1
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Du J, Yin H, Lu Y, Lu T, Chen T. Effects of Surface Tethering on the Thermodynamics and Kinetics of Frustrated Protein Folding. J Phys Chem B 2022; 126:4776-4786. [PMID: 35731862 DOI: 10.1021/acs.jpcb.2c01982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The interaction between the protein and surface plays an important role in biology and biotechnology. To understand how surface tethering influences the folding behavior of frustrated proteins, in this work, we systematically study the thermodynamics and folding kinetics of the bacterial immunity protein Im7 and Fyn SH3 domain tethered to a surface using Langevin dynamics simulations. Upon surface tethering, the stabilization often results from the entropic effect, whereas the destabilization is usually caused by either an energetic or entropic effect. For the Fyn SH3 domain with a two-state folding manner, the influence of nonnative interactions on thermodynamic stability is not significant, while nonnative interactions can weaken the effect of surface tethering on the change in the folding rate. By contrast, for the frustrated protein Im7, depending on where the protein is tethered, the surface tethering can promote or suppress misfolding by modulating specific nonnative contacts, thereby altering the folding rate and folding mechanism. Because surface tethering can change the intrachain diffusivity of unfolding, the kinetic stability cannot be well captured by the thermodynamic stability at some tether points. This study should be helpful in general to understand how surface tethering affects the folding energy landscape of frustrated proteins.
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Affiliation(s)
- Jiang Du
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, P. R. China
| | - Hongmei Yin
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, P. R. China
| | - Yanfang Lu
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, P. R. China
| | - Teng Lu
- Computer Network Information Center of the Chinese Academy of Sciences, Beijing 100083, P. R. China
| | - Tao Chen
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, P. R. China.,Key Laboratory of Polymer Processing Engineering (South China University of Technology), Ministry of Education, Guangzhou 510641, P. R. China
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2
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Ortega G, Aguilar MA, Gautam BK, Plaxco KW. The effect of charged residue substitutions on the thermodynamics of protein-surface interactions. Protein Sci 2021; 30:2408-2417. [PMID: 34719069 DOI: 10.1002/pro.4215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 01/07/2023]
Abstract
The interactions of proteins with surfaces are important in both biological processes and biotechnologies. In contrast to decades of study regarding the biophysics of proteins in bulk solution, however, our mechanistic understanding of the biophysics of proteins interacting with surfaces remains largely qualitative. In response, we have set to explore quantitatively the thermodynamics of protein-surface interactions. In this work, we explore systematically the role of electrostatics in modulating the interaction between proteins and charged surfaces. In particular, we use electrochemistry to explore the extent to which a macroscopic, hydroxyl-coated surface held at a slightly negative potential affects the folding thermodynamics of surface-attached protein variants with different composition of charged amino acids. Doing so, we find that attachment to the surface generally leads to a net stabilization, presumably due to excluded volume effects that reduce the entropy of the unfolded state. The magnitude of this stabilization, however, is strongly correlated with the charged-residue content of the protein. In particular, we find statistically significant correlations with both the net charge of the protein, with greater negative charge leading to less stabilization by the surface, and with the number of arginines, with more arginines leading to greater stabilization. Such findings refine our understanding of protein-surface interactions, providing in turn a guiding rationale to achieve the functional deposition of proteins on artificial surfaces for implementation in, for example, protein-based biotechnologies.
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Affiliation(s)
- Gabriel Ortega
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California, USA.,Center for Bioengineering, University of California Santa Barbara, Santa Barbara, California, USA.,Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance, Parque Tecnológico de Bizkaia, Derio, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Bizkaia, Spain
| | - Miguel A Aguilar
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California, USA
| | - Bishal K Gautam
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California, USA
| | - Kevin W Plaxco
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California, USA.,Center for Bioengineering, University of California Santa Barbara, Santa Barbara, California, USA
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3
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Idili A, Parolo C, Alvarez-Diduk R, Merkoçi A. Rapid and Efficient Detection of the SARS-CoV-2 Spike Protein Using an Electrochemical Aptamer-Based Sensor. ACS Sens 2021; 6:3093-3101. [PMID: 34375076 PMCID: PMC8370117 DOI: 10.1021/acssensors.1c01222] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
The
availability of sensors able to rapidly detect SARS-CoV-2 directly
in biological fluids in a single step would allow performing massive
diagnostic testing to track in real time and contain the spread of
COVID-19. Motivated by this, here, we developed an electrochemical
aptamer-based (EAB) sensor able to achieve the rapid, reagentless,
and quantitative measurement of the SARS-CoV-2 spike (S) protein.
