1
|
Effects of ionic strength on the folding and stability of SAMP1, a ubiquitin-like halophilic protein. Biophys J 2022; 121:552-564. [PMID: 35063455 PMCID: PMC8874027 DOI: 10.1016/j.bpj.2022.01.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 12/13/2021] [Accepted: 01/13/2022] [Indexed: 11/21/2022] Open
Abstract
Our knowledge of the folding behavior of proteins from extremophiles is limited at this time. These proteins may more closely resemble the primordial proteins selected in early evolution under extreme conditions. The small archaeal modifier protein 1 (SAMP1) studied in this report is an 87-residue protein with a β-grasp fold found in the halophile Haloferax volcanii from the Dead Sea. To gain insight into the effects of salt on the stability and folding mechanism of SAMP1, we conducted equilibrium and kinetic folding experiments as a function of sodium chloride concentration. The results revealed that increasing ionic strength accelerates refolding and slows down unfolding of SAMP1, giving rise to a pronounced salt-induced stabilization. With increasing NaCl concentration, the rate of folding observed via a combination of continuous-flow (0.1-2 ms time range) and stopped-flow measurements (>2 ms) exhibited a >100-fold increase between 0.1 and 1.5 M NaCl and leveled off at higher concentrations. Using the Linderström-Lang smeared charge formalism to model electrostatic interactions in ground and transition states encountered during folding, we showed that the observed salt dependence is dominated by Debye-Hückel screening of electrostatic repulsion among numerous negatively charged residues. Comparisons are also drawn with three well-studied mesophilic members of the β-grasp superfamily: protein G, protein L, and ubiquitin. Interestingly, the folding rate of SAMP1 in 3 M sodium chloride is comparable to that of protein G, ubiquitin, and protein L at lower ionic strength. The results indicate the important role of electrostatic interactions in protein folding and imply that proteins have evolved to minimize unfavorable charge-charge interactions under their specific native conditions.
Collapse
|
2
|
Baba M, Kojima K, Nakase R, Imai S, Yamasaki T, Takita T, Crouch RJ, Yasukawa K. Effects of neutral salts and pH on the activity and stability of human RNase H2. J Biochem 2017; 162:211-219. [PMID: 28402412 DOI: 10.1093/jb/mvx021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 02/13/2017] [Indexed: 11/14/2022] Open
Abstract
Ribonuclease H (RNase H) specifically degrades the RNA of RNA/DNA hybrid. Recent study has shown that a single ribonucleotide is embedded in DNA double strand at every few thousand base pairs in human genome, and human RNase H2 is involved in its removal. Here, we examined the effects of neutral salts and pH on the activity and stability of human RNase H2. NaCl, KCl, RbCl and NaBr increased the activity to 170-390% at 10-60 mM, while LiCl, LiBr and CsCl inhibited it, suggesting that species of cation, but not anion, is responsible for the effect on activity. NaCl and KCl increased the stability by decreasing the first-order rate constant of the inactivation to 50-60% at 60-80 mM. The activity at 25-35 °C exhibited a narrow bell-shaped pH-dependence with the acidic and alkaline pKe (pKe1 and pKe2) values of 7.3 - 7.6 and 8.1 - 8.8, respectively. Enthalpy changes (ΔH°) of deprotonation were 5 ± 21 kJ mol-1 for pKe1 and 68 ± 25 kJ mol-1 for pKe2. These results suggest that the ionizable groups responsible for pKe1 may be two out of Asp34, Glu35 and Asp141 of DEDD motif, and that for pKe2 may be Lys69 of DSK motif.
Collapse
Affiliation(s)
- Misato Baba
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Oiwakecho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kenji Kojima
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Oiwakecho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Rihoko Nakase
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Oiwakecho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Shota Imai
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Oiwakecho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Tomomi Yamasaki
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Oiwakecho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Oiwakecho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Robert J Crouch
- Section on Formation of RNA, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Oiwakecho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| |
Collapse
|