1
|
Nordahl L, Akkuratov EE, Heimgärtner J, Schach K, Meineke B, Elsässer S, Wennmalm S, Brismar H. Detection and quantification of Na,K-ATPase dimers in the plasma membrane of living cells by FRET-FCS. Biochim Biophys Acta Gen Subj 2024; 1868:130619. [PMID: 38643888 DOI: 10.1016/j.bbagen.2024.130619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/25/2024] [Accepted: 04/12/2024] [Indexed: 04/23/2024]
Abstract
The sodium potassium pump, Na,K-ATPase (NKA), is an integral plasma membrane protein, expressed in all eukaryotic cells. It is responsible for maintaining the transmembrane Na+ gradient and is the major determinant of the membrane potential. Self-interaction and oligomerization of NKA in cell membranes has been proposed and discussed but is still an open question. Here, we have used a combination of FRET and Fluorescence Correlation Spectroscopy, FRET-FCS, to analyze NKA in the plasma membrane of living cells. Click chemistry was used to conjugate the fluorescent labels Alexa 488 and Alexa 647 to non-canonical amino acids introduced in the NKA α1 and β1 subunits. We demonstrate that FRET-FCS can detect an order of magnitude lower concentration of green-red labeled protein pairs in a single-labeled red and green background than what is possible with cross-correlation (FCCS). We show that a significant fraction of NKA is expressed as a dimer in the plasma membrane. We also introduce a method to estimate not only the number of single and double labeled NKA, but the number of unlabeled, endogenous NKA and estimate the density of endogenous NKA at the plasma membrane to 1400 ± 800 enzymes/μm2.
Collapse
Affiliation(s)
- Linnea Nordahl
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Box 1031, 171 21 Solna, Sweden
| | - Evgeny E Akkuratov
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Johannes Heimgärtner
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Box 1031, 171 21 Solna, Sweden
| | - Katja Schach
- Graduate Training Centre of Neuroscience, University of Tübingen, Otfried-Müller-Str. 27, 72076 Tübingen, Germany
| | - Birthe Meineke
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Box 1031, 171 21 Solna, Sweden
| | - Simon Elsässer
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Box 1031, 171 21 Solna, Sweden
| | - Stefan Wennmalm
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Box 1031, 171 21 Solna, Sweden.
| | - Hjalmar Brismar
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Box 1031, 171 21 Solna, Sweden; Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Box 1031, 171 21 Solna, Sweden
| |
Collapse
|
2
|
Halder R, Warshel A. Energetic and structural insights behind calcium induced conformational transition in calmodulin. Proteins 2024; 92:384-394. [PMID: 37915244 PMCID: PMC10872638 DOI: 10.1002/prot.26620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 10/01/2023] [Accepted: 10/10/2023] [Indexed: 11/03/2023]
Abstract
Calmodulin (CaM) is a key signaling protein that triggers several cellular and physiological processes inside the cell. Upon binding with calcium ion, CaM undergoes large scale conformational transition from a closed state to an open state that facilitates its interaction with various target protein and regulates their activity. This work explores the origin of the energetic and structural variation of the wild type and mutated CaM and explores the molecular origin for the structural differences between them. We first calculated the sequential calcium binding energy to CaM using the PDLD/S-LRA/β approach. This study shows a very good correlation with experimental calcium binding energies. Next we calculated the calcium binding energies to the wild type CaM and several mutated CaM systems which were reported experimentally. On the structural aspect, it has been reported experimentally that certain mutation (Q41L-K75I) in calcium bound CaM leads to complete conformational transition from an open to a closed state. By using equilibrium molecular dynamics simulation, free energy calculation and contact frequency map analysis, we have shown that the formation of a cluster of long-range hydrophobic contacts, initiated by the Q41L-K75I CaM variant is the driving force behind its closing motion. This study unravels the energetics and structural aspects behind calcium ion induced conformational changes in wild type CaM and its variant.
Collapse
Affiliation(s)
- Ritaban Halder
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| |
Collapse
|
3
|
Sano Y, Itoh Y, Kamonprasertsuk S, Suzuki L, Fukasawa A, Oikawa H, Takahashi S. Simple and Efficient Detection Scheme of Two-Color Fluorescence Correlation Spectroscopy for Protein Dynamics Investigation from Nanoseconds to Milliseconds. ACS PHYSICAL CHEMISTRY AU 2024; 4:85-93. [PMID: 38283787 PMCID: PMC10811772 DOI: 10.1021/acsphyschemau.3c00040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/29/2023] [Accepted: 10/30/2023] [Indexed: 01/30/2024]
Abstract
Nanosecond resolved fluorescence correlation spectroscopy (ns-FCS) based on two-color fluorescence detection is a powerful strategy for investigating the fast dynamics of biological macromolecules labeled with donor and acceptor fluorophores. The standard methods of ns-FCS use two single-photon avalanche diodes (SPADs) for the detection of single-color signals (four SPADs for two-color signals) to eliminate the afterpulse artifacts of SPAD at the expense of the efficiency of utilizing photon data in the calculation of correlograms. Herein, we demonstrated that hybrid photodetectors (HPDs) enable the recording of fluorescence photons in ns-FCS based on the minimal system using two HPDs for the detection of two-color signals. However, HPD exhibited afterpulses at a yield with respect to the rate of photodetection (<10-4) much lower than that of SPADs (∼10-2), which could still hamper correlation measurements. We demonstrated that the simple subtraction procedure could eliminate afterpulse artifacts. While the quantum efficiency of photodetection for HPDs is lower than that for high-performance SPADs, the developed system can be practically used for two-color ns-FCS in a time domain longer than a few nanoseconds. The fast chain dynamics of the B domain of protein A in the unfolded state was observed using the new method.
