 1995. Denaturant m values and heat capacity changes: Relation to changes in accessible surface areas of protein unfolding. Protein Sci. 4: 21382148.[Abstract]
Nojima H., Ikai A., Oshima T., Noda H. 1977. Reversible thermal unfolding of thermostable phosphoglycerate kinase. Thermostability associated with mean zero enthalpy change. J. Mol. Biol. 116: 429442.[CrossRef][Medline]
Nojima H., Hon-Nami K., Oshima T., Noda H. 1978. Reversible thermal unfolding of thermostable cytochrome c-552. J. Mol. Biol. 122: 3342.[CrossRef][Medline]
Ohmae E., Kurumiya T., Makino S., Gekko K. 1996. Acid and thermal unfolding of Escherichia coli dihydrofolate reductase. J. Biochem. 120: 946953.
Pace C.N. 1975. The stability of globular proteins. CRC Crit. Rev. Biochem. 3: 143.[Medline]
Pace C.N. 1992. Contribution of the hydrophobic effect to globular protein stability. J. Mol. Biol. 226: 2935.[CrossRef][Medline]
Pace C.N. 2000. Single surface stabilizer. Nat. Struct. Biol. 7: 345346.
Pace C.N., Shirley B.A., McNutt M., Gajiwala K. 1996. Forces contributing to the conformational stability of proteins. FASEB J. 10: 7583.[Abstract]
Perl D., Mueller U., Heinemann U., Schmid F.X. 2000. Two exposed amino acid residues confer thermostability on a cold shock protein. Nat. Struct. Biol. 7: 380383.[CrossRef][Medline]
Perutz M.F. 1978. Electrostatic effects in proteins. Science 201: 11871191.
Perutz M.F. and Raidt H. 1975. Stereochemical basis of heat stability in bacterial ferredoxins and in haemoglobin A2. Nature 255: 256259.[CrossRef][Medline]
Petsko G.A. 2001. Structural basis of thermostability in hyperthermophilic proteins, or "there's more than one way to skin a cat". Methods Enzymol. 334: 469478.[Medline]
Pfeil W., Gesierich U., Kleemann G.R., Sterner R. 1997. Ferredoxin from the hyperthermophile Thermotoga maritima is stable beyond the boiling point of water. J. Mol. Biol. 272: 591596.[CrossRef][Medline]
Razvi A. and Scholtz J.M. 2006. A thermodynamic comparison of HPr proteins from extremophilic organisms. Biochemistry 45: 40844092.[CrossRef][Medline]
Rees D.C. and Adams M.W. 1995. Hyperthermophiles: Taking the heat and loving it. Structure 3: 251254.[Medline]
Robic S., Guzman-Casado M., Sanchez-Ruiz J.M., Marqusee S. 2003. Role of residual structure in the unfolded state of a thermophilic protein. Proc. Natl. Acad. Sci. 100: 1134511349.
Rose G.D. and Wolfenden R. 1993. Hydrogen bonding, hydrophobicity, packing, and protein folding. Annu. Rev. Biophys. Biomol. Struct. 22: 381415.[Medline]
Ruiz-Sanz J., Filimonov V.V., Christodoulou E., Vorgias C.E., Mateo P.L. 2004. Thermodynamic analysis of the unfolding and stability of the dimeric DNA-binding protein HU from the hyperthermophilic eubacterium Thermotoga maritima and its E34D mutant. Eur. J. Biochem. 271: 14971507.[Medline]
Russell N.J. and Fukunaga N. 1990. A comparison of thermal adaptation of membrane lipids in psychrophilic and thermophilic bacteria. FEMS Microbiol. Rev. 75: 171182.
