1
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Irukuvajjula SS, Jithender Reddy G, Rao K, Vadrevu LR. Contrasting effect of ficoll on apo and holo forms of bacterial chemotaxis protein Y: Selective destabilization of the conformationally altered holo form. Int J Biol Macromol 2023; 232:123505. [PMID: 36736516 DOI: 10.1016/j.ijbiomac.2023.123505] [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: 11/03/2022] [Revised: 01/13/2023] [Accepted: 01/28/2023] [Indexed: 02/04/2023]
Abstract
Chemotaxis Y (CheY), upon metal binding, displays a drastic alteration in its structure and stability. This premise prompted us to study the effect of crowding on the two conformationally distinct states of the same test protein. A comparative analysis on the structure and thermal stability in the presence and absence of the macromolecular crowder, ficoll, and its monomeric unit, sucrose, revealed a contrasting effect of ficoll on the apo and holo forms. In the presence of ficoll while the thermal stability (Tm) of the apo form is enhanced, the thermal stability of the holo form is reduced. The selective lowering of Tm for the holo form in the combined presence of ficoll and sucrose and not in sucrose alone suggests that the contrasting effect is due to the macromolecular nature of ficoll. Since metal-protein interaction remains unperturbed in the presence of ficoll and Mg2+ sequestration is ruled out in a systematic manner the alternative possibility for the exclusive reduction in the thermal stability of the holo form is the ficoll-induced modulation of the relative population of apo and holo forms of CheY.
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Affiliation(s)
- Shivkumar Sharma Irukuvajjula
- Department of Biological Sciences, Birla Institute of Science and Technology - Pilani, Hyderabad Campus, Shamirpet, Hyderabad 500078, India.
| | - G Jithender Reddy
- NMR Division, Department of Analytical & Structural Chemistry, CSIR-Indian Institute of Chemical Technology, Ministry of Science and Technology, Uppal Road, Tarnaka, Hyderabad 500007, India
| | - Krishna Rao
- Tata Institute of Fundamental Research, 36/P, Gopanpally Mandal, Ranga Reddy District, Hyderabad, Telangana State 500107, India
| | - Late Ramakrishna Vadrevu
- Department of Biological Sciences, Birla Institute of Science and Technology - Pilani, Hyderabad Campus, Shamirpet, Hyderabad 500078, India
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2
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Nde J, Zhang P, Ezerski JC, Lu W, Knapp K, Wolynes PG, Cheung MS. Coarse-Grained Modeling and Molecular Dynamics Simulations of Ca 2+-Calmodulin. Front Mol Biosci 2021; 8:661322. [PMID: 34504868 PMCID: PMC8421859 DOI: 10.3389/fmolb.2021.661322] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 07/21/2021] [Indexed: 12/21/2022] Open
Abstract
Calmodulin (CaM) is a calcium-binding protein that transduces signals to downstream proteins through target binding upon calcium binding in a time-dependent manner. Understanding the target binding process that tunes CaM’s affinity for the calcium ions (Ca2+), or vice versa, may provide insight into how Ca2+-CaM selects its target binding proteins. However, modeling of Ca2+-CaM in molecular simulations is challenging because of the gross structural changes in its central linker regions while the two lobes are relatively rigid due to tight binding of the Ca2+ to the calcium-binding loops where the loop forms a pentagonal bipyramidal coordination geometry with Ca2+. This feature that underlies the reciprocal relation between Ca2+ binding and target binding of CaM, however, has yet to be considered in the structural modeling. Here, we presented a coarse-grained model based on the Associative memory, Water mediated, Structure, and Energy Model (AWSEM) protein force field, to investigate the salient features of CaM. Particularly, we optimized the force field of CaM and that of Ca2+ ions by using its coordination chemistry in the calcium-binding loops to match with experimental observations. We presented a “community model” of CaM that is capable of sampling various conformations of CaM, incorporating various calcium-binding states, and carrying the memory of binding with various targets, which sets the foundation of the reciprocal relation of target binding and Ca2+ binding in future studies.
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Affiliation(s)
- Jules Nde
- Department of Physics, University of Houston, Houston, TX, United States.,Center for Theoretical Biological Physics, Rice University, Houston, TX, United States
| | - Pengzhi Zhang
- Department of Physics, University of Houston, Houston, TX, United States
| | - Jacob C Ezerski
- Department of Physics, University of Houston, Houston, TX, United States
| | - Wei Lu
- Center for Theoretical Biological Physics, Rice University, Houston, TX, United States
| | - Kaitlin Knapp
- Center for Theoretical Biological Physics, Rice University, Houston, TX, United States
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, TX, United States
| | - Margaret S Cheung
- Department of Physics, University of Houston, Houston, TX, United States.,Center for Theoretical Biological Physics, Rice University, Houston, TX, United States
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3
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Subadini S, Bera K, Hritz J, Sahoo H. Polyethylene glycol perturbs the unfolding of CRABP I: A correlation between experimental and theoretical approach. Colloids Surf B Biointerfaces 2021; 202:111696. [PMID: 33770701 DOI: 10.1016/j.colsurfb.2021.111696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/25/2021] [Accepted: 03/11/2021] [Indexed: 10/21/2022]
Abstract
The importance of macromolecules paves the way towards a detailed molecular level investigation as all most all cellular processes occurring at the interior of cells in the form of proteins, enzymes, and other biological molecules are significantly affected because of their crowding. Thus, exploring the role of crowding environment on the denaturation and renaturation kinetics of protein molecules is of great importance. Here, CRABP I (cellular retinoic acid binding protein I) is employed as a model protein along with different molecular weights of Polyethylene glycol (PEG) as molecular crowders. The experimental evaluations are done by accessing the protein secondary structure analysis using circular dichroism (CD) spectroscopy and unfolding kinetics using intrinsic fluorescence of CRABP I at 37 °C to mimic the in vivo crowding environment. The unfolding kinetics results indicated that both PEG 2000 and PEG 4000 act as stabilizers by retarding the unfolding kinetic rates. Both kinetic and stability outcomes presented the importance of crowding environment on stability and kinetics of CRABP I. The molecular dynamics (MD) studies revealed that thirteen PEG 2000 molecules assembled during the 500 ns simulation, which increases the stability and percentage of β-sheet. The experimental findings are well supported by the molecular dynamics simulation results.
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Affiliation(s)
- Suchismita Subadini
- Biophysical and Protein Chemistry Lab, Department of Chemistry, NIT Rourkela, Rourkela, 769008, India
| | - Krishnendu Bera
- CEITEC MU, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Jozef Hritz
- CEITEC MU, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic; Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Harekrushna Sahoo
- Biophysical and Protein Chemistry Lab, Department of Chemistry, NIT Rourkela, Rourkela, 769008, India; Center of Nanomaterials, NIT Rourkela, Rourkela, 769008, India.
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4
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Hu Y, Cheng K, He L, Zhang X, Jiang B, Jiang L, Li C, Wang G, Yang Y, Liu M. NMR-Based Methods for Protein Analysis. Anal Chem 2021; 93:1866-1879. [PMID: 33439619 DOI: 10.1021/acs.analchem.0c03830] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a well-established method for analyzing protein structure, interaction, and dynamics at atomic resolution and in various sample states including solution state, solid state, and membranous environment. Thanks to rapid NMR methodology development, the past decade has witnessed a growing number of protein NMR studies in complex systems ranging from membrane mimetics to living cells, which pushes the research frontier further toward physiological environments and offers unique insights in elucidating protein functional mechanisms. In particular, in-cell NMR has become a method of choice for bridging the huge gap between structural biology and cell biology. Herein, we review the recent developments and applications of NMR methods for protein analysis in close-to-physiological environments, with special emphasis on in-cell protein structural determination and the analysis of protein dynamics, both difficult to be accessed by traditional methods.