Collapse
Affiliation(s)
- Yutaka Sano
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi 980-8577, Japan
- Department of Chemistry, Graduate School of Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Yuji Itoh
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi 980-8577, Japan
- Department of Chemistry, Graduate School of Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan
| | - Supawich Kamonprasertsuk
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi 980-8577, Japan
- Department of Chemistry, Graduate School of Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Leo Suzuki
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi 980-8577, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan
| | - Atsuhito Fukasawa
- Electron Tube Division, Hamamatsu Photonics K. K., Iwata, Shizuoka 438-0193, Japan
| | - Hiroyuki Oikawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi 980-8577, Japan
- Department of Chemistry, Graduate School of Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan
- MOLCURE, Kawasaki, Kanagawa 212-0032, Japan
| | - Satoshi Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi 980-8577, Japan
- Department of Chemistry, Graduate School of Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan
| |
Collapse
|
4
|
Coñuecar R, Asela I, Rivera M, Galaz-Davison P, González-Higueras J, Hamilton GL, Engelberger F, Ramírez-Sarmiento CA, Babul J, Sanabria H, Medina E. DNA facilitates heterodimerization between human transcription factors FoxP1 and FoxP2 by increasing their conformational flexibility. iScience 2023; 26:107228. [PMID: 37485372 PMCID: PMC10362293 DOI: 10.1016/j.isci.2023.107228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 05/15/2023] [Accepted: 06/20/2023] [Indexed: 07/25/2023] Open
Abstract
Transcription factors regulate gene expression by binding to DNA. They have disordered regions and specific DNA-binding domains. Binding to DNA causes structural changes, including folding and interactions with other molecules. The FoxP subfamily of transcription factors in humans is unique because they can form heterotypic interactions without DNA. However, it is unclear how they form heterodimers and how DNA binding affects their function. We used computational and experimental methods to study the structural changes in FoxP1's DNA-binding domain when it forms a heterodimer with FoxP2. We found that FoxP1 has complex and diverse conformational dynamics, transitioning between compact and extended states. Surprisingly, DNA binding increases the flexibility of FoxP1, contrary to the typical folding-upon-binding mechanism. In addition, we observed a 3-fold increase in the rate of heterodimerization after FoxP1 binds to DNA. These findings emphasize the importance of structural flexibility in promoting heterodimerization to form transcriptional complexes.
Collapse
Affiliation(s)
- Ricardo Coñuecar
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Isabel Asela
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Maira Rivera
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Pablo Galaz-Davison
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Jorge González-Higueras
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - George L. Hamilton
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Felipe Engelberger
- Institute for Drug Discovery, Leipzig University Medical School, 04107 Leipzig, Germany
| | - César A. Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Jorge Babul
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Hugo Sanabria
- Department of Physics & Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Exequiel Medina
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
- Department of Physics & Astronomy, Clemson University, Clemson, SC 29634, USA
| |
Collapse
|
5
|
Guan X, Tan C, Li W, Wang W, Thirumalai D. Role of water-bridged interactions in metal ion coupled protein allostery. PLoS Comput Biol 2022; 18:e1010195. [PMID: 35653400 PMCID: PMC9197054 DOI: 10.1371/journal.pcbi.1010195] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 06/14/2022] [Accepted: 05/10/2022] [Indexed: 11/18/2022] Open
Abstract
Allosteric communication between distant parts of proteins controls many cellular functions, in which metal ions are widely utilized as effectors to trigger the allosteric cascade. Due to the involvement of strong coordination interactions, the energy landscape dictating the metal ion binding is intrinsically rugged. How metal ions achieve fast binding by overcoming the landscape ruggedness and thereby efficiently mediate protein allostery is elusive. By performing molecular dynamics simulations for the Ca2+ binding mediated allostery of the calmodulin (CaM) domains, each containing two Ca2+ binding helix-loop-helix motifs (EF-hands), we revealed the key role of water-bridged interactions in Ca2+ binding and protein allostery. The bridging water molecules between Ca2+ and binding residue reduces the ruggedness of ligand exchange landscape by acting as a lubricant, facilitating the Ca2+ coupled protein allostery. Calcium-induced rotation of the helices in the EF-hands, with the hydrophobic core serving as the pivot, leads to exposure of hydrophobic sites for target binding. Intriguingly, despite being structurally similar, the response of the two symmetrically arranged EF-hands upon Ca2+ binding is asymmetric. Breakage of symmetry is needed for efficient allosteric communication between the EF-hands. The key roles that water molecules play in driving allosteric transitions are likely to be general in other metal ion mediated protein allostery. Natural proteins often utilize allostery in executing a variety of functions. Metal ions are typical cofactors to trigger the allosteric cascade. In this work, using the Ca2+ sensor protein calmodulin as the model system, we revealed crucial roles of water-bridged interactions in the metal ion coupled protein allostery. The coordination of the Ca2+ to the binding site involves an intermediate in which the water molecule bridges the Ca2+ and the liganding residue. The bridging water reduces the free energy barrier height of ligand exchange, therefore facilitating the ligand exchange and allosteric coupling by acting as a lubricant. We also showed that the response of the two symmetrically arranged EF-hand motifs of CaM domains upon Ca2+ binding is asymmetric, which is directly attributed to the differing dehydration process of the Ca2+ ions and is needed for efficient allosteric communication.
