1
|
Regulation of Protein Structural Changes by Incorporation of a Small-Molecule Linker. Int J Mol Sci 2018; 19:ijms19123714. [PMID: 30469528 PMCID: PMC6321067 DOI: 10.3390/ijms19123714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 11/16/2018] [Accepted: 11/19/2018] [Indexed: 12/12/2022] Open
Abstract
Proteins have the potential to serve as nanomachines with well-controlled structural movements, and artificial control of their conformational changes is highly desirable for successful applications exploiting their dynamic structural characteristics. Here, we demonstrate an experimental approach for regulating the degree of conformational change in proteins by incorporating a small-molecule linker into a well-known photosensitive protein, photoactive yellow protein (PYP), which is sensitized by blue light and undergoes a photo-induced N-terminal protrusion coupled with chromophore-isomerization-triggered conformational changes. Specifically, we introduced thiol groups into specific sites of PYP through site-directed mutagenesis and then covalently conjugated a small-molecule linker into these sites, with the expectation that the linker is likely to constrain the structural changes associated with the attached positions. To investigate the structural dynamics of PYP incorporated with the small-molecule linker (SML-PYP), we employed the combination of small-angle X-ray scattering (SAXS), transient absorption (TA) spectroscopy and experiment-restrained rigid-body molecular dynamics (MD) simulation. Our results show that SML-PYP exhibits much reduced structural changes during photo-induced signaling as compared to wild-type PYP. This demonstrates that incorporating an external molecular linker can limit photo-induced structural dynamics of the protein and may be used as a strategy for fine control of protein structural dynamics in nanomachines.
Collapse
|
2
|
Yang C, Kim TW, Kim Y, Choi J, Lee SJ, Ihee H. Kinetics of the E46Q mutant of photoactive yellow protein investigated by transient grating spectroscopy. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.03.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
3
|
Yang C, Kim SO, Kim Y, Yun SR, Choi J, Ihee H. Photocycle of Photoactive Yellow Protein in Cell-Mimetic Environments: Molecular Volume Changes and Kinetics. J Phys Chem B 2017; 121:769-779. [PMID: 28058827 DOI: 10.1021/acs.jpcb.6b13076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using various spectroscopic techniques such as UV-visible spectroscopy, circular dichroism spectroscopy, NMR spectroscopy, small-angle X-ray scattering, transient grating, and transient absorption techniques, we investigated how cell-mimetic environments made by crowding influence the photocycle of photoactive yellow protein (PYP) in terms of the molecular volume change and kinetics. Upon addition of molecular crowding agents, the ratio of the diffusion coefficient of the blue-shifted intermediate (pB) to that of the ground species (pG) significantly changes from 0.92 and approaches 1.0. This result indicates that the molecular volume change accompanied by the photocycle of PYP in molecularly crowded environments is much smaller than that which occurs in vitro and that the pB intermediate under crowded environments favors a compact conformation due to the excluded volume effect. The kinetics of the photocycle of PYP in cell-mimetic environments is greatly decelerated by the dehydration, owing to the interaction between the protein and small crowding agents, but is barely affected by the excluded volume effect. The results lead to the inference that the signaling transducer of PYP may not necessarily utilize the conformational change of PYP to sense the signaling state.
Collapse
Affiliation(s)
- Cheolhee Yang
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science , Daejeon 305-701, Republic of Korea.,Department of Chemistry, KAIST , Daejeon 305-701, Republic of Korea
| | - Seong Ok Kim
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science , Daejeon 305-701, Republic of Korea.,Department of Chemistry, KAIST , Daejeon 305-701, Republic of Korea
| | - Yonggwan Kim
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science , Daejeon 305-701, Republic of Korea.,Department of Chemistry, KAIST , Daejeon 305-701, Republic of Korea
| | - So Ri Yun
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science , Daejeon 305-701, Republic of Korea.,Department of Chemistry, KAIST , Daejeon 305-701, Republic of Korea
| | - Jungkweon Choi
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science , Daejeon 305-701, Republic of Korea.,Department of Chemistry, KAIST , Daejeon 305-701, Republic of Korea
| | - Hyotcherl Ihee
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science , Daejeon 305-701, Republic of Korea.,Department of Chemistry, KAIST , Daejeon 305-701, Republic of Korea
| |
Collapse
|