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Affiliation(s)
- Yunfei Hu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Kai Cheng
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China
| | - Lichun He
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Xu Zhang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Bin Jiang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Ling Jiang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Guan Wang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Yunhuang Yang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
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5
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Cozzolino S, Graziano G. The magnitude of macromolecular crowding caused by Dextran and Ficoll for the conformational stability of globular proteins. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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6
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Perez CP, Elmore DE, Radhakrishnan ML. Computationally Modeling Electrostatic Binding Energetics in a Crowded, Dynamic Environment: Physical Insights from a Peptide–DNA System. J Phys Chem B 2019; 123:10718-10734. [DOI: 10.1021/acs.jpcb.9b09478] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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7
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Folding of poly-amino acids and intrinsically disordered proteins in overcrowded milieu induced by pH change. Int J Biol Macromol 2018; 125:244-255. [PMID: 30529354 DOI: 10.1016/j.ijbiomac.2018.12.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/27/2018] [Accepted: 12/02/2018] [Indexed: 12/24/2022]
Abstract
pH-induced structural changes of the synthetic homopolypeptides poly-E, poly-K, poly-R, and intrinsically disordered proteins (IDPs) prothymosin α (ProTα) and linker histone H1, in concentrated PEG solutions simulating macromolecular crowding conditions within the membrane-less organelles, were characterized. The conformational transitions of the studied poly-amino acids in the concentrated PEG solutions depend on the polymerization degree of these homopolypeptides, the size of their side chains, the charge distribution of the side chains, and the crowding agent concentration. The results obtained for poly-amino acids are valid for IDPs having a significant total charge. The overcrowded conditions promote a significant increase in the cooperativity of the pH-induced coil-α-helix transition of ProTα and provoke histone H1 aggregation. The most favorable conditions for the pH-induced structural transitions in concentrated PEG solutions are realized when the charged residues are grouped in blocks, and when the distance between the end of the side group carrying charge and the backbone is small. Therefore, the block-wise distribution of charged residues within the IDPs not only plays an important role in the liquid-liquid phase transitions, but may also define the expressivity of structural transitions of these proteins in the overcrowded conditions of the membrane-less organelles.
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8
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Morea EGO, Viviescas MA, Fernandes CAH, Matioli FF, Lira CBB, Fernandez MF, Moraes BS, da Silva MS, Storti CB, Fontes MRM, Cano MIN. A calmodulin-like protein (LCALA) is a new Leishmania amazonensis candidate for telomere end-binding protein. Biochim Biophys Acta Gen Subj 2017; 1861:2583-2597. [PMID: 28844976 DOI: 10.1016/j.bbagen.2017.08.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 08/06/2017] [Accepted: 08/14/2017] [Indexed: 11/26/2022]
Abstract
BACKGROUND Leishmania spp. telomeres are composed of 5'-TTAGGG-3' repeats associated with proteins. We have previously identified LaRbp38 and LaRPA-1 as proteins that bind the G-rich telomeric strand. At that time, we had also partially characterized a protein: DNA complex, named LaGT1, but we could not identify its protein component. METHODS AND RESULTS Using protein-DNA interaction and competition assays, we confirmed that LaGT1 is highly specific to the G-rich telomeric single-stranded DNA. Three protein bands, with LaGT1 activity, were isolated from affinity-purified protein extracts in-gel digested, and sequenced de novo using mass spectrometry analysis. In silico analysis of the digested peptide identified them as a putative calmodulin with sequences identical to the T. cruzi calmodulin. In the Leishmania genome, the calmodulin ortholog is present in three identical copies. We cloned and sequenced one of the gene copies, named it LCalA, and obtained the recombinant protein. Multiple sequence alignment and molecular modeling showed that LCalA shares homology to most eukaryotes calmodulin. In addition, we demonstrated that LCalA is nuclear, partially co-localizes with telomeres and binds in vivo the G-rich telomeric strand. Recombinant LCalA can bind specifically and with relative affinity to the G-rich telomeric single-strand and to a 3'G-overhang, and DNA binding is calcium dependent. CONCLUSIONS We have described a novel candidate component of Leishmania telomeres, LCalA, a nuclear calmodulin that binds the G-rich telomeric strand with high specificity and relative affinity, in a calcium-dependent manner. GENERAL SIGNIFICANCE LCalA is the first reported calmodulin that binds in vivo telomeric DNA.
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Affiliation(s)
- Edna G O Morea
- Genetics Dept., Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | | | - Carlos A H Fernandes
- Biophysics and Physics Dept., Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Fabio F Matioli
- Biophysics and Physics Dept., Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Cristina B B Lira
- Genetics Dept., Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Maribel F Fernandez
- Instituto Tocantinense Presidente Antonio Carlos LTDA., ITPAC-Porto Nacional S.A., TO, Brazil
| | - Barbara S Moraes
- PROAHSA - Programa de Estudos Avançados em Administração Hospitalar e Sistemas de Saúde, São Paulo, Brazil
| | - Marcelo S da Silva
- Laboratório Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo, SP, Brazil
| | - Camila B Storti
- Genetics Dept., Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Marcos R M Fontes
- Biophysics and Physics Dept., Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Maria Isabel N Cano
- Genetics Dept., Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil.
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9
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Hovey L, Fowler CA, Mahling R, Lin Z, Miller MS, Marx DC, Yoder JB, Kim EH, Tefft KM, Waite BC, Feldkamp MD, Yu L, Shea MA. Calcium triggers reversal of calmodulin on nested anti-parallel sites in the IQ motif of the neuronal voltage-dependent sodium channel Na V1.2. Biophys Chem 2017; 224:1-19. [PMID: 28343066 PMCID: PMC5503752 DOI: 10.1016/j.bpc.2017.02.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 02/23/2017] [Accepted: 02/23/2017] [Indexed: 01/26/2023]
Abstract
Several members of the voltage-gated sodium channel family are regulated by calmodulin (CaM) and ionic calcium. The neuronal voltage-gated sodium channel NaV1.2 contains binding sites for both apo (calcium-depleted) and calcium-saturated CaM. We have determined equilibrium dissociation constants for rat NaV1.2 IQ motif [IQRAYRRYLLK] binding to apo CaM (~3nM) and (Ca2+)4-CaM (~85nM), showing that apo CaM binding is favored by 30-fold. For both apo and (Ca2+)4-CaM, NMR demonstrated that NaV1.2 IQ motif peptide (NaV1.2IQp) exclusively made contacts with C-domain residues of CaM (CaMC). To understand how calcium triggers conformational change at the CaM-IQ interface, we determined a solution structure (2M5E.pdb) of (Ca2+)2-CaMC bound to NaV1.2IQp. The polarity of (Ca2+)2-CaMC relative to the IQ motif was opposite to that seen in apo CaMC-Nav1.2IQp (2KXW), revealing that CaMC recognizes nested, anti-parallel sites in Nav1.2IQp. Reversal of CaM may require transient release from the IQ motif during calcium binding, and facilitate a re-orientation of CaMN allowing interactions with non-IQ NaV1.2 residues or auxiliary regulatory proteins interacting in the vicinity of the IQ motif.