Collapse
Affiliation(s)
- Xingyue Guan
- Department of Physics, National Laboratory of Solid State Microstructure, Nanjing University, Nanjing, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, China
| | - Cheng Tan
- Department of Physics, National Laboratory of Solid State Microstructure, Nanjing University, Nanjing, China
| | - Wenfei Li
- Department of Physics, National Laboratory of Solid State Microstructure, Nanjing University, Nanjing, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, China
- * E-mail: (WL); (WW); (DT)
| | - Wei Wang
- Department of Physics, National Laboratory of Solid State Microstructure, Nanjing University, Nanjing, China
- * E-mail: (WL); (WW); (DT)
| | - D. Thirumalai
- Department of Chemistry, University of Texas, Texas, United States of America
- * E-mail: (WL); (WW); (DT)
| |
Collapse
|
6
|
Varvdekar B, Prabhakant A, Krishnan M. Response of Terahertz Protein Vibrations to Ligand Binding: Calmodulin-Peptide Complexes as a Case Study. J Chem Inf Model 2022; 62:1669-1679. [PMID: 35312312 DOI: 10.1021/acs.jcim.1c01344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Terahertz vibrations are sensitive reporters of the structure and interactions of proteins. Ligand binding alters the nature and distribution of these collective vibrations. The ligand-induced changes in the terahertz protein vibrations contribute to the binding entropy and to the overall thermodynamic stability of the resultant protein-ligand complexes. Here, we have examined the response of the low-frequency (below 6 terahertz) collective vibrations of the calcium-loaded calmodulin (CaM) to binding to five different ligands, both in the presence and absence of water, using normal-mode analysis and molecular dynamics simulations. A comparison of the vibrational spectra of hydrated and dry systems reveals that protein-solvent interactions stiffen the terahertz protein vibrations and that these solvent-coupled collective vibrations contribute significantly to the hydration-sensitive variation in the vibrational entropy of CaM. In the absence of water, the low-frequency vibrations of CaM are stiffened by ligand binding. On the contrary, the number and the cumulative vibrational entropy of low-frequency vibrational modes (ω < 200 cm-1) of the hydrated CaM are increased noticeably after binding to the peptides, indicating binding-induced softening of collective vibrations of the protein. Although the calculated and experimental binding affinities of the chosen complexes correlated reasonably well, no systematic correlation was observed between the protein vibrational entropy and the binding affinity. The results underscored the importance of the interplay of protein-ligand and solvent interactions in modulating the low-frequency vibrations of proteins.
Collapse
Affiliation(s)
- Bhagyesh Varvdekar
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology, Gachibowli, Hyderabad 500032, India
| | - Akshay Prabhakant
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology, Gachibowli, Hyderabad 500032, India
| | - Marimuthu Krishnan
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology, Gachibowli, Hyderabad 500032, India
| |
Collapse
|
7
|
Kay TM, Aplin CP, Simonet R, Beenken J, Miller RC, Libal C, Boersma AJ, Sheets ED, Heikal AA. Molecular Brightness Approach for FRET Analysis of Donor-Linker-Acceptor Constructs at the Single Molecule Level: A Concept. Front Mol Biosci 2021; 8:730394. [PMID: 34595208 PMCID: PMC8476790 DOI: 10.3389/fmolb.2021.730394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/30/2021] [Indexed: 11/13/2022] Open
Abstract
In this report, we have developed a simple approach using single-detector fluorescence autocorrelation spectroscopy (FCS) to investigate the Förster resonance energy transfer (FRET) of genetically encoded, freely diffusing crTC2.1 (mTurquoise2.1-linker-mCitrine) at the single molecule level. We hypothesize that the molecular brightness of the freely diffusing donor (mTurquoise2.1) in the presence of the acceptor (mCitrine) is lower than that of the donor alone due to FRET. To test this hypothesis, the fluorescence fluctuation signal and number of molecules of freely diffusing construct were measured using FCS to calculate the molecular brightness of the donor, excited at 405 nm and detected at 475/50 nm, in the presence and absence of the acceptor. Our results indicate that the molecular brightness of cleaved crTC2.1 in a buffer is larger than that of the intact counterpart under 405-nm excitation. The energy transfer efficiency at the single molecule level is larger and more spread in values as compared with the ensemble-averaging time-resolved fluorescence measurements. In contrast, the molecular brightness of the intact crTC2.1, under 488 nm excitation of the acceptor (531/40 nm detection), is the same or slightly larger than that of the cleaved counterpart. These FCS-FRET measurements on freely diffusing donor-acceptor pairs are independent of the precise time constants associated with autocorrelation curves due to the presence of potential photophysical processes. Ultimately, when used in living cells, the proposed approach would only require a low expression level of these genetically encoded constructs, helping to limit potential interference with the cell machinery.
