1
|
Hong YK, Nakamoto M, Matsusaki M. Engineering metabolic cycle-inspired hydrogels with enzyme-fueled programmable transient volume changes. J Mater Chem B 2023; 11:8136-8141. [PMID: 37565488 DOI: 10.1039/d3tb00638g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
An enzyme-fueled transient volume phase transition (TVPT) of hydrogels under out-of-equilibrium conditions is reported. The approach takes inspiration from the metabolic cycle, comprising nutrient intake and anabolism/catabolism followed by waste excretion. The incorporation of methacrylic acid and acrylated trypsin in a polymeric hydrogel allowed the TVPT of the gel to be fueled by lysozyme. With the intake of lysozyme as fuel, the construction/destruction of electrostatic cross-linkages induced transient shrinkage/swelling of the gel accompanied by the depletion of lysozyme activity. The system's transient response could be flexibly programmed by adjusting not only the fuel concentration but the chemical composition of materials. The lysozyme-fueled TVPT of the gel could be exploited to transient changes in the mechanical properties of the gel. Our work opens a route toward a new class of stimuli-responsive hydrogels for biomedical applications.
Collapse
Affiliation(s)
- Young Kyoung Hong
- School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Masahiko Nakamoto
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan.
| | - Michiya Matsusaki
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan.
| |
Collapse
|
2
|
Yang B, Li S, Mu W, Wang Z, Han X. Light-Harvesting Artificial Cells Containing Cyanobacteria for CO 2 Fixation and Further Metabolism Mimicking. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2201305. [PMID: 35905491 DOI: 10.1002/smll.202201305] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/29/2022] [Indexed: 06/15/2023]
Abstract
The bottom-up constructed artificial cells help to understand the cell working mechanism and provide the evolution clues for organisms. The energy supply and metabolism mimicry are the key issues in the field of artificial cells. Herein, an artificial cell containing cyanobacteria capable of light harvesting and carbon dioxide fixation is demonstrated to produce glucose molecules by converting light energy into chemical energy. Two downstream "metabolic" pathways starting from glucose molecules are investigated. One involves enzyme cascade reaction to produce H2 O2 (assisted by glucose oxidase) first, followed by converting Amplex red to resorufin (assisted by horseradish peroxidase). The other pathway is more biologically relevant. Glucose molecules are dehydrogenated to transfer hydrogens to nicotinamide adenine dinucleotide (NAD+ ) for the production of nicotinamide adenine dinucleotide hydride (NADH) molecules in the presence of glucose dehydrogenase. Further, NADH molecules are oxidized into NAD+ by pyruvate catalyzed by lactate dehydrogenase, meanwhile, lactate is obtained. Therefore, the cascade cycling of NADH/NAD+ is built. The artificial cells built here pave the way for investigating more complicated energy-supplied metabolism inside artificial cells.
Collapse
Affiliation(s)
- Boyu Yang
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin, 150001, China
| | - Shubin Li
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin, 150001, China
| | - Wei Mu
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin, 150001, China
| | - Zhao Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin, 150001, China
| | - Xiaojun Han
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin, 150001, China
| |
Collapse
|
3
|
Cao Y, Gabrielli L, Frezzato D, Prins LJ. Persistent ATP-Concentration Gradients in a Hydrogel Sustained by Chemical Fuel Consumption. Angew Chem Int Ed Engl 2023; 62:e202215421. [PMID: 36420591 DOI: 10.1002/anie.202215421] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/19/2022] [Accepted: 11/23/2022] [Indexed: 11/25/2022]
Abstract
We show the formation of macroscopic ATP-concentrations in an agarose gel and demonstrate that these gradients can be sustained in time at the expense of the consumption of a chemical fuel. The approach relies on the spatially controlled activation of ATP-producing and ATP-consuming reactions through the local injection of enzymes in the matrix. The reaction-diffusion system is maintained in a stationary non-equilibrium state as long as chemical fuel, phosphocreatine, is present. The reaction-diffusion system is coupled to a supramolecular system composed of monolayer protected gold nanoparticles and a fluorescent probe. As a result of this coupling, fluorescence signals emerge spontaneously in response to the ATP-concentration gradients. We show that the approach permits the rational formation of complex fluorescence patterns that change over time as a function of the evolution of the ATP-concentrations present in the system.