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Affiliation(s)
- Liam Hovey
- Department of Biochemistry, University of Iowa, 52242-1109 Iowa City, United States
| | - C Andrew Fowler
- NMR Facility, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, 52242-1109 Iowa City, United States
| | - Ryan Mahling
- Department of Biochemistry, University of Iowa, 52242-1109 Iowa City, United States
| | - Zesen Lin
- Department of Biochemistry, University of Iowa, 52242-1109 Iowa City, United States
| | - Mark Stephen Miller
- Department of Biochemistry, University of Iowa, 52242-1109 Iowa City, United States
| | - Dagan C Marx
- Department of Biochemistry, University of Iowa, 52242-1109 Iowa City, United States
| | - Jesse B Yoder
- Department of Biochemistry, University of Iowa, 52242-1109 Iowa City, United States
| | - Elaine H Kim
- Department of Biochemistry, University of Iowa, 52242-1109 Iowa City, United States
| | - Kristin M Tefft
- Department of Biochemistry, University of Iowa, 52242-1109 Iowa City, United States
| | - Brett C Waite
- Department of Biochemistry, University of Iowa, 52242-1109 Iowa City, United States
| | - Michael D Feldkamp
- Department of Biochemistry, University of Iowa, 52242-1109 Iowa City, United States
| | - Liping Yu
- NMR Facility, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, 52242-1109 Iowa City, United States
| | - Madeline A Shea
- Department of Biochemistry, University of Iowa, 52242-1109 Iowa City, United States.
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10
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Moroz P, Razgoniaeva N, He Y, Jensen G, Eckard H, Lu HP, Zamkov M. Tracking the Energy Flow on Nanoscale via Sample-Transmitted Excitation Photoluminescence Spectroscopy. ACS NANO 2017; 11:4191-4197. [PMID: 28324655 DOI: 10.1021/acsnano.7b01141] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Tracking the energy flow in nanoscale materials is an important yet challenging goal. Experimental methods for probing the intermolecular energy transfer (ET) are often burdened by the spectral crosstalk between donor and acceptor species, which complicates unraveling their individual contributions. This issue is particularly prominent in inorganic nanoparticles and biological macromolecules featuring broad absorbing profiles. Here, we demonstrate a general spectroscopic strategy for measuring the ET efficiency between nanostructured or molecular dyes exhibiting a significant donor-acceptor spectral overlap. The reported approach is enabled through spectral shaping of the broadband excitation light with solutions of donor molecules, which inhibits the excitation of respective donor species in the sample. The resulting changes in the acceptor emission induced by the spectral modulation of the excitation beam are then used to determine the quantum efficiency and the rate of ET processes between arbitrary fluorophores (molecules, nanoparticles, polymers) with high accuracy. The feasibility of the reported method was demonstrated using a control donor-acceptor system utilizing a protein-bridged Cy3-Cy5 dye pair and subsequently applied for studying the energy flow in a CdSe560-CdSe600 binary nanocrystal film.
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Affiliation(s)
- Pavel Moroz
- The Center for Photochemical Sciences, ‡Department of Physics, and §Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
| | - Natalia Razgoniaeva
- The Center for Photochemical Sciences, ‡Department of Physics, and §Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
| | - Yufan He
- The Center for Photochemical Sciences, ‡Department of Physics, and §Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
| | - Gregory Jensen
- The Center for Photochemical Sciences, ‡Department of Physics, and §Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
| | - Holly Eckard
- The Center for Photochemical Sciences, ‡Department of Physics, and §Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
| | - H Peter Lu
- The Center for Photochemical Sciences, ‡Department of Physics, and §Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
| | - Mikhail Zamkov
- The Center for Photochemical Sciences, ‡Department of Physics, and §Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
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11
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Fonin AV, Silonov SA, Sitdikova AK, Kuznetsova IM, Uversky VN, Turoverov KK. Structure and Conformational Properties of d-Glucose/d-Galactose-Binding Protein in Crowded Milieu. Molecules 2017; 22:molecules22020244. [PMID: 28178192 PMCID: PMC6155729 DOI: 10.3390/molecules22020244] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/26/2017] [Accepted: 01/29/2017] [Indexed: 11/18/2022] Open
Abstract
Conformational changes of d-glucose/d-galactose-binding protein (GGBP) were studied under molecular crowding conditions modeled by concentrated solutions of polyethylene glycols (PEG-12000, PEG-4000, and PEG-600), Ficoll-70, and Dextran-70, addition of which induced noticeable structural changes in the GGBP molecule. All PEGs promoted compaction of GGBP and lead to the increase in ordering of its structure. Concentrated solutions of PEG-12000 and PEG-4000 caused GGBP aggregation. Although Ficoll-70 and Dextran-70 also promoted increase in the GGBP ordering, the structural outputs were different for different crowders. For example, in comparison with the GGBP in buffer, the intrinsic fluorescence spectrum of this protein was shifted to short-wave region in the presence of PEGs but was red-shifted in the presence of Ficoll-70 and Dextran-70. It was hypothesized that this difference could be due to the specific interaction of GGBP with the sugar-based polymers (Ficoll-70 and Dextran-70), indicating that protein can adopt different conformations in solutions containing molecular crowders of different chemical nature. It was also shown that all tested crowding agents were able to stabilize GGBP structure shifting the GGBP guanidine hydrochloride (GdnHCl)-induced unfolding curves to higher denaturant concentrations, but their stabilization capabilities did not depend on the hydrodynamic dimensions of the polymers molecules. Refolding of GGBP was complicated by protein aggregation in all tested solutions of crowding agents. The lowest yield of refolded protein was achieved in the highly concentrated solutions of PEG-12000. These data support the previous notion that the influence of macromolecular crowders on proteins is rather complex phenomenon that extends beyond the excluded volume effects.
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Affiliation(s)
- Alexander V Fonin
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Structural Dynamics, Stability and Folding of Proteins, Tikhoretsky av. 4, St. Petersburg 197046, Russia.
| | - Sergey A Silonov
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Structural Dynamics, Stability and Folding of Proteins, Tikhoretsky av. 4, St. Petersburg 197046, Russia.
- Saint-Petersburg Technological Institute (Technical University), Moskovsky av. 26, Saint-Petersburg 190013, Russia.
| | - Asiya K Sitdikova
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Structural Dynamics, Stability and Folding of Proteins, Tikhoretsky av. 4, St. Petersburg 197046, Russia.
- Department of Biophysics, St. Petersburg State Polytechnical University, Polytechnicheskaya av. 29, St. Petersburg 195251, Russia.
| | - Irina M Kuznetsova
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Structural Dynamics, Stability and Folding of Proteins, Tikhoretsky av. 4, St. Petersburg 197046, Russia.
| | - Vladimir N Uversky
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Structural Dynamics, Stability and Folding of Proteins, Tikhoretsky av. 4, St. Petersburg 197046, Russia.
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
| | - Konstantin K Turoverov
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Structural Dynamics, Stability and Folding of Proteins, Tikhoretsky av. 4, St. Petersburg 197046, Russia.
- Department of Biophysics, St. Petersburg State Polytechnical University, Polytechnicheskaya av. 29, St. Petersburg 195251, Russia.
