A consensus zinc finger peptide: design, high-affinity metal binding, a pH-dependent structure, and a His to Cys sequence variant

Krizek, Beth A.; Amann, Barbara; Kilfoil, Valda J.; Merkle, Denise L.; Berg, Jeremy M.

doi:10.1021/ja00012a021

Cited by 241 publications

(336 citation statements)

References 0 publications

Supporting

Mentioning

312

Contrasting

Order By: Relevance

“…This structure differs from what has traditionally been called a molten globule (Kuwajima, 1989), since there is no substantial disruption of tertiary interactions as probed by near-UV circular dichroism and absorption spectroscopy. Moreover, the chemical shift dispersion in the proton NMR spectrum remains fully preserved.…”

Section: Response Of Rdpf To Environmental Changesmentioning

confidence: 71%

“…ANS is a polycyclic aromatic fluorescent probe that interacts with proteins whose hydrophobic sites are, to some extent, solvent-exposed (Semisotnov et al, 1991). It has been used extensively to probe the molten globular states (Kuwajima, 1989) of proteins; we have applied this approach to RdPf to probe the overall folding of the protein at low pH. Figure 5 shows that, at pH 2, room temperature, and low ionic strength, the quantum yield for the ANS fluorescence emission increases dramatically upon addition of RdPf to the solution in nearly equimolar amounts.…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Response of Rubredoxin from Pyrococcus furiosus to Environmental Changes: Implications for the Origin of Hyperthermostability

Cavagnero¹,

Zhou²,

Adams³

et al. 1995

Biochemistry

View full text Add to dashboard Cite

The bases of the hyperthennostability of rubredoxin from Py~ococcus furiosus (RdPf) have been probed by structural perturbations induced by solution pH and ionic strength changes. Comparison of the solution behavior at pH 7 and pH 2, as probed by far-and near-UV circular dichroism, Trp fluorescence emission, 1 -anilinonaphthalene-8-sulfonate (ANS) binding, and NMR spectroscopy, reveals the presence of only minimal structural variations at room temperature. At pH 2, the protein displays a surprising nearly native-like behavior at high ionic strength while, at low ionic strength, it is capable of strongly binding the hydrophobic probe ANS. All the secondary and tertiary structural features, including the environment of the hydrophobic core, appear to be intact regardless of pH and ionic strength. The apparent "melting" or denaturation temperature at pH 2, however, is 42 "C lower than at pH 7. This is attributed to the perturbation of many electrostatic interactions, including the disruption of all the ion pairs, which is complete at pH 2, as indicated by electrometric pH titrations. The implications of these findings for the origins of the hyperthennostability of rubredoxin are discussed.The existence of life forms that live at elevated temperature and pressure is an open manifestation of nature's ingenuity in managing to support life even under the most adverse conditions. A variety of so-called hyperthermophilic microorganisms have been isolated in recent years (Stetter et al., 1990;Adams, 1990;Stetter, 1986) in the vicinity of both terrestrial and submarine hydrothermal vents. The majority of them are classified as Archaea (Woese et al., 1990) and thrive at temperatures up to 110 "C, the highest temperature known to be compatible with life. They are also the most slowly evolving or "primitive" of known organisms. Little is known of the novel biochemistry that must be required to sustain life above 100 "C. However, the quest for biomolecules displaying unusual and interesting physicochemical properties has recently led to the discovery and isolation of specific enzymes from these hyperthermophilic organisms. Among those that have been purified so far are proteases (Eggen et al., 1990;Cowan et al., 1987), redox proteins (Aono et al., 1989;Blake et al., 1991), hydrogenases Juszczak et al., 1991;Pihl & Maier, 1991), dehydrogenases (Robb et al., 1992), ferredoxin-dependent oxidoreductases (Mukund & Adams, 1990), DNA polymerases (Lundberg et al., 1991), and enzymes involved in carbohydrate metabolism (Koch & Zablowski, 1990;Constantino et al., 1990). These enzymes are composed of the regular 20 amino acids and display a thermal stability unknown to their mesophilic counterparts. Yet, sequence comparisons reveal no apparent striking differences. At this juncture, the origin of protein hyperthermostability (Flam, * To whom correspondence should be addressed.