Collapse
Affiliation(s)
- Yingjuan Cao
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Luca Gabrielli
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Diego Frezzato
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Leonard J Prins
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131, Padova, Italy
| |
Collapse
|
4
|
Hu R, Ding X, Yu P, He X, Watts A, Zhao X, Wang J. Ultrafast Two-Dimensional Infrared Spectroscopy Resolved a Structured Lysine 159 on the Cytoplasmic Surface of the Microbial Photoreceptor Bacteriorhodopsin. J Am Chem Soc 2022; 144:22083-22092. [PMID: 36399663 DOI: 10.1021/jacs.2c09435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Bacteriorhodopsin (bR) is a light-driven microbial receptor, and lysine 159 (K159) is a charged residue on the cytoplasmic (CP) side of its E-F loop. However, its conformation and function remain unknown due to fast surface dynamics. By utilizing a 13C, 15N-labeled lysine (K) as an isotope probe, we created a network of site-specific amide-I vibrational signatures (backbone carbonyl stretch) to identify the frequency contribution of the labeled residues to the amide-I excitonic band structure. Thus, the red-shifted amide-I frequency in the 13C, 15N-lysine-labeled bR (uK-bR) to the unlabeled bR (WT-bR) could be differentiated and examined by ultrafast two-dimensional vibrational echo infrared (2D IR) spectroscopy. Our results showed that the backbone carbonyl of K159 is located at a high frequency of ca. 1693 cm-1 and has a vibrational excited-state relaxation time shorter than the bulk helical amide-I mode at the same frequency, suggesting that K159 may possess a hydrogen-bonded γ-turn structure with E161, one of the carboxylate residues on the CP surface of bR. The 2D solid-state NMR study of uK-bR also revealed conformational dependent lysine residues, from which K159 was found to involve the turn motif. This γ-turn structure maintained by K159 may help to stabilize the E-F loop and support E161 in attracting protons from the bulk during the late stage of the bR photocycle. The combined spectroscopic approach illustrated in this work may be applied to map residue-specific local structures and dynamics of other receptors and large proteins.
Collapse
Affiliation(s)
- Rong Hu
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Xiaoyan Ding
- Department of Physics, School of Physics and Electronic Science, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai 200241, P.R. China.,Department of Biochemistry, University of Oxford, South Park Road, Oxford OX1 3QU, U.K
| | - Pengyun Yu
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Xuemei He
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Anthony Watts
- Department of Biochemistry, University of Oxford, South Park Road, Oxford OX1 3QU, U.K
| | - Xin Zhao
- Department of Physics, School of Physics and Electronic Science, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai 200241, P.R. China
| | - Jianping Wang
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| |
Collapse
|
5
|
Del Grosso E, Irmisch P, Gentile S, Prins LJ, Seidel R, Ricci F. Dissipative Control over the Toehold-Mediated DNA Strand Displacement Reaction. Angew Chem Int Ed Engl 2022; 61:e202201929. [PMID: 35315568 PMCID: PMC9324813 DOI: 10.1002/anie.202201929] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Indexed: 12/31/2022]
Abstract
Here we show a general approach to achieve dissipative control over toehold‐mediated strand‐displacement, the most widely employed reaction in the field of DNA nanotechnology. The approach relies on rationally re‐engineering the classic strand displacement reaction such that the high‐energy invader strand (fuel) is converted into a low‐energy waste product through an energy‐dissipating reaction allowing the spontaneous return to the original state over time. We show that such dissipative control over the toehold‐mediated strand displacement process is reversible (up to 10 cycles), highly controllable and enables unique temporal activation of DNA systems. We show here two possible applications of this strategy: the transient labelling of DNA structures and the additional temporal control of cascade reactions.