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12
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Xu G, Cheng K, Wu Q, Liu M, Li C. Confinement Alters the Structure and Function of Calmodulin. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609639] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Guohua Xu
- Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P.R. China
| | - Kai Cheng
- Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P.R. China
- Graduate University of Chinese Academy of Sciences; Beijing 100029 P.R. China
| | - Qiong Wu
- Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P.R. China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P.R. China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P.R. China
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Xu G, Cheng K, Wu Q, Liu M, Li C. Confinement Alters the Structure and Function of Calmodulin. Angew Chem Int Ed Engl 2016; 56:530-534. [DOI: 10.1002/anie.201609639] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 11/11/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Guohua Xu
- Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P.R. China
| | - Kai Cheng
- Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P.R. China
- Graduate University of Chinese Academy of Sciences; Beijing 100029 P.R. China
| | - Qiong Wu
- Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P.R. China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P.R. China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P.R. China
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Biswas S, Chowdhury PK. Correlated and Anticorrelated Domain Movement of Human Serum Albumin: A Peek into the Complexity of the Crowded Milieu. J Phys Chem B 2016; 120:4897-911. [DOI: 10.1021/acs.jpcb.6b01671] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Saikat Biswas
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Pramit Kumar Chowdhury
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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15
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Hoffman L, Wang X, Sanabria H, Cheung MS, Putkey JA, Waxham MN. Relative Cosolute Size Influences the Kinetics of Protein-Protein Interactions. Biophys J 2016; 109:510-20. [PMID: 26244733 DOI: 10.1016/j.bpj.2015.06.043] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 05/29/2015] [Accepted: 06/22/2015] [Indexed: 12/18/2022] Open
Abstract
Protein signaling occurs in crowded intracellular environments, and while high concentrations of macromolecules are postulated to modulate protein-protein interactions, analysis of their impact at each step of the reaction pathway has not been systematically addressed. Potential cosolute-induced alterations in target association are particularly important for a signaling molecule like calmodulin (CaM), where competition among >300 targets governs which pathways are selectively activated. To explore how high concentrations of cosolutes influence CaM-target affinity and kinetics, we methodically investigated each step of the CaM-target binding mechanism under crowded or osmolyte-rich environments mimicked by ficoll-70, dextran-10, and sucrose. All cosolutes stabilized compact conformers of CaM and modulated association kinetics by affecting diffusion and rates of conformational change; however, the results showed that differently sized molecules had variable effects to enhance or impede unique steps of the association pathway. On- and off-rates were modulated by all cosolutes in a compensatory fashion, producing little change in steady-state affinity. From this work insights were gained on how high concentrations of inert crowding agents and osmolytes fit into a kinetic framework to describe protein-protein interactions relevant for cellular signaling.
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Affiliation(s)
- Laurel Hoffman
- Department of Neurobiology and Anatomy, University of Texas Medical School at Houston, Houston, Texas
| | - Xu Wang
- Department of Biochemistry and Molecular Biology, University of Texas Medical School at Houston, Houston, Texas
| | - Hugo Sanabria
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina
| | - Margaret S Cheung
- Department of Physics, University of Houston, Houston, Texas; The Center for Theoretical Biological Physics, Rice University, Houston, Texas
| | - John A Putkey
- Department of Biochemistry and Molecular Biology, University of Texas Medical School at Houston, Houston, Texas
| | - M Neal Waxham
- Department of Neurobiology and Anatomy, University of Texas Medical School at Houston, Houston, Texas.
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16
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Yoshitake T, Toyooka T, Nakasone Y, Zikihara K, Tokutomi S, Terazima M. Macromolecular crowding effect for photoreactions of LOV2 domains of Arabidopsis thaliana phototropin 1. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2015.08.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Mondal S, Kallianpur MV, Udgaonkar JB, Krishnamoorthy G. Molecular crowding causes narrowing of population heterogeneity and restricts internal dynamics in a protein. Methods Appl Fluoresc 2015. [DOI: 10.1088/2050-6120/4/1/014003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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18
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Ye Y, Liu X, Xu G, Liu M, Li C. Direct Observation of Ca2+-Induced Calmodulin Conformational Transitions in IntactXenopus laevisOocytes by19F NMR Spectroscopy. Angew Chem Int Ed Engl 2015; 54:5328-30. [DOI: 10.1002/anie.201500261] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Indexed: 01/04/2023]
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19
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Ye Y, Liu X, Xu G, Liu M, Li C. Direct Observation of Ca2+-Induced Calmodulin Conformational Transitions in IntactXenopus laevisOocytes by19F NMR Spectroscopy. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201500261] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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20
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Tripathi S, Wang Q, Zhang P, Hoffman L, Waxham MN, Cheung MS. Conformational frustration in calmodulin-target recognition. J Mol Recognit 2015; 28:74-86. [PMID: 25622562 DOI: 10.1002/jmr.2413] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 07/30/2014] [Accepted: 07/31/2014] [Indexed: 11/10/2022]
Abstract
Calmodulin (CaM) is a primary calcium (Ca(2+) )-signaling protein that specifically recognizes and activates highly diverse target proteins. We explored the molecular basis of target recognition of CaM with peptides representing the CaM-binding domains from two Ca(2+) -CaM-dependent kinases, CaMKI and CaMKII, by employing experimentally constrained molecular simulations. Detailed binding route analysis revealed that the two CaM target peptides, although similar in length and net charge, follow distinct routes that lead to a higher binding frustration in the CaM-CaMKII complex than in the CaM-CaMKI complex. We discovered that the molecular origin of the binding frustration is caused by intermolecular contacts formed with the C-domain of CaM that need to be broken before the formation of intermolecular contacts with the N-domain of CaM. We argue that the binding frustration is important for determining the kinetics of the recognition process of proteins involving large structural fluctuations.
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Affiliation(s)
- Swarnendu Tripathi
- Department of Physics, University of Houston, Houston, TX, 77204, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX, 77005, USA
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21
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Kuznetsova IM, Zaslavsky BY, Breydo L, Turoverov KK, Uversky VN. Beyond the excluded volume effects: mechanistic complexity of the crowded milieu. Molecules 2015; 20:1377-409. [PMID: 25594347 PMCID: PMC6272634 DOI: 10.3390/molecules20011377] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 01/09/2015] [Indexed: 11/16/2022] Open
Abstract
Macromolecular crowding is known to affect protein folding, binding of small molecules, interaction with nucleic acids, enzymatic activity, protein-protein interactions, and protein aggregation. Although for a long time it was believed that the major mechanism of the action of crowded environments on structure, folding, thermodynamics, and function of a protein can be described in terms of the excluded volume effects, it is getting clear now that other factors originating from the presence of high concentrations of “inert” macromolecules in crowded solution should definitely be taken into account to draw a more complete picture of a protein in a crowded milieu. This review shows that in addition to the excluded volume effects important players of the crowded environments are viscosity, perturbed diffusion, direct physical interactions between the crowding agents and proteins, soft interactions, and, most importantly, the effects of crowders on solvent properties.
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Affiliation(s)
- Irina M. Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russia; E-Mails: (I.M.K.); (K.K.T.)
- St. Petersburg State Polytechnical University, 29 Polytechnicheskaya st., St. Petersburg 195251, Russia
| | - Boris Y. Zaslavsky
- Cleveland Diagnostics, 3615 Superior Ave., Suite 4407B, Cleveland, OH 44114, USA; E-Mail:
| | - Leonid Breydo
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL 33612, USA; E-Mails:
| | - Konstantin K. Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russia; E-Mails: (I.M.K.); (K.K.T.)
- St. Petersburg State Polytechnical University, 29 Polytechnicheskaya st., St. Petersburg 195251, Russia
| | - Vladimir N. Uversky
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russia; E-Mails: (I.M.K.); (K.K.T.)
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL 33612, USA; E-Mails:
- Biology Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-813-974-5816; Fax: +1-813-974-7357
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22
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Biswas S, Chowdhury PK. Unusual domain movement in a multidomain protein in the presence of macromolecular crowders. Phys Chem Chem Phys 2015; 17:19820-33. [DOI: 10.1039/c5cp02674a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
FRET-based distance changes between domains I and II of HSA reveal significant differences in the manner in which dextran based macromolecular crowding agents influence the serum protein.