Collapse
Affiliation(s)
- Taryn M Kay
- Department of Physics and Astronomy, University of Minnesota Duluth, Duluth, MN, United States
| | - Cody P Aplin
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, United States
| | - Rowan Simonet
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, United States
| | - Julie Beenken
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, United States
| | - Robert C Miller
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, United States
| | - Christin Libal
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, United States
| | - Arnold J Boersma
- DWI-Leibniz Institute for Interactive Materials, Aachen, Germany
| | - Erin D Sheets
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, United States
| | - Ahmed A Heikal
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, United States
| |
Collapse
|
8
|
Xu L, Tian S, Peng X, Hua Y, Yang W, Chen L, Liu S, Wu W, Zhao J, He J, Wu L, Yang J, Zheng Y. Clusterin inhibits Aβ 42 aggregation through a "strawberry model" as detected by FRET-FCS. J Neurochem 2021; 158:444-454. [PMID: 33694231 DOI: 10.1111/jnc.15344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 02/19/2021] [Accepted: 03/07/2021] [Indexed: 11/28/2022]
Abstract
Extracellular plaque deposits of β-amyloid peptide (Aβ) are one of the main pathological features of Alzheimer's disease (AD). The aggregation of Aβ42 species, especially Aβ42 oligomers, is still an active research field in AD pathogenesis. Secretory clusterin protein (sCLU), an extracellular chaperone, plays an important role in AD pathogenesis. Although sCLU interacts directly with Aβ42 in vitro and in vivo, the mechanism is not clear. In this paper, His-tagged sCLU (sCLU-His) was cloned, expressed and purified, and we applied florescence resonance energy transfer-fluorescence correlation spectroscopy (FRET-FCS) to investigate the direct interaction of sCLU-His and Aβ42 at the single-molecule fluorescence level in vitro. Here, we chose four different fluorescently labeled Aβ42 oligomers to form two different groups of aggregation models, easy or difficult to aggregate. The results showed that sCLU-His could form complexes with both aggregation models, and sCLU-His inhibited the aggregation of Aβ42/RB ~ Aβ42/Atto647 (easy to aggregate model). The complexes were produced as the Aβ42/Label adhered to the sCLU-His, which is similar to a "strawberry model," as strawberry seeds are dotted on the outer surface of strawberries. This work provided additional insight into the interaction mechanism of sCLU and Aβ42 .
Collapse
Affiliation(s)
- Lingwan Xu
- School of Sciences, Beijing Jiaotong University, Beijing, China
| | - Shijun Tian
- Hebei Agriculture University, Baoding, China
| | - Xianglei Peng
- School of Sciences, Beijing Jiaotong University, Beijing, China
| | - Ying Hua
- School of Sciences, Beijing Jiaotong University, Beijing, China
| | - Wenxuan Yang
- School of Sciences, Beijing Jiaotong University, Beijing, China
| | - Longwei Chen
- School of Sciences, Beijing Jiaotong University, Beijing, China
| | - Shilei Liu
- School of Sciences, Beijing Jiaotong University, Beijing, China
| | - Wenzheng Wu
- School of Sciences, Beijing Jiaotong University, Beijing, China
| | - Jiang Zhao
- Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Jinsheng He
- School of Sciences, Beijing Jiaotong University, Beijing, China
| | - Liqing Wu
- National Institute of Metrology, Beijing, China
| | - Jingfa Yang
- Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Yanpeng Zheng
- School of Sciences, Beijing Jiaotong University, Beijing, China
| |
Collapse
|
9
|
Medina E, Villalobos P, Hamilton GL, Komives EA, Sanabria H, Ramírez-Sarmiento CA, Babul J. Intrinsically Disordered Regions of the DNA-Binding Domain of Human FoxP1 Facilitate Domain Swapping. J Mol Biol 2020; 432:5411-5429. [PMID: 32735805 DOI: 10.1016/j.jmb.2020.07.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 01/01/2023]
Abstract
Forkhead box P (FoxP) proteins are unique transcription factors that spatiotemporally regulate gene expression by tethering two chromosome loci together via functional domain-swapped dimers formed through their DNA-binding domains. Further, the differential kinetics on this dimerization mechanism underlie an intricate gene regulation network at physiological conditions. Nonetheless, poor understanding of the structural dynamics and steps of the association process impedes to link the functional domain swapping to human-associated diseases. Here, we have characterized the DNA-binding domain of human FoxP1 by integrating single-molecule Förster resonance energy transfer and hydrogen-deuterium exchange mass spectrometry data with molecular dynamics simulations. Our results confirm the formation of a previously postulated domain-swapped (DS) FoxP1 dimer in solution and reveal the presence of highly populated, heterogeneous, and locally disordered dimeric intermediates along the dimer dissociation pathway. The unique features of FoxP1 provide a glimpse of how intrinsically disordered regions can facilitate domain swapping oligomerization and other tightly regulated association mechanisms relevant in biological processes.
