Crystal structures of mutant forms of the Bacillus caldolyticus cold shock protein differing in thermal stability

Delbrück, Heinrich; Muêller, U.; Perl, Dieter; Schmid, Franz X.; Heinemann, Udo

doi:10.1006/jmbi.2001.5051

Cited by 40 publications

(50 citation statements)

References 29 publications

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“…This method has been widely used to study electrostatic contribution to protein folding stabilities through mutations that involve charged or polar residues. For example, Bacillus caldolyticus cold shock protein (Bc-Csp) is a thermophilic protein, which differs from Bacillus subtilis cold shock protein B (Bs-CspB), its mesophilic homolog, in 11 of its 66 residues Delbruck et al, 2001). Through mutational studies which reduced the sequence differences between these two protein molecules, both experiment Pace, 2000;Perl et al, 2000;Delbruck et al, 2001;) and PB calculations demonstrated that the difference in stability of these two proteins arises mostly from the interactions among three residues: Arg 3, Glu 46, and Leu 66 in Bc-Csp, as compared with Glu 3, Ala 46, and Glu 66 in Bs-CspB.…”

Section: Ivc Folding Free Energiesmentioning

confidence: 99%

“…For example, Bacillus caldolyticus cold shock protein (Bc-Csp) is a thermophilic protein, which differs from Bacillus subtilis cold shock protein B (Bs-CspB), its mesophilic homolog, in 11 of its 66 residues Delbruck et al, 2001). Through mutational studies which reduced the sequence differences between these two protein molecules, both experiment Pace, 2000;Perl et al, 2000;Delbruck et al, 2001;) and PB calculations demonstrated that the difference in stability of these two proteins arises mostly from the interactions among three residues: Arg 3, Glu 46, and Leu 66 in Bc-Csp, as compared with Glu 3, Ala 46, and Glu 66 in Bs-CspB. The removal of the repulsion between Glu 3 and Glu 66 and creation of a favorable salt bridge between Arg 3 and Glu 46 are the main reasons that BcCsp is more stable than Bs-CspB at higher temperatures.…”

Section: Ivc Folding Free Energiesmentioning

confidence: 99%

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Computational Methods for Biomolecular Electrostatics

Dong

Olsen

Baker

2008

Methods in Cell Biology

116

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An understanding of intermolecular interactions is essential for insight into how cells develop, operate, communicate and control their activities. Such interactions include several components: contributions from linear, angular, and torsional forces in covalent bonds, van der Waals forces, as well as electrostatics. Among the various components of molecular interactions, electrostatics are of special importance because of their long range and their influence on polar or charged molecules, including water, aqueous ions, and amino or nucleic acids, which are some of the primary components of living systems. Electrostatics, therefore, play important roles in determining the structure, motion and function of a wide range of biological molecules. This chapter presents a brief overview of electrostatic interactions in cellular systems with a particular focus on how computational tools can be used to investigate these types of interactions.

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Section: Ivc Folding Free Energiesmentioning

confidence: 99%

Section: Ivc Folding Free Energiesmentioning

confidence: 99%

Computational Methods for Biomolecular Electrostatics

Dong

Olsen

Baker

2008

Methods in Cell Biology

116

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“…Previously, studies investigating the cause of thermostability (23) in proteins from thermophilic eubacteria have either focused in detail on the variation of relatively small families of folds from thermophile to mesophile (24,25) or else have directed their attention principally toward particular sequence-based means for thermal stabilization (26,27), such as salt-bridge formation (28,29) or disulfide bridges (15). In contrast to previous studies, here we focus on comparative analysis of patterns of fold usage across whole thermophilic and mesophilic proteomes by calculating the normalized contact trace distributions for sets of fully sequenced thermophilic and mesophilic genomes.…”

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confidence: 99%

Natural selection of more designable folds: A mechanism for thermophilic adaptation

England

Shakhnovich

2003

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

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An open question of great interest in biophysics is whether variations in structure cause protein folds to differ in the number of amino acid sequences that can fold to them stably, i.e., in their designability. Recently, we have shown that a novel quantitative measure of a fold's tertiary topology, called its contact trace, strongly correlates with the fold's designability. Here, we investigate the relationship between a fold's contact trace and its relative frequency of usage in mesophilic vs. thermophilic eubacteria. We observe that thermophilic organisms exhibit a bias toward using folds of higher contact trace when compared with mesophiles. We establish this difference both for the distributions of folds at the whole-proteome level and also through more focused structural comparisons of orthologous proteins. Our findings suggest that thermophilic adaptation in bacterial genomes occurs in part through natural selection of more designable folds, pointing to designability as a key component of protein fitness.U nderstanding the adaptations that enable thermophilic organisms to survive at extreme temperatures is a challenge that has interested researchers since 1897 (1), and great strides have been made along this line of inquiry since the recent publications of complete genomes for several hyperthermophilic species (2). However, most research in this area has focused on amino acid sequence variations that increase the thermodynamic stability of thermophilic proteins while leaving their structures unchanged (2, 3). Far less is known about what structural differences exist between thermophilic and mesophilic proteomes. One interesting possibility is that a thermophilic bias in structure may manifest as a preference for folds that are able to accommodate a large number of low-energy sequences, because such folds have a higher probability of being able to maintain their stability while adapting by mutation to new pressures. This hypothesis relates to another problem of great interest in biophysics: how the structural topology of a protein fold affects its designability (4-9). Here, we present results that point to an important connection between these two problems. Making use of what is known analytically about the relationship between a fold's topology and its designability and thermostability, we report an adaptation mechanism of thermophillic bacteria: one that proceeds by selection of more designable folds.Recently, a new theoretical treatment of designability has been developed within the framework of a residue-residue contact Hamiltonian (10). This Hamiltonian is a well established model for protein energetics that defines the conformational energy of a polypeptide chain as the sum of the pairwise interaction energies of all of the amino acid pairs whose ␣ carbons are separated by a distance less than some contact cutoff, typically chosen to be Ϸ7.5 Å (11). More formally, for a chain of length N with a monomer alphabet containing M amino acid types (of course, M ϭ 20 for real proteins), we can define the ene...

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“…[1] A disulphide bond (Cys509-Cys695) is present towards the N and C termini. A1 has an overall cuboid shape with distinct positively and negatively charged areas on the surface.…”

mentioning

confidence: 99%

“…We have investigated the native-state dynamics of the 66-residue beta-barrel protein Bc-Csp L66E (PDB code 1HZB [1]), using parallel tempering simulations. Loop fluctuations were identified.…”

mentioning

confidence: 99%