show abstract

Section: Response Of Rdpf To Environmental Changesmentioning

confidence: 71%

Section: Resultsmentioning

confidence: 99%

Response of Rubredoxin from Pyrococcus furiosus to Environmental Changes: Implications for the Origin of Hyperthermostability

Cavagnero¹,

Zhou²,

Adams³

et al. 1995

Biochemistry

View full text Add to dashboard Cite

show abstract

“…The second motif contains a cysteine in place of the terminal histidine residue. Such a substitution has been observed in a number of zinc fingers in various organisms (especially in the last zinc finger in a tandem array of zinc fingers) and has been demonstrated to allow formation of a functional zinc finger domain (23).…”

Section: Discussionmentioning

confidence: 96%

The Cia5 gene controls formation of the carbon concentrating mechanism in Chlamydomonas reinhardtii

Xiang

Zhang

Weeks

2001

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

135

117

View full text Add to dashboard Cite

Wild-type Chlamydomonas reinhardtii cells shifted from high concentrations (5%) of CO 2 to low, ambient levels (0.03%) rapidly increase transcription of mRNAs from several CO 2-responsive genes. Simultaneously, they develop a functional carbon concentrating mechanism that allows the cells to greatly increase internal levels of CO 2 and HCO 3 ؊ . The cia5 mutant is defective in all of these phenotypes. A newly isolated gene, designated Cia5, restores transformed cia5 cells to the phenotype of wild-type cells. The 6,481-bp gene produces a 5.1-kb mRNA that is present constitutively in light in high and low CO 2 both in wild-type cells and the cia5 mutant. It encodes a protein that has features of a putative transcription factor and that, likewise, is present constitutively in low and high CO 2 conditions. Complementation of cia5 can be achieved with a truncated Cia5 gene that is missing the coding information for 54 C-terminal amino acids. Unlike wild-type cells or cia5 mutants transformed with an intact Cia5 gene, cia5 mutants complemented with the truncated gene exhibit constitutive synthesis of mRNAs from CO 2-responsive genes in light under both high and low CO 2 conditions. These discoveries suggest that posttranslational changes to the C-terminal domain control the ability of CIA5 to act as an inducer and directly or indirectly control transcription of CO 2-responsive genes. Thus, CIA5 appears to be a master regulator of the carbon concentrating mechanism and is intimately involved in the signal transduction mechanism that senses and allows immediate responses to fluctuations in environmental CO 2 and HCO 3 ؊ concentrations.

show abstract

“…This approach uses large multiple sequence alignments of related protein sequences to determine the most over represented amino acids at each position within a domain [20][21][22][23] . Because of their enrichment over vast evolutionary timescales, these amino acids are predicted to be best suited to enhance that domain's activity or stability.…”

Section: A Consensus Ppr Protein Scaffoldmentioning

confidence: 99%

An artificial PPR scaffold for programmable RNA recognition

et al. 2014

View full text Add to dashboard Cite

Pentatricopeptide repeat (PPR) proteins control diverse aspects of RNA metabolism in eukaryotic cells. Although recent computational and structural studies have provided insights into RNA recognition by PPR proteins, their highly insoluble nature and inconsistencies between predicted and observed modes of RNA binding have restricted our understanding of their biological functions and their use as tools. Here we use a consensus design strategy to create artificial PPR domains that are structurally robust and can be programmed for sequence-specific RNA binding. The atomic structures of these artificial PPR domains elucidate the structural basis for their stability and modelling of RNA-protein interactions provides mechanistic insights into the importance of RNA-binding residues and suggests modes of PPR-RNA association. The modular mode of RNA binding by PPR proteins holds great promise for the engineering of new tools to target RNA and to understand the mechanisms of gene regulation by natural PPR proteins.

show abstract

A consensus zinc finger peptide: design, high-affinity metal binding, a pH-dependent structure, and a His to Cys sequence variant

Cited by 241 publications

References 0 publications

Response of Rubredoxin from Pyrococcus furiosus to Environmental Changes: Implications for the Origin of Hyperthermostability

Response of Rubredoxin from Pyrococcus furiosus to Environmental Changes: Implications for the Origin of Hyperthermostability

The Cia5 gene controls formation of the carbon concentrating mechanism in Chlamydomonas reinhardtii

An artificial PPR scaffold for programmable RNA recognition

Contact Info

Product

Resources

About