Collapse
Affiliation(s)
- Exequiel Medina
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile
| | - Pablo Villalobos
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile
| | - George L Hamilton
- Department of Physics & Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Elizabeth A Komives
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Hugo Sanabria
- Department of Physics & Astronomy, Clemson University, Clemson, SC 29634, USA.
| | - César A Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile; Millennium Institute for Integrative Biology (iBio), Santiago, Chile.
| | - Jorge Babul
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile.
| |
Collapse
|
10
|
Halder R, Jana B. Exploring and Engineering the Conformational Landscape of Calmodulin through Specific Interactions. J Phys Chem B 2019; 123:9321-9327. [DOI: 10.1021/acs.jpcb.9b06343] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Ritaban Halder
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Biman Jana
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| |
Collapse
|
11
|
Heidarinejad M, Nakamura H, Inoue T. Stimulation-induced changes in diffusion and structure of calmodulin and calmodulin-dependent protein kinase II proteins in neurons. Neurosci Res 2018; 136:13-32. [PMID: 29395358 DOI: 10.1016/j.neures.2018.01.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 01/11/2018] [Accepted: 01/11/2018] [Indexed: 11/28/2022]
Abstract
Calcium/calmodulin-dependent protein kinase II (CaMKII) and calmodulin (CaM) play essential roles in synaptic plasticity, which is an elementary process of learning and memory. In this study, fluorescence correlation spectroscopy (FCS) revealed diffusion properties of CaM, CaMKIIα and CaMKIIβ proteins in human embryonic kidney 293 (HEK293) cells and hippocampal neurons. A simultaneous multiple-point FCS recording system was developed on a random-access two-photon microscope, which facilitated efficient analysis of molecular dynamics in neuronal compartments. The diffusion of CaM in neurons was slower than that in HEK293 cells at rest, while the diffusion in stimulated neurons was accelerated and indistinguishable from that in HEK293 cells. This implied that activity-dependent binding partners of CaM exist in neurons, which slow down the diffusion at rest. Diffusion properties of CaMKIIα and β proteins implied that major populations of these proteins exist as holoenzymatic forms. Upon stimulation of neurons, the diffusion of CaMKIIα and β proteins became faster with reduced particle brightness, indicating drastic structural changes of the proteins such as dismissal from holoenzyme structure and further fragmentation.
Collapse
Affiliation(s)
- Morteza Heidarinejad
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan.
| | - Hideki Nakamura
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan.
| | - Takafumi Inoue
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan.
| |
Collapse
|
12
|
Voith von Voithenberg L, Lamb DC. Single Pair Förster Resonance Energy Transfer: A Versatile Tool To Investigate Protein Conformational Dynamics. Bioessays 2018; 40. [DOI: 10.1002/bies.201700078] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 12/05/2017] [Indexed: 01/23/2023]
Affiliation(s)
- Lena Voith von Voithenberg
- Department Chemie; Center for Nanoscience (CeNS); Center for Integrated Protein Science Munich (CIPSM); Nanosystem Initiative Munich (NIM); Ludwig-Maximilians-Universität München; Butenandtstr. 5-13 81377 München Germany
- BIOSS Centre for Signalling Studies; Schänzlestr. 18 79104 Freiburg Germany
| | - Don C. Lamb
- Department Chemie; Center for Nanoscience (CeNS); Center for Integrated Protein Science Munich (CIPSM); Nanosystem Initiative Munich (NIM); Ludwig-Maximilians-Universität München; Butenandtstr. 5-13 81377 München Germany
| |
Collapse
|
13
|
The use of fluorescence correlation spectroscopy to characterize the molecular mobility of fluorescently labelled G protein-coupled receptors. Biochem Soc Trans 2016; 44:624-9. [PMID: 27068980 PMCID: PMC5264494 DOI: 10.1042/bst20150285] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Indexed: 01/10/2023]
Abstract
The membranes of living cells have been shown to be highly organized into distinct microdomains, which has spatial and temporal consequences for the interaction of membrane bound receptors and their signalling partners as complexes. Fluorescence correlation spectroscopy (FCS) is a technique with single cell sensitivity that sheds light on the molecular dynamics of fluorescently labelled receptors, ligands or signalling complexes within small plasma membrane regions of living cells. This review provides an overview of the use of FCS to probe the real time quantification of the diffusion and concentration of G protein-coupled receptors (GPCRs), primarily to gain insights into ligand–receptor interactions and the molecular composition of signalling complexes. In addition we document the use of photon counting histogram (PCH) analysis to investigate how changes in molecular brightness (ε) can be a sensitive indicator of changes in molecular mass of fluorescently labelled moieties.