Collapse
Affiliation(s)
- Erica Del Grosso
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Patrick Irmisch
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103, Leipzig, Germany
| | - Serena Gentile
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Leonard J Prins
- Department of Chemical fSciences, University of Padua, Via Marzolo 1, 35131, Padua, Italy
| | - Ralf Seidel
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103, Leipzig, Germany
| | - Francesco Ricci
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| |
Collapse
|
6
|
Del Grosso E, Irmisch P, Gentile S, Prins LJ, Seidel R, Ricci F. Dissipative Control over the Toehold‐Mediated DNA Strand Displacement Reaction. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Erica Del Grosso
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Patrick Irmisch
- Molecular Biophysics Group Peter Debye Institute for Soft Matter Physics Universität Leipzig 04103 Leipzig Germany
| | - Serena Gentile
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Leonard J. Prins
- Department of Chemical fSciences University of Padua Via Marzolo 1 35131 Padua Italy
| | - Ralf Seidel
- Molecular Biophysics Group Peter Debye Institute for Soft Matter Physics Universität Leipzig 04103 Leipzig Germany
| | - Francesco Ricci
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| |
Collapse
|
7
|
Nie X, Hu Z, Xiao T, Li L, Jin J, Liu K, Liu Z. Light-Powered Ion Pumping in a Cation-Selective Conducting Polymer Membrane. Angew Chem Int Ed Engl 2022; 61:e202201138. [PMID: 35133687 DOI: 10.1002/anie.202201138] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Indexed: 11/09/2022]
Abstract
The simulation of the ion pumping against a proton gradient energized by light in photosynthesis is of significant importance for the energy conversion in a non-biological environment. Herein, we report light-powered ion pumping in a polystyrene sulfonate anion (PSS) doped polypyrrole (PPy) conducting polymer membrane (PSS-PPy) with a symmetric geometry. This PSS-PPy conducting polymer membrane exhibits a cationic selectivity and a light-responsive surface-charge-governed ion transport attributed to the negatively charged PSS groups. An asymmetric visible irradiation on one side of the PSS-PPy membrane induces a built-in electric field across the membrane due to the intrinsic photoelectronic property of PPy, which drives the cationic transport against the concentration gradient, demonstrating an ion-pumping effect. This work is a prototype that uses a geometry-symmetric conducting polymer membrane as a light-powered artificial ion pump for active ion transport, which exhibits potential applications in nanofluidic energy conversion.
Collapse
Affiliation(s)
- Xiaoyan Nie
- School of Chemistry, Beihang University, Beijing, 100191, P. R. China
| | - Ziying Hu
- Querrey Simpson Institute for Bioelectronics, Northwestern University, Evanston, IL 60208, USA
| | - Tianliang Xiao
- School of Energy and Power Engineering, Beihang University, Beijing, 100191, P. R. China
| | - Li Li
- School of Chemistry, Beihang University, Beijing, 100191, P. R. China
| | - Jiao Jin
- School of Chemistry, Beihang University, Beijing, 100191, P. R. China
| | - Kesong Liu
- School of Chemistry, Beihang University, Beijing, 100191, P. R. China
| | - Zhaoyue Liu
- School of Chemistry, Beihang University, Beijing, 100191, P. R. China
| |
Collapse
|
8
|
Nie X, Hu Z, Xiao T, Li L, Jin J, Liu K, Liu Z. Light‐Powered Ion Pumping in a Cation‐Selective Conducting Polymer Membrane. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Xiaoyan Nie
- School of Chemistry Beihang University Beijing 100191 P. R. China
| | - Ziying Hu
- Querrey Simpson Institute for Bioelectronics Northwestern University Evanston IL 60208 USA
| | - Tianliang Xiao
- School of Energy and Power Engineering Beihang University Beijing 100191 P. R. China
| | - Li Li
- School of Chemistry Beihang University Beijing 100191 P. R. China
| | - Jiao Jin
- School of Chemistry Beihang University Beijing 100191 P. R. China
| | - Kesong Liu
- School of Chemistry Beihang University Beijing 100191 P. R. China
| | - Zhaoyue Liu
- School of Chemistry Beihang University Beijing 100191 P. R. China
| |
Collapse
|
9
|
Chen R, Das K, Cardona MA, Gabrielli L, Prins LJ. Progressive Local Accumulation of Self-Assembled Nanoreactors in a Hydrogel Matrix through Repetitive Injections of ATP. J Am Chem Soc 2022; 144:2010-2018. [PMID: 35061942 PMCID: PMC8815075 DOI: 10.1021/jacs.1c13504] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Cellular functions
are regulated with high spatial control through
the local activation of chemical processes in a complex inhomogeneous
matrix. The development of synthetic macroscopic systems with a similar
capacity allows fundamental studies aimed at understanding the relationship
between local molecular events and the emergence of functional properties
at the macroscopic level. Here, we show that a kinetically stable
inhomogeneous hydrogel matrix is spontaneously formed upon the local
injection of ATP. Locally, ATP templates the self-assembly of amphiphiles
into large nanoreactors with a much lower diffusion rate compared
to unassembled amphiphiles. The local depletion of unassembled amphiphiles
near the injection point installs a concentration gradient along which
unassembled amphiphiles diffuse from the surroundings to the center.