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Affiliation(s)
- Saikat Biswas
- Department of Chemistry
- Indian Institute of Technology Delhi
- New Delhi 110016
- India
| | - Pramit K. Chowdhury
- Department of Chemistry
- Indian Institute of Technology Delhi
- New Delhi 110016
- India
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23
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What macromolecular crowding can do to a protein. Int J Mol Sci 2014; 15:23090-140. [PMID: 25514413 PMCID: PMC4284756 DOI: 10.3390/ijms151223090] [Citation(s) in RCA: 355] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/04/2014] [Accepted: 12/05/2014] [Indexed: 01/17/2023] Open
Abstract
The intracellular environment represents an extremely crowded milieu, with a limited amount of free water and an almost complete lack of unoccupied space. Obviously, slightly salted aqueous solutions containing low concentrations of a biomolecule of interest are too simplistic to mimic the “real life” situation, where the biomolecule of interest scrambles and wades through the tightly packed crowd. In laboratory practice, such macromolecular crowding is typically mimicked by concentrated solutions of various polymers that serve as model “crowding agents”. Studies under these conditions revealed that macromolecular crowding might affect protein structure, folding, shape, conformational stability, binding of small molecules, enzymatic activity, protein-protein interactions, protein-nucleic acid interactions, and pathological aggregation. The goal of this review is to systematically analyze currently available experimental data on the variety of effects of macromolecular crowding on a protein molecule. The review covers more than 320 papers and therefore represents one of the most comprehensive compendia of the current knowledge in this exciting area.
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24
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Goldenberg DP, Argyle B. Minimal effects of macromolecular crowding on an intrinsically disordered protein: a small-angle neutron scattering study. Biophys J 2014; 106:905-14. [PMID: 24559993 DOI: 10.1016/j.bpj.2013.12.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 11/26/2013] [Accepted: 12/02/2013] [Indexed: 01/04/2023] Open
Abstract
Small-angle neutron scattering was used to study the effects of macromolecular crowding by two globular proteins, i.e., bovine pancreatic trypsin inhibitor and equine metmyoglobin, on the conformational ensemble of an intrinsically disordered protein, the N protein of bacteriophage λ. The λ N protein was uniformly labeled with (2)H, and the concentrations of D2O in the samples were adjusted to match the neutron scattering contrast of the unlabeled crowding proteins, thereby masking their contribution to the scattering profiles. Scattering from the deuterated λ N was recorded for samples containing up to 0.12 g/mL bovine pancreatic trypsin inhibitor or 0.2 g/mL metmyoglobin. The radius of gyration of the uncrowded protein was estimated to be 30 Å and was found to be remarkably insensitive to the presence of crowders, varying by <2 Å for the highest crowder concentrations. The scattering profiles were also used to estimate the fractal dimension of λ N, which was found to be ∼1.8 in the absence or presence of crowders, indicative of a well-solvated and expanded random coil under all of the conditions examined. These results are contrary to the predictions of theoretical treatments and previous experimental studies demonstrating compaction of unfolded proteins by crowding with polymers such as dextran and Ficoll. A computational simulation suggests that some previous treatments may have overestimated the effective volumes of disordered proteins and the variation of these volumes within an ensemble. The apparent insensitivity of λ N to crowding may also be due in part to weak attractive interactions with the crowding proteins, which may compensate for the effects of steric exclusion.
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Affiliation(s)
| | - Brian Argyle
- Department of Biology, University of Utah, Salt Lake City, Utah
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25
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The effect of macromolecular crowding on the electrostatic component of barnase-barstar binding: a computational, implicit solvent-based study. PLoS One 2014; 9:e98618. [PMID: 24915485 PMCID: PMC4051634 DOI: 10.1371/journal.pone.0098618] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 05/05/2014] [Indexed: 02/02/2023] Open
Abstract
Macromolecular crowding within the cell can impact both protein folding and binding. Earlier models of cellular crowding focused on the excluded volume, entropic effect of crowding agents, which generally favors compact protein states. Recently, other effects of crowding have been explored, including enthalpically-related crowder–protein interactions and changes in solvation properties. In this work, we explore the effects of macromolecular crowding on the electrostatic desolvation and solvent-screened interaction components of protein–protein binding. Our simple model enables us to focus exclusively on the electrostatic effects of water depletion on protein binding due to crowding, providing us with the ability to systematically analyze and quantify these potentially intuitive effects. We use the barnase–barstar complex as a model system and randomly placed, uncharged spheres within implicit solvent to model crowding in an aqueous environment. On average, we find that the desolvation free energy penalties incurred by partners upon binding are lowered in a crowded environment and solvent-screened interactions are amplified. At a constant crowder density (fraction of total available volume occupied by crowders), this effect generally increases as the radius of model crowders decreases, but the strength and nature of this trend can depend on the water probe radius used to generate the molecular surface in the continuum model. In general, there is huge variation in desolvation penalties as a function of the random crowder positions. Results with explicit model crowders can be qualitatively similar to those using a lowered “effective” solvent dielectric to account for crowding, although the “best” effective dielectric constant will likely depend on multiple system properties. Taken together, this work systematically demonstrates, quantifies, and analyzes qualitative intuition-based insights into the effects of water depletion due to crowding on the electrostatic component of protein binding, and it provides an initial framework for future analyses.
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26
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Sulmann S, Dell'Orco D, Marino V, Behnen P, Koch KW. Conformational Changes in Calcium-Sensor Proteins under Molecular Crowding Conditions. Chemistry 2014; 20:6756-62. [DOI: 10.1002/chem.201402146] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Indexed: 11/05/2022]
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27
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Ramanathan A, Savol A, Burger V, Chennubhotla CS, Agarwal PK. Protein conformational populations and functionally relevant substates. Acc Chem Res 2014; 47:149-56. [PMID: 23988159 DOI: 10.1021/ar400084s] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Functioning proteins do not remain fixed in a unique structure, but instead they sample a range of conformations facilitated by motions within the protein. Even in the native state, a protein exists as a collection of interconverting conformations driven by thermodynamic fluctuations. Motions on the fast time scale allow a protein to sample conformations in the nearby area of its conformational landscape, while motions on slower time scales give it access to conformations in distal areas of the landscape. Emerging evidence indicates that protein landscapes contain conformational substates with dynamic and structural features that support the designated function of the protein. Nuclear magnetic resonance (NMR) experiments provide information about conformational ensembles of proteins. X-ray crystallography allows researchers to identify the most populated states along the landscape, and computational simulations give atom-level information about the conformational substates of different proteins. This ability to characterize and obtain quantitative information about the conformational substates and the populations of proteins within them is allowing researchers to better understand the relationship between protein structure and dynamics and the mechanisms of protein function. In this Account, we discuss recent developments and challenges in the characterization of functionally relevant conformational populations and substates of proteins. In some enzymes, the sampling of functionally relevant conformational substates is connected to promoting the overall mechanism of catalysis. For example, the conformational landscape of the enzyme dihydrofolate reductase has multiple substates, which facilitate the binding and the release of the cofactor and substrate and catalyze the hydride transfer. For the enzyme cyclophilin A, computational simulations reveal that the long time scale conformational fluctuations enable the enzyme to access conformational substates that allow it to attain the transition state, therefore promoting the reaction mechanism. In the long term, this emerging view of proteins with conformational substates has broad implications for improving our understanding of enzymes, enzyme engineering, and better drug design. Researchers have already used photoactivation to modulate protein conformations as a strategy to develop a hypercatalytic enzyme. In addition, the alteration of the conformational substates through binding of ligands at locations other than the active site provides the basis for the design of new medicines through allosteric modulation.