Collapse
|
14
|
Nandigrami P, Portman JJ. Comparing allosteric transitions in the domains of calmodulin through coarse-grained simulations. J Chem Phys 2016; 144:105102. [PMID: 26979706 DOI: 10.1063/1.4943130] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Calmodulin (CaM) is a ubiquitous Ca(2+)-binding protein consisting of two structurally similar domains with distinct stabilities, binding affinities, and flexibilities. We present coarse grained simulations that suggest that the mechanism for the domain's allosteric transitions between the open and closed conformations depends on subtle differences in the folded state topology of the two domains. Throughout a wide temperature range, the simulated transition mechanism of the N-terminal domain (nCaM) follows a two-state transition mechanism while domain opening in the C-terminal domain (cCaM) involves unfolding and refolding of the tertiary structure. The appearance of the unfolded intermediate occurs at a higher temperature in nCaM than it does in cCaM consistent with nCaM's higher thermal stability. Under approximate physiological conditions, the simulated unfolded state population of cCaM accounts for 10% of the population with nearly all of the sampled transitions (approximately 95%) unfolding and refolding during the conformational change. Transient unfolding significantly slows the domain opening and closing rates of cCaM, which can potentially influence its Ca(2+)-binding mechanism.
Collapse
Affiliation(s)
| | - John J Portman
- Department of Physics, Kent State University, Kent, Ohio 44242, USA
| |
Collapse
|
15
|
Shao Q. Enhanced conformational sampling technique provides an energy landscape view of large-scale protein conformational transitions. Phys Chem Chem Phys 2016; 18:29170-29182. [DOI: 10.1039/c6cp05634b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A novel in silico approach (NMA–ITS) is introduced to rapidly and effectively sample the configuration space and give quantitative data for exploring the conformational changes of proteins.
Collapse
Affiliation(s)
- Qiang Shao
- Drug Discovery and Design Center
- CAS Key Laboratory of Receptor Research
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai
| |
Collapse
|
16
|
Wennmalm S, Chmyrov V, Widengren J, Tjernberg L. Highly Sensitive FRET-FCS Detects Amyloid β-Peptide Oligomers in Solution at Physiological Concentrations. Anal Chem 2015; 87:11700-5. [PMID: 26489794 DOI: 10.1021/acs.analchem.5b02630] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Oligomers formed by the amyloid β-peptide (Aβ) are pathogens in Alzheimer's disease. Increased knowledge on the oligomerization process is crucial for understanding the disease and for finding treatments. Ideally, Aβ oligomerization should be studied in solution and at physiologically relevant concentrations, but most popular techniques of today are not capable of such analyses. We demonstrate here that the combination of Förster Resonance Energy Transfer and Fluorescence Correlation Spectroscopy (FRET-FCS) has a unique ability to detect small subpopulations of FRET-active molecules and oligomers. FRET-FCS could readily detect a FRET-active oligonucleotide present at levels as low as 0.5% compared to FRET-inactive dye molecules. In contrast, three established fluorescence fluctuation techniques (FCS, FCCS, and PCH) required fractions between 7 and 11%. When applied to the analysis of Aβ, FRET-FCS detected oligomers consisting of less than 10 Aβ molecules, which coexisted with the monomers at fractions as low as 2 ± 2%. Thus, we demonstrate for the first time direct detection of small fractions of Aβ oligomers in solution at physiological concentrations. This ability of FRET-FCS could be an indispensable tool for studying biological oligomerization processes, in general, and for finding therapeutically useful oligomerization inhibitors.
Collapse
Affiliation(s)
- Stefan Wennmalm
- Royal Institute of Technology-KTH, Department of Applied Physics, Experimental Biomolecular Physics Group, Scilifelab , 171 65 Solna, Sweden
| | - Volodymyr Chmyrov
- Royal Institute of Technology-KTH , Department of Applied Physics, Experimental Biomolecular Physics Group, AlbaNova, 106 91 Stockholm, Sweden
| | - Jerker Widengren
- Royal Institute of Technology-KTH , Department of Applied Physics, Experimental Biomolecular Physics Group, AlbaNova, 106 91 Stockholm, Sweden
| | - Lars Tjernberg
- Karolinska Institutet , Department of NVS, Center for Alzheimer Research, Division for Neurogeriatrics, Novum plan 5, 141 86 Stockholm, Sweden
| |
Collapse
|
17
|
Microsecond protein dynamics observed at the single-molecule level. Nat Commun 2015; 6:7685. [PMID: 26151767 PMCID: PMC4506535 DOI: 10.1038/ncomms8685] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/01/2015] [Indexed: 01/27/2023] Open
Abstract
How polypeptide chains acquire specific conformations to realize unique biological functions is a central problem of protein science. Single-molecule spectroscopy, combined with fluorescence resonance energy transfer, is utilized to study the conformational heterogeneity and the state-to-state transition dynamics of proteins on the submillisecond to second timescales. However, observation of the dynamics on the microsecond timescale is still very challenging. This timescale is important because the elementary processes of protein dynamics take place and direct comparison between experiment and simulation is possible. Here we report a new single-molecule technique to reveal the microsecond structural dynamics of proteins through correlation of the fluorescence lifetime. This method, two-dimensional fluorescence lifetime correlation spectroscopy, is applied to clarify the conformational dynamics of cytochrome c. Three conformational ensembles and the microsecond transitions in each ensemble are indicated from the correlation signal, demonstrating the importance of quantifying microsecond dynamics of proteins on the folding free energy landscape. Single molecule spectroscopy can visualise dynamic changes in protein conformation on the submillisecond timescale. Here, Otosu et al. apply two-dimensional fluorescence lifetime correlation spectroscopy to visualise dynamics between seven conformers of cytochrome c on the microsecond timescale.