First, we demonstrated the ability of the selected aptamer to undergo
a binding-induced conformational change in the presence of its target
using fluorescence spectroscopy. Then, we engineered the aptamer to
work as a bioreceptor in the EAB platform and we demonstrated its
sensitivity and specificity. Finally, to demonstrate the clinical
potential of the sensor, we tested it directly in biological fluids
(serum and artificial saliva), achieving the rapid (minutes) and single-step
detection of the S protein in its clinical range.
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Affiliation(s)
- Andrea Idili
- Institut Català de Nanociència i Nanotecnologia (ICN2), Campus UAB, Bellaterra 08193 Barcelona, Spain
| | - Claudio Parolo
- Institut Català de Nanociència i Nanotecnologia (ICN2), Campus UAB, Bellaterra 08193 Barcelona, Spain
- Barcelona Institute for Global Health, 08036 Barcelona, Spain
| | - Ruslán Alvarez-Diduk
- Institut Català de Nanociència i Nanotecnologia (ICN2), Campus UAB, Bellaterra 08193 Barcelona, Spain
| | - Arben Merkoçi
- Institut Català de Nanociència i Nanotecnologia (ICN2), Campus UAB, Bellaterra 08193 Barcelona, Spain
- CSIC and the Barcelona Institute of Science and Technology (BIST), 08036 Barcelona, Spain
- Institucio′ Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
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4
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Ortega G, Kurnik M, Gautam BK, Plaxco KW. Attachment of Proteins to a Hydroxyl-Terminated Surface Eliminates the Stabilizing Effects of Polyols. J Am Chem Soc 2020; 142:15349-15354. [PMID: 32786756 DOI: 10.1021/jacs.0c05719] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The physics of proteins interacting with surfaces can differ significantly from those seen when the same proteins are free in bulk solution. As an example, we describe here the extent to which site-specific attachment to a chemically well-defined macroscopic surface alters the ability of several stabilizing and destabilizing cosolutes to modulate protein folding thermodynamics. We determined this via guanidinium denaturations performed in the presence of varying concentrations of cosolutes when proteins were either site-specifically attached to self-assembled monolayers on gold or free in bulk solution. Doing this we found that the extent to which guanidinium (a destabilizing Hofmeister cation), sulfate (a stabilizing Hofmeister anion), and urea (a neutral denaturant) alter the folding free energy remains indistinguishable whether proteins are surface-attached or free in bulk solution. In sharp contrast, however, neutral osmolytes sucrose and glycerol, which significantly stabilize proteins in bulk solution, do not measurably affect their stability when they are attached to a hydroxyl-terminated surface. In contrast, we recovered bulk solution-like stabilization when the attachment surface was instead carboxyl-terminated. It thus appears that chemistry-specific surface interactions can dramatically alter the way in which biomolecules interact with other components of the system.
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Affiliation(s)
- Gabriel Ortega
- Department of Chemistry and Biochemistry, University of California-Santa Barbara, Santa Barbara, California 93106, United States.,Center for Bioengineering, University of California-Santa Barbara, Santa Barbara, California 93106, United States
| | - Martin Kurnik
- Department of Chemistry and Biochemistry, University of California-Santa Barbara, Santa Barbara, California 93106, United States.,Center for Bioengineering, University of California-Santa Barbara, Santa Barbara, California 93106, United States
| | - Bishal K Gautam
- Department of Chemistry and Biochemistry, University of California-Santa Barbara, Santa Barbara, California 93106, United States
| | - Kevin W Plaxco
- Department of Chemistry and Biochemistry, University of California-Santa Barbara, Santa Barbara, California 93106, United States.,Center for Bioengineering, University of California-Santa Barbara, Santa Barbara, California 93106, United States
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5
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Sanchez-Guzman D, Giraudon-Colas G, Marichal L, Boulard Y, Wien F, Degrouard J, Baeza-Squiban A, Pin S, Renault JP, Devineau S. In Situ Analysis of Weakly Bound Proteins Reveals Molecular Basis of Soft Corona Formation. ACS NANO 2020; 14:9073-9088. [PMID: 32633939 DOI: 10.1021/acsnano.0c04165] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Few experimental techniques allow the analysis of the protein corona in situ. As a result, little is known on the effects of nanoparticles on weakly bound proteins that form the soft corona. Despite its biological importance, our understanding of the molecular bases driving its formation is limited. Here, we show that hemoglobin can form either a hard or a soft corona on silica nanoparticles depending on the pH conditions. Using cryoTEM and synchrotron-radiation circular dichroism, we show that nanoparticles alter the structure and the stability of weakly bound proteins in situ. Molecular dynamics simulation identified the structural elements driving protein-nanoparticle interaction. Based on thermodynamic analysis, we show that nanoparticles stabilize partially unfolded protein conformations by enthalpy-driven molecular interactions. We suggest that nanoparticles alter weakly bound proteins by shifting the equilibrium toward the unfolded states at physiological temperature. We show that the classical approach based on nanoparticle separation from the biological medium fails to detect destabilization of weakly bound proteins, and therefore cannot be used to fully predict the biological effects of nanomaterials in situ.