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Affiliation(s)
- Arvind Ramanathan
- Computational Science and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Andrej Savol
- Joint Carnegie Mellon University−University of Pittsburgh Ph.D Program in Computational Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Virginia Burger
- Joint Carnegie Mellon University−University of Pittsburgh Ph.D Program in Computational Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Chakra S. Chennubhotla
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Pratul K. Agarwal
- Annavitas Biosciences, 2519 Caspian Drive, Knoxville, Tennessee 37932, United States
- Computational Biology Institute, and Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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28
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Protein recognition and selection through conformational and mutually induced fit. Proc Natl Acad Sci U S A 2013; 110:20545-50. [PMID: 24297894 DOI: 10.1073/pnas.1312788110] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein-protein interactions drive most every biological process, but in many instances the domains mediating recognition are disordered. How specificity in binding is attained in the absence of defined structure contrasts with well-established experimental and theoretical work describing ligand binding to protein. The signaling protein calmodulin presents a unique opportunity to investigate mechanisms for target recognition given that it interacts with several hundred different targets. By advancing coarse-grained computer simulations and experimental techniques, mechanistic insights were gained in defining the pathways leading to recognition and in how target selectivity can be achieved at the molecular level. A model requiring mutually induced conformational changes in both calmodulin and target proteins was necessary and broadly informs how proteins can achieve both high affinity and high specificity.
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29
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Feig M, Sugita Y. Reaching new levels of realism in modeling biological macromolecules in cellular environments. J Mol Graph Model 2013; 45:144-56. [PMID: 24036504 DOI: 10.1016/j.jmgm.2013.08.017] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 08/14/2013] [Accepted: 08/19/2013] [Indexed: 12/21/2022]
Abstract
An increasing number of studies are aimed at modeling cellular environments in a comprehensive and realistic fashion. A major challenge in these efforts is how to bridge spatial and temporal scales over many orders of magnitude. Furthermore, there are additional challenges in integrating different aspects ranging from questions about biomolecular stability in crowded environments to the description of reactive processes on cellular scales. In this review, recent studies with models of biomolecules in cellular environments at different levels of detail are discussed in terms of their strengths and weaknesses. In particular, atomistic models, implicit representations of cellular environments, coarse-grained and spheroidal models of biomolecules, as well as the inclusion of reactive processes via reaction-diffusion models are described. Furthermore, strategies for integrating the different models into a comprehensive description of cellular environments are discussed.
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Affiliation(s)
- Michael Feig
- Department of Biochemistry & Molecular Biology and Department of Chemistry, Michigan State University, 603 Wilson Road, BCH 218, East Lansing, MI 48824, United States; RIKEN Quantitative Biology Center, International Medical Device Alliance (IMDA) 6F, 1-6-5 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
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30
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Direct observation of protein unfolded state compaction in the presence of macromolecular crowding. Biophys J 2013; 104:694-704. [PMID: 23442920 DOI: 10.1016/j.bpj.2012.12.020] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 11/20/2012] [Accepted: 12/06/2012] [Indexed: 11/22/2022] Open
Abstract
Proteins fold and function in cellular environments that are crowded with other macromolecules. As a consequence of excluded volume effects, compact folded states of proteins should be indirectly stabilized due to destabilization of extended unfolded conformations. Here, we assess the role of excluded volume in terms of protein stability, structural dimensions and folding dynamics using a sugar-based crowding agent, dextran 20, and the small ribosomal protein S16 as a model system. To specifically address dimensions, we labeled the protein with BODIPY at two positions and measured Trp-BODIPY distances under different conditions. As expected, we found that dextran 20 (200 mg/ml) stabilized the variants against urea-induced unfolding. At conditions where the protein is unfolded, Förster resonance energy transfer measurements reveal that in the presence of dextran, the unfolded ensemble is more compact and there is residual structure left as probed by far-ultraviolet circular dichroism. In the presence of a crowding agent, folding rates are faster in the two-state regime, and at low denaturant concentrations, a kinetic intermediate is favored. Our study provides direct evidence for protein unfolded-state compaction in the presence of macromolecular crowding along with its energetic and kinetic consequences.
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31
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Where soft matter meets living matter--protein structure, stability, and folding in the cell. Curr Opin Struct Biol 2013; 23:212-7. [PMID: 23474325 DOI: 10.1016/j.sbi.2013.02.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Revised: 02/08/2013] [Accepted: 02/13/2013] [Indexed: 01/06/2023]
Abstract
A protein is a biopolymer that self-assembles through the process of protein folding. A cell is a crowded space where the surrounding macromolecules of a protein can limit the number of ways of folding. These crowding macromolecules can also affect the shape and the size of a physically malleable, or 'soft, squishy', protein with regulatory purposes. In this review, we focus on the in silico approaches of coarse-grained molecular simulations that enable the investigation of protein folding in a cell-like environment. When these simulation results were compared with experimentally measured properties of a protein, such joint effort has yielded new ideas on the specific function of a protein in cells. We also highlighted the recent developments of computer modeling and simulations that encompass the importance of the shape of a macromolecule, the interactions between macromolecules, and the hydrodynamic interactions on the kinetics and thermodynamics of a protein in a high concentration of protein solution and in cytoplasmic environments.
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Christiansen A, Wang Q, Cheung MS, Wittung-Stafshede P. Effects of macromolecular crowding agents on protein folding in vitro and in silico. Biophys Rev 2013; 5:137-145. [PMID: 28510156 DOI: 10.1007/s12551-013-0108-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 01/31/2013] [Indexed: 01/24/2023] Open
Abstract
Proteins fold and function inside cells which are environments very different from that of dilute buffer solutions most often used in traditional experiments. The crowded milieu results in excluded-volume effects, increased bulk viscosity and amplified chances for inter-molecular interactions. These environmental factors have not been accounted for in most mechanistic studies of protein folding executed during the last decades. The question thus arises as to how these effects-present when polypeptides normally fold in vivo-modulate protein biophysics. To address excluded volume effects, we use synthetic macromolecular crowding agents, which take up significant volume but do not interact with proteins, in combination with strategically selected proteins and a range of equilibrium and time-resolved biophysical (spectroscopic and computational) methods. In this review, we describe key observations on macromolecular crowding effects on protein stability, folding and structure drawn from combined in vitro and in silico studies. As expected based on Minton's early predictions, many proteins (apoflavodoxin, VlsE, cytochrome c, and S16) became more thermodynamically stable (magnitude depends inversely on protein stability in buffer) and, unexpectedly, for apoflavodoxin and VlsE, the folded states changed both secondary structure content and, for VlsE, overall shape in the presence of macromolecular crowding. For apoflavodoxin and cytochrome c, which have complex kinetic folding mechanisms, excluded volume effects made the folding energy landscapes smoother (i.e., less misfolding and/or kinetic heterogeneity) than in buffer.