Collapse
|
18
|
Liu B, Chia D, Csizmok V, Farber P, Forman-Kay JD, Gradinaru CC. The effect of intrachain electrostatic repulsion on conformational disorder and dynamics of the Sic1 protein. J Phys Chem B 2014; 118:4088-97. [PMID: 24673507 DOI: 10.1021/jp500776v] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The yeast cyclin-dependent kinase inhibitor Sic1 is a disordered protein that, upon multisite phosphorylation, forms a dynamic complex with the Cdc4 subunit of an SCF ubiquitin ligase. To understand the multisite phosphorylation dependence of the Sic1:Cdc4 interaction, which ultimately leads to a sharp cell cycle transition, the conformational properties of the disordered Sic1 N-terminal targeting region were studied using single-molecule fluorescence spectroscopy. Multiple conformational populations with different sensitivities to charge screening were identified by performing experiments in nondenaturing salts and ionic denaturants. Both the end-to-end distance and the hydrodynamic radius decrease monotonically with increasing the salt concentration, and a rollover of the chain dimensions in high denaturant conditions is observed. The data were fit to the polyelectrolyte binding-screening model, yielding parameters such as the excluded volume of the uncharged chain and the binding constant to denaturant. An overall scaling factor of ∼1.2 was needed for fitting the data, which implies that Sic1 cannot be approximated by a random Gaussian chain. Fluorescence correlation spectroscopy reveals Sic1 structure fluctuations occurring on both fast (10-100 ns) and slow (∼10 ms) time scales, with the fast phase absent in low salt solutions. The results of this study provide direct evidence that long-range intrachain electrostatic repulsions are a significant factor for the conformational landscape of Sic1, and support the role of electrostatics in determining the overall shape and hydrodynamic properties of intrinsically disordered proteins.
Collapse
Affiliation(s)
- Baoxu Liu
- Department of Chemical and Physical Sciences, University of Toronto Mississauga , Mississauga, Ontario L5L 1C6, Canada
| | | | | | | | | | | |
Collapse
|
19
|
Das A, Chakrabarti J, Ghosh M. Conformational thermodynamics of metal-ion binding to a protein. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.07.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
20
|
Mazouchi A, Bahram A, Gradinaru CC. Sub-diffusion decays in fluorescence correlation spectroscopy: dye photophysics or protein dynamics? J Phys Chem B 2013; 117:11100-11. [PMID: 23675915 DOI: 10.1021/jp4010746] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transitions between bright and dark fluorescent states of several rhodamine dyes were investigated by fluorescence correlation spectroscopy. We resolved two sub-diffusion exponential decays for free rhodamines in aqueous solutions, of which the slower component scales linearly with the viscosity of the solution. Correlation data for proteins and DNA labeled with tetramethylrhodamine were fitted with three to four exponential decays describing flickering dynamics on a time scale between 0.5 and 100 μs. We investigated the nature of these processes by performing experiments under different experimental conditions and for different samples. On the basis of how their population and lifetime change with viscosity, the oxygen content of the solution, the laser irradiance, and the detection geometry, we assigned these states, in the order of increasing lifetimes, to a triplet state, a hybrid between twisted-intramolecular-charge-transfer state and a ground state lactonic state, a lactonic state, and a photoionized state, respectively. Our data suggests that none of the observed sub-diffusion correlation decays can be directly assigned to the intramolecular dynamics of the labeled biomolecules. However, we found evidence that the intrinsic conformational dynamics of the biomolecule appears in the correlation curves as a modulation of the photophysics of the dye label. This shows the importance of accurate control measurements and appropriate modeling of the dye photophysics in fluorescence correlation studies, and it cautions against direct assignments of dark-state relaxation times to folding kinetics in proteins and nucleic acids.