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Affiliation(s)
| | | | - Laurent Marichal
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, 91405 Orsay Cedex, France
| | - Yves Boulard
- Université Paris-Saclay, CEA, CNRS, I2BC, B3S, Gif-sur-Yvette 91190, France
| | - Frank Wien
- Synchrotron SOLEIL, 91192 Gif-sur-Yvette, France
| | - Jéril Degrouard
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, 91405 Orsay Cedex, France
| | | | - Serge Pin
- Université Paris-Saclay, CEA, CNRS, NIMBE, Gif-sur-Yvette 91190, France
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6
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Curtis SD, Ploense KL, Kurnik M, Ortega G, Parolo C, Kippin TE, Plaxco KW, Arroyo-Currás N. Open Source Software for the Real-Time Control, Processing, and Visualization of High-Volume Electrochemical Data. Anal Chem 2019; 91:12321-12328. [PMID: 31462040 PMCID: PMC7336365 DOI: 10.1021/acs.analchem.9b02553] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
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Electrochemical sensors
are major players in the race for improved
molecular diagnostics due to their convenience, temporal resolution,
manufacturing scalability, and their ability to support real-time
measurements. This is evident in the ever-increasing number of health-related
electrochemical sensing platforms, ranging from single-measurement
point-of-care devices to wearable devices supporting immediate and
continuous monitoring. In support of the need for such systems to
rapidly process large data volumes, we describe here an open-source,
easily customizable, multiplatform compatible program for the real-time
control, processing, and visualization of electrochemical data. The
software’s architecture is modular and fully documented, allowing
the easy customization of the code to support the processing of voltammetric
(e.g., square-wave and cyclic) and chronoamperometric data. The program,
which we have called Software for the Analysis and Continuous Monitoring of Electrochemical Systems (SACMES), also includes a graphical interface
allowing the user to easily change analysis parameters (e.g., signal/noise
processing, baseline correction) in real-time. To demonstrate the
versatility of SACMES we use it here to analyze the real-time data
output by (1) the electrochemical, aptamer-based measurement of a
specific small-molecule target, (2) a monoclonal antibody-detecting
DNA-scaffold sensor, and (3) the determination of the folding thermodynamics
of an electrode-attached, redox-reporter-modified protein.
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Affiliation(s)
- Samuel D Curtis
- Center for Bioengineering , University of California Santa Barbara , Santa Barbara , California 93106 , United States.,Department of Pharmacology and Molecular Sciences , Johns Hopkins School of Medicine , Baltimore , Maryland 21205 , United States
| | - Kyle L Ploense
- Center for Bioengineering , University of California Santa Barbara , Santa Barbara , California 93106 , United States
| | - Martin Kurnik
- Center for Bioengineering , University of California Santa Barbara , Santa Barbara , California 93106 , United States.,Department of Chemistry and Biochemistry , University of California Santa Barbara , Santa Barbara , California 93106 , United States
| | - Gabriel Ortega
- Center for Bioengineering , University of California Santa Barbara , Santa Barbara , California 93106 , United States.,Department of Chemistry and Biochemistry , University of California Santa Barbara , Santa Barbara , California 93106 , United States
| | - Claudio Parolo
- Center for Bioengineering , University of California Santa Barbara , Santa Barbara , California 93106 , United States.,Department of Chemistry and Biochemistry , University of California Santa Barbara , Santa Barbara , California 93106 , United States
| | - Tod E Kippin
- Department of Psychological and Brain Sciences , University of California Santa Barbara , Santa Barbara , California 93106 , United States.,Neuroscience Research Institute , University of California Santa Barbara , Santa Barbara , California 93106 , United States.,Department of Molecular Cellular and Developmental Biology , University of California Santa Barbara , Santa Barbara , California 93106 , United States
| | - Kevin W Plaxco
- Center for Bioengineering , University of California Santa Barbara , Santa Barbara , California 93106 , United States.,Department of Chemistry and Biochemistry , University of California Santa Barbara , Santa Barbara , California 93106 , United States
| | - Netzahualcóyotl Arroyo-Currás
- Department of Pharmacology and Molecular Sciences , Johns Hopkins School of Medicine , Baltimore , Maryland 21205 , United States
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