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Affiliation(s)
| | - Qian Wang
- Department of Physics, University of Houston, Houston, TX, 77204, USA
| | - Margaret S Cheung
- Department of Physics, University of Houston, Houston, TX, 77204, USA
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Saha R, Rakshit S, Verma PK, Mitra RK, Pal SK. Protein-cofactor binding and ultrafast electron transfer in riboflavin binding protein under the spatial confinement of nanoscopic reverse micelles. J Mol Recognit 2013; 26:59-66. [DOI: 10.1002/jmr.2246] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 10/09/2012] [Indexed: 11/10/2022]
Affiliation(s)
- Ranajay Saha
- Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences; Block JD, Sector III Salt Lake; Kolkata 700098; India
| | - Surajit Rakshit
- Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences; Block JD, Sector III Salt Lake; Kolkata 700098; India
| | - Pramod Kumar Verma
- Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences; Block JD, Sector III Salt Lake; Kolkata 700098; India
| | - Rajib Kumar Mitra
- Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences; Block JD, Sector III Salt Lake; Kolkata 700098; India
| | - Samir Kumar Pal
- Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences; Block JD, Sector III Salt Lake; Kolkata 700098; India
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Crowding, molecular volume and plasticity: An assessment involving crystallography, NMR and simulations. J Biosci 2012; 37:953-63. [DOI: 10.1007/s12038-012-9276-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Latham MP, Kay LE. Is buffer a good proxy for a crowded cell-like environment? A comparative NMR study of calmodulin side-chain dynamics in buffer and E. coli lysate. PLoS One 2012; 7:e48226. [PMID: 23118958 PMCID: PMC3484071 DOI: 10.1371/journal.pone.0048226] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 09/24/2012] [Indexed: 11/18/2022] Open
Abstract
Biophysical studies of protein structure and dynamics are typically performed in a highly controlled manner involving only the protein(s) of interest. Comparatively fewer such studies have been carried out in the context of a cellular environment that typically involves many biomolecules, ions and metabolites. Recently, solution NMR spectroscopy, focusing primarily on backbone amide groups as reporters, has emerged as a powerful technique for investigating protein structure and dynamics in vivo and in crowded “cell-like” environments. Here we extend these studies through a comparative analysis of Ile, Leu, Val and Met methyl side-chain motions in apo, Ca2+-bound and Ca2+, peptide-bound calmodulin dissolved in aqueous buffer or in E. coli lysate. Deuterium spin relaxation experiments, sensitive to pico- to nano-second time-scale processes and Carr-Purcell-Meiboom-Gill relaxation dispersion experiments, reporting on millisecond dynamics, have been recorded. Both similarities and differences in motional properties are noted for calmodulin dissolved in buffer or in lysate. These results emphasize that while significant insights can be obtained through detailed “test-tube” studies, experiments performed under conditions that are “cell-like” are critical for obtaining a comprehensive understanding of protein motion in vivo and therefore for elucidating the relation between motion and function.
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Affiliation(s)
- Michael P Latham
- Departments of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto, Toronto, Ontario, Canada.
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Wang Q, Cheung MS. A physics-based approach of coarse-graining the cytoplasm of Escherichia coli (CGCYTO). Biophys J 2012; 102:2353-61. [PMID: 22677389 DOI: 10.1016/j.bpj.2012.04.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 03/15/2012] [Accepted: 04/04/2012] [Indexed: 01/26/2023] Open
Abstract
We have investigated protein stability in an environment of Escherichia coli cytoplasm using coarse-grained computer simulations. To coarse-grain a small slide of E. coli's cytoplasm consisting of over 16 million atoms, we have developed a self-assembled clustering algorithm (CGCYTO). CGCYTO uses the shape parameter and asphericity as well as a parameter λ (ranging from 0 to 1) that measures the covolume of a test protein and a macromolecule against the covolume of a test protein and a sphere of equal volume as that of a macromolecule for the criteria of coarse-graining a cytoplasmic model. A cutoff λ(c) = 0.8 was chosen based on the size of a test protein and computational resources and it determined the resolution of a coarse-grained cytoplasm. We compared the results from a polydisperse cytoplasmic model (PD model) produced by CGCYTO with two other coarse-grained hard-sphere cytoplasmic models: 1), F70 model, macromolecules in the cytoplasm were modeled by homogeneous hard spheres with a radius of 55 Å, the size of Ficoll70 and 2), HS model, each macromolecule in the cytoplasm was modeled by a hard sphere of equal volume. It was found that the folding temperature T(f) of a test protein (apoazurin) in a PD model is ~5° greater than that in a F70 model. In addition, the deviation of T(f) in a PD model is twice as much as that in a HS model when an apoazurin is randomly placed at different voids formed by particle fluctuations in PD models.
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Affiliation(s)
- Qian Wang
- Department of Physics, University of Houston, Houston, Texas, USA
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Samiotakis A, Cheung MS. Folding dynamics of Trp-cage in the presence of chemical interference and macromolecular crowding. I. J Chem Phys 2012; 135:175101. [PMID: 22070323 DOI: 10.1063/1.3656691] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Proteins fold and function in the crowded environment of the cell's interior. In the recent years it has been well established that the so-called "macromolecular crowding" effect enhances the folding stability of proteins by destabilizing their unfolded states for selected proteins. On the other hand, chemical and thermal denaturation is often used in experiments as a tool to destabilize a protein by populating the unfolded states when probing its folding landscape and thermodynamic properties. However, little is known about the complicated effects of these synergistic perturbations acting on the kinetic properties of proteins, particularly when large structural fluctuations, such as protein folding, have been involved. In this study, we have first investigated the folding mechanism of Trp-cage dependent on urea concentration by coarse-grained molecular simulations where the impact of urea is implemented into an energy function of the side chain and/or backbone interactions derived from the all-atomistic molecular dynamics simulations with urea through a Boltzmann inversion method. In urea solution, the folding rates of a model miniprotein Trp-cage decrease and the folded state slightly swells due to a lack of contact formation between side chains at the terminal regions. In addition, the equilibrium m-values of Trp-cage from the computer simulations are in agreement with experimental measurements. We have further investigated the combined effects of urea denaturation and macromolecular crowding on Trp-cage's folding mechanism where crowding agents are modeled as hard-spheres. The enhancement of folding rates of Trp-cage is most pronounced by macromolecular crowding effect when the extended conformations of Trp-cast dominate at high urea concentration. Our study makes quantitatively testable predictions on protein folding dynamics in a complex environment involving both chemical denaturation and macromolecular crowding effects.
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Atilgan AR, Aykut AO, Atilgan C. Subtle pH differences trigger single residue motions for moderating conformations of calmodulin. J Chem Phys 2011; 135:155102. [DOI: 10.1063/1.3651807] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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The effect of macromolecular crowding, ionic strength and calcium binding on calmodulin dynamics. PLoS Comput Biol 2011; 7:e1002114. [PMID: 21829336 PMCID: PMC3145654 DOI: 10.1371/journal.pcbi.1002114] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 05/23/2011] [Indexed: 11/20/2022] Open
Abstract
The flexibility in the structure of calmodulin (CaM) allows its binding to over 300 target proteins in the cell. To investigate the structure-function relationship of CaM, we combined methods of computer simulation and experiments based on circular dichroism (CD) to investigate the structural characteristics of CaM that influence its target recognition in crowded cell-like conditions. We developed a unique multiscale solution of charges computed from quantum chemistry, together with protein reconstruction, coarse-grained molecular simulations, and statistical physics, to represent the charge distribution in the transition from apoCaM to holoCaM upon calcium binding. Computationally, we found that increased levels of macromolecular crowding, in addition to calcium binding and ionic strength typical of that found inside cells, can impact the conformation, helicity and the EF hand orientation of CaM. Because EF hand orientation impacts the affinity of calcium binding and the specificity of CaM's target selection, our results may provide unique insight into understanding the promiscuous behavior of calmodulin in target selection inside cells. Proteins are workhorses for driving biological functions inside cells. Calmodulin (CaM) is a protein that can carry cellular signals by triggered conformational changes due to calcium binding that alters target binding. Interestingly, CaM is able to bind over 300 targets. One of the challenges in characterizing CaM's ability to bind multiple targets lies in that CaM is a flexible protein and its structure is easily modulated by the physicochemical changes in its surroundings, particularly inside a complex cellular milieu. In order to determine structure-function relationships of CaM, we employed a combined approach of experiments, computer simulations and statistical physics in the investigation of the effect of calcium-binding, salt concentration, and macromolecular crowding on CaM. The results revealed unique folding energy landscapes of CaM in the absence and presence of calcium ions and the structural implications of CaM are interpreted under cell-like conditions. Further, a large conformational change in CaM in response to environmental impacts, dictates the packing of local helices that may be critical to its function of target binding and recognition among vast target selections.