Collapse
Affiliation(s)
- Amir Mazouchi
- Department of Physics, University of Toronto , and Department of Chemical and Physical Sciences, University of Toronto Mississauga , Mississauga, Ontario L5L 1C6, Canada
| | | | | |
Collapse
|
21
|
Felekyan S, Sanabria H, Kalinin S, Kühnemuth R, Seidel CAM. Analyzing Förster resonance energy transfer with fluctuation algorithms. Methods Enzymol 2013; 519:39-85. [PMID: 23280107 DOI: 10.1016/b978-0-12-405539-1.00002-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) in combination with Förster resonance energy transfer (FRET) has been developed to a powerful statistical tool, which allows for the analysis of FRET fluctuations in the huge time of nanoseconds to seconds. FRET-FCS utilizes the strong distance dependence of the FRET efficiency on the donor (D)-acceptor (A) distance so that it developed to a perfect method for studying structural fluctuation in biomolecules involved in conformational flexibility, structural dynamics, complex formation, folding, and catalysis. Structural fluctuations thereby result in anticorrelated donor and acceptor signals, which are analyzed by FRET-FCS in order to characterize underlying structural dynamics. Simulated and experimental examples are discussed. First, we review experimental implementations of FRET-FCS and present theory for a two-state interconverting system. Additionally, we consider a very common case of FRET dynamics in the presence of donor-only labeled species. We demonstrate that the mean relaxation time for the structural dynamics can be easily obtained in most of cases, whereas extracting meaningful information from correlation amplitudes can be challenging. We present a strategy to avoid a fit with an underdetermined model function by restraining the D and A brightnesses of the at least one involved state, so that both FRET efficiencies and both rate constants (i.e., the equilibrium constant) can be determined. For samples containing several fluorescent species, the use of pulsed polarized excitation with multiparameter fluorescence detection allows for filtered FCS (fFCS), where species-specific correlation functions can be obtained, which can be directly interpreted. The species selection is achieved by filtering using fluorescence decays of individual species. Analytical functions for species auto- and cross-correlation functions are given. Moreover, fFCS is less affected by photophysical artifacts and often offers higher contrast, which effectively increases its time resolution and significantly enhances its capability to resolve multistate kinetics. fFCS can also differentiate between species even when their brightnesses are the same and thus opens up new possibilities to characterize complex dynamics. Alternative fluctuation algorithms to study FRET dynamics are also briefly reviewed.
Collapse
Affiliation(s)
- Suren Felekyan
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Düsseldorf, Germany
| | | | | | | | | |
Collapse
|
22
|
Direct observation of T4 lysozyme hinge-bending motion by fluorescence correlation spectroscopy. Biophys J 2012; 103:1525-36. [PMID: 23062345 DOI: 10.1016/j.bpj.2012.07.053] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 07/16/2012] [Accepted: 07/16/2012] [Indexed: 10/27/2022] Open
Abstract
Bacteriophage T4 Lysozyme (T4L) catalyzes the hydrolysis of the peptidoglycan layer of the bacterial cell wall late in the infection cycle. It has long been postulated that equilibrium dynamics enable substrate access to the active site located at the interface between the N- and C-terminal domains. Crystal structures of WT-T4L and point mutants captured a range of conformations that differ by the hinge-bending angle between the two domains. Evidence of equilibrium between open and closed conformations in solution was gleaned from distance measurements between the two domains but the nature of the equilibrium and the timescale of the underlying motion have not been investigated. Here, we used fluorescence fluctuation spectroscopy to directly detect T4L equilibrium conformational fluctuations in solution. For this purpose, Tetramethylrhodamine probes were introduced at pairs of cysteines in regions of the molecule that undergo relative displacement upon transition from open to closed conformations. Correlation analysis of Tetramethylrhodamine intensity fluctuations reveals hinge-bending motion that changes the relative distance and orientation of the N- and C-terminal domains with ≅ 15 μs relaxation time. That this motion involves interconversion between open and closed conformations was further confirmed by the dampening of its amplitude upon covalent substrate trapping. In contrast to the prevalent two-state model of T4L equilibrium, molecular brightness and number of particles obtained from cumulant analysis suggest that T4L populates multiple intermediate states, consistent with the wide range of hinge-bending angles trapped in the crystal structure of T4L mutants.
Collapse
|
23
|
Tripathi S, Portman JJ. Conformational flexibility and the mechanisms of allosteric transitions in topologically similar proteins. J Chem Phys 2011; 135:075104. [PMID: 21861587 DOI: 10.1063/1.3625636] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Conformational flexibility plays a central role in allosteric transition of proteins. In this paper, we extend the analysis of our previous study [S. Tripathi and J. J. Portman, Proc. Natl. Acad. Sci. U.S.A. 106, 2104 (2009)] to investigate how relatively minor structural changes of the meta-stable states can significantly influence the conformational flexibility and allosteric transition mechanism. We use the allosteric transitions of the domains of calmodulin as an example system to highlight the relationship between the transition mechanism and the inter-residue contacts present in the meta-stable states. In particular, we focus on the origin of transient local unfolding (cracking), a mechanism that can lower free energy barriers of allosteric transitions, in terms of the inter-residue contacts of the meta-stable states and the pattern of local strain that develops during the transition. We find that the magnitude of the local strain in the protein is not the sole factor determining whether a region will ultimately crack during the transition. These results emphasize that the residue interactions found exclusively in one of the two meta-stable states is the key in understanding the mechanism of allosteric conformational change.
Collapse
|