Schindler T. and Schmid F.X. 1996. Thermodynamic properties of an extremely rapid protein folding reaction. Biochemistry 35: 1683316842.[CrossRef][Medline]
Shiraki K., Nishikori S., Fujiwara S., Hashimoto H., Kai Y., Takagi M., Imanaka T. 2001. Comparative analyses of the conformational stability of a hyperthermophilic protein and its mesophilic counterpart. Eur. J. Biochem. 268: 41444150.[Medline]
Sieber V., Pluckthun A., Schmid F.X. 1998. Selecting proteins with improved stability by a phage-based method. Nat. Biotechnol. 16: 955960.[CrossRef][Medline]
Somero G.N. 1995. Proteins and temperature. Annu. Rev. Physiol. 57: 4368.[CrossRef][Medline]
Spolar R.S., Livingstone J.R., Record Jr. M.T. 1992. Use of liquid hydrocarbon and amide transfer data to estimate contributions to thermodynamic functions of protein folding from the removal of nonpolar and polar surface from water. Biochemistry 31: 39473955.[CrossRef][Medline]
Sridharan S., Razvi A., Scholtz J.M., Sacchettini J.C. 2005. The HPr proteins from the thermophile Bacillus stearothermophilus can form domain-swapped dimers. J. Mol. Biol. 346: 919931.[CrossRef][Medline]
Sterner R. and Liebl W. 2001. Thermophilic adaptation of proteins. Crit. Rev. Biochem. Mol. Biol. 36: 39106.[CrossRef][Medline]
Szilagyi A. and Zavodszky P. 2000. Structural differences between mesophilic, moderately thermophilic and extremely thermophilic protein subunits: Results of a comprehensive survey. Struct. Fold. Des. 8: 493504.[Medline]
Thompson J.D., Higgins D.G., Gibson T.J. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 46734680.
van de Vossenberg J.L., Driessen A.J., Konings W.N. 1998. The essence of being extremophilic: The role of the unique archaeal membrane lipids. Extremophiles 2: 163170.[CrossRef][Medline]
Vieille C. and Zeikus J.G. 1996. Thermozymes: Identifying molecular determinants of protein structural and functional stability. Trends Biotechnol. 14: 183190.[CrossRef]
Vogt G. and Argos P. 1997. Protein thermal stability: Hydrogen bonds or internal packing? Fold. Des. 2: S40S46.[CrossRef][Medline]
Vogt G., Woell S., Argos P. 1997. Protein thermal stability, hydrogen bonds, and ion pairs. J. Mol. Biol. 269: 631643.[CrossRef][Medline]
Wassenberg D., Welker C., Jaenicke R. 1999. Thermodynamics of the unfolding of the cold-shock protein from Thermotoga maritima. J. Mol. Biol. 289: 187193.[CrossRef][Medline]
Wintrode P.L. and Arnold F.H. 2000. Temperature adaptation of enzymes: Lessons from laboratory evolution. Adv. Protein Chem. 55: 161225.[Medline]
Xu S., Qin S., Pan X.M. 2004. Thermal and conformational stability of Ssh10b protein from archaeon Sulfolobus shibattae. Biochem. J. 382: 433440.[CrossRef][Medline]
Yancey P.H., Clark M.E., Hand S.C., Bowlus R.D., Somero G.N. 1982. Living with water stress: Evolution of osmolyte systems. Science 217: 12141222.
![]()
CiteULike
Connotea
Del.icio.us
Digg
Reddit
Technorati What's this?
This article has been cited by other articles:
![]() |
L. Montanucci, P. Fariselli, P. L. Martelli, and R. Casadio Predicting protein thermostability changes from sequence upon multiple mutations Bioinformatics, July 1, 2008; 24(13): i190 - i195. [Abstract] [PDF] |
||||
![]() |
Y. Dehouck, B. Folch, and M. Rooman Revisiting the correlation between proteins' thermoresistance and organisms' thermophilicity Protein Eng. Des. Sel., April 1, 2008; 21(4): 275 - 278. [Abstract] [Full Text] [PDF] |
||||
![]() |
L. Wang, A. B. Cowley, and D. R. Benson Enhancing the thermal stability of mitochondrial cytochrome b5 by introducing a structural motif characteristic of the less stable microsomal isoform Protein Eng. Des. Sel., October 24, 2007; (2007) gzm053v1. [Abstract] [Full Text] [PDF] |
||||
![]() |
A. Sujak, N. J. M. Sanghamitra, O. Maneg, B. Ludwig, and S. Ma |