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Aguilar X, F. Weise C, Sparrman T, Wolf-Watz M, Wittung-Stafshede P. Macromolecular Crowding Extended to a Heptameric System: The Co-chaperonin Protein 10. Biochemistry 2011; 50:3034-44. [DOI: 10.1021/bi2002086] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ximena Aguilar
- Department of Chemistry, Chemical Biological Center, Umeå University, 901 87 Umeå, Sweden
| | - Christoph F. Weise
- Department of Chemistry, Chemical Biological Center, Umeå University, 901 87 Umeå, Sweden
| | - Tobias Sparrman
- Department of Chemistry, Chemical Biological Center, Umeå University, 901 87 Umeå, Sweden
| | - Magnus Wolf-Watz
- Department of Chemistry, Chemical Biological Center, Umeå University, 901 87 Umeå, Sweden
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41
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Kim YC, Best RB, Mittal J. Macromolecular crowding effects on protein–protein binding affinity and specificity. J Chem Phys 2010; 133:205101. [DOI: 10.1063/1.3516589] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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42
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Structure, function, and folding of phosphoglycerate kinase are strongly perturbed by macromolecular crowding. Proc Natl Acad Sci U S A 2010; 107:17586-91. [PMID: 20921368 DOI: 10.1073/pnas.1006760107] [Citation(s) in RCA: 257] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We combine experiment and computer simulation to show how macromolecular crowding dramatically affects the structure, function, and folding landscape of phosphoglycerate kinase (PGK). Fluorescence labeling shows that compact states of yeast PGK are populated as the amount of crowding agents (Ficoll 70) increases. Coarse-grained molecular simulations reveal three compact ensembles: C (crystal structure), CC (collapsed crystal), and Sph (spherical compact). With an adjustment for viscosity, crowded wild-type PGK and fluorescent PGK are about 15 times or more active in 200 mg/ml Ficoll than in aqueous solution. Our results suggest a previously undescribed solution to the classic problem of how the ADP and diphosphoglycerate binding sites of PGK come together to make ATP: Rather than undergoing a hinge motion, the ADP and substrate sites are already located in proximity under crowded conditions that mimic the in vivo conditions under which the enzyme actually operates. We also examine T-jump unfolding of PGK as a function of crowding experimentally. We uncover a nonmonotonic folding relaxation time vs. Ficoll concentration. Theory and modeling explain why an optimum concentration exists for fastest folding. Below the optimum, folding slows down because the unfolded state is stabilized relative to the transition state. Above the optimum, folding slows down because of increased viscosity.
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43
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Tsao D, Minton AP, Dokholyan NV. A didactic model of macromolecular crowding effects on protein folding. PLoS One 2010; 5:e11936. [PMID: 20689808 PMCID: PMC2914742 DOI: 10.1371/journal.pone.0011936] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Accepted: 07/08/2010] [Indexed: 12/27/2022] Open
Abstract
A didactic model is presented to illustrate how the effect of macromolecular crowding on protein folding and association is modeled using current analytical theory and discrete molecular dynamics. While analytical treatments of crowding may consider the effect as a potential of average force acting to compress a polypeptide chain into a compact state, the use of simulations enables the presence of crowding reagents to be treated explicitly. Using an analytically solvable toy model for protein folding, an approximate statistical thermodynamic method is directly compared to simulation in order to gauge the effectiveness of current analytical crowding descriptions. Both methodologies are in quantitative agreement under most conditions, indication that both current theory and simulation methods are capable of recapitulating aspects of protein folding even by utilizing a simplistic protein model.
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Affiliation(s)
- Douglas Tsao
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Allen P. Minton
- Section on Physical Biochemistry, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, United States Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Nikolay V. Dokholyan
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
- * E-mail:
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Christiansen A, Wang Q, Samiotakis A, Cheung MS, Wittung-Stafshede P. Factors Defining Effects of Macromolecular Crowding on Protein Stability: An in Vitro/in Silico Case Study Using Cytochrome c. Biochemistry 2010; 49:6519-30. [DOI: 10.1021/bi100578x] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexander Christiansen
- Department of Chemistry, Chemical Biological Center, Umeå University, 901 87 Umeå, Sweden
| | - Qian Wang
- Department of Physics, University of Houston, Houston, Texas 77204
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45
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McGuffee SR, Elcock AH. Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm. PLoS Comput Biol 2010; 6:e1000694. [PMID: 20221255 PMCID: PMC2832674 DOI: 10.1371/journal.pcbi.1000694] [Citation(s) in RCA: 524] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Accepted: 01/30/2010] [Indexed: 01/24/2023] Open
Abstract
A longstanding question in molecular biology is the extent to which the behavior of macromolecules observed in vitro accurately reflects their behavior in vivo. A number of sophisticated experimental techniques now allow the behavior of individual types of macromolecule to be studied directly in vivo; none, however, allow a wide range of molecule types to be observed simultaneously. In order to tackle this issue we have adopted a computational perspective, and, having selected the model prokaryote Escherichia coli as a test system, have assembled an atomically detailed model of its cytoplasmic environment that includes 50 of the most abundant types of macromolecules at experimentally measured concentrations. Brownian dynamics (BD) simulations of the cytoplasm model have been calibrated to reproduce the translational diffusion coefficients of Green Fluorescent Protein (GFP) observed in vivo, and “snapshots” of the simulation trajectories have been used to compute the cytoplasm's effects on the thermodynamics of protein folding, association and aggregation events. The simulation model successfully describes the relative thermodynamic stabilities of proteins measured in E. coli, and shows that effects additional to the commonly cited “crowding” effect must be included in attempts to understand macromolecular behavior in vivo. The interior of a typical bacterial cell is a highly crowded place in which molecules must jostle and compete with each other in order to carry out their biological functions. The conditions under which such molecules are typically studied in vitro, however, are usually quite different: one or a few different types of molecules are studied as they freely diffuse in a dilute, aqueous solution. There is therefore a significant disconnect between the conditions under which molecules can be most usefully studied and the conditions under which such molecules usually “live”, and developing ways to bridge this gap is likely to be important for properly understanding molecular behavior in vivo. Toward this end, we show in this work that computer simulations can be used to model the interior of bacterial cells at a near atomic level of detail: the rates of diffusion of proteins are matched to known experimental values, and their thermodynamic stabilities are found to be in good agreement with the few measurements that have so far been performed in vivo. While the simulation approach is certainly not free of assumptions, it offers a potentially important complement to experimental techniques and provides a vivid illustration of molecular behavior inside a biological cell that is likely to be of significant educational value.
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Affiliation(s)
- Sean R. McGuffee
- Department of Biochemistry, University of Iowa, Iowa City, Iowa, United States of America
| | - Adrian H. Elcock
- Department of Biochemistry, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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46
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Elcock AH. Models of macromolecular crowding effects and the need for quantitative comparisons with experiment. Curr Opin Struct Biol 2010; 20:196-206. [PMID: 20167475 DOI: 10.1016/j.sbi.2010.01.008] [Citation(s) in RCA: 232] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Revised: 01/17/2010] [Accepted: 01/21/2010] [Indexed: 01/19/2023]
Abstract
In recent years significant effort has been devoted to exploring the potential effects of macromolecular crowding on protein folding and association phenomena. Theoretical calculations and molecular simulations have, in particular, been exploited to describe aspects of protein behavior in crowded and confined conditions and many aspects of the simulated behavior have reflected, at least at a qualitative level, the behavior observed in experiments. One major and immediate challenge for the theorists is to now produce models capable of making quantitatively accurate predictions of in vitro behavior. A second challenge is to derive models that explain results obtained from experiments performed in vivo, the results of which appear to call into question the assumed dominance of excluded-volume effects in vivo.
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Affiliation(s)
- Adrian H Elcock
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA.
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