This allows for a progressive local accumulation of self-assembled
nanoreactors in the matrix upon repetitive cycles of ATP injection
separated by time intervals during which diffusion of unassembled
amphiphiles takes place. Contrary to the homogeneous matrix containing
the same components, in the inhomogeneous matrix the local upregulation
of a chemical reaction occurs. Depending on the way the same amount
of injected ATP is administered to the hydrogel matrix different macroscopic
distributions of nanoreactors are obtained, which affect the location
in the matrix where the chemical reaction is upregulated.
Collapse
Affiliation(s)
- Rui Chen
- Department of Chemical Sciences, University of Padova, Padova, 35131, Italy
| | - Krishnendu Das
- Department of Chemical Sciences, University of Padova, Padova, 35131, Italy
| | - Maria A. Cardona
- Department of Chemical Sciences, University of Padova, Padova, 35131, Italy
| | - Luca Gabrielli
- Department of Chemical Sciences, University of Padova, Padova, 35131, Italy
| | - Leonard J. Prins
- Department of Chemical Sciences, University of Padova, Padova, 35131, Italy
| |
Collapse
|
10
|
Dhamija A, Das CK, Ko YH, Kim Y, Mukhopadhyay RD, Gunnam A, Yu X, Hwang IC, Schäfer LV, Kim K. Remotely controllable supramolecular rotor mounted inside a porphyrinic cage. Chem 2022. [DOI: 10.1016/j.chempr.2021.12.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
|
11
|
Gentile S, Del Grosso E, Pungchai PE, Franco E, Prins LJ, Ricci F. Spontaneous Reorganization of DNA-Based Polymers in Higher Ordered Structures Fueled by RNA. J Am Chem Soc 2021; 143:20296-20301. [PMID: 34843256 PMCID: PMC8662731 DOI: 10.1021/jacs.1c09503] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
We demonstrate a strategy that allows
for the spontaneous reconfiguration
of self-assembled DNA polymers exploiting RNA as chemical fuel. To
do this, we have rationally designed orthogonally addressable DNA
building blocks that can be transiently deactivated by RNA fuels and
subtracted temporarily from participation in the self-assembly process.
Through a fine modulation of the rate at which the building blocks
are reactivated we can carefully control the final composition of
the polymer and convert a disordered polymer in a higher order polymer,
which is disfavored from a thermodynamic point of view. We measure
the dynamic reconfiguration via fluorescent signals and confocal microscopy,
and we derive a kinetic model that captures the experimental results.
Our approach suggests a novel route toward the development of biomolecular
materials in which engineered chemical reactions support the autonomous
spatial reorganization of multiple components.
Collapse
Affiliation(s)
- Serena Gentile
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Erica Del Grosso
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Passa E Pungchai
- Department of Bioengineering, University of California at Los Angeles, 410 Westwood Plaza, Los Angeles, California 90095, United States
| | - Elisa Franco
- Department of Mechanical and Aerospace Engineering and of Bioengineering, University of California at Los Angeles, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Leonard J Prins
- Department of Chemical Sciences, University of Padua, Via Marzolo 1, 35131 Padua, Italy
| | - Francesco Ricci
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| |
Collapse
|
12
|
Das K, Gabrielli L, Prins LJ. Chemically Fueled Self-Assembly in Biology and Chemistry. Angew Chem Int Ed Engl 2021; 60:20120-20143. [PMID: 33704885 PMCID: PMC8453758 DOI: 10.1002/anie.202100274] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/12/2021] [Indexed: 12/23/2022]
Abstract
Life is a non-equilibrium state of matter maintained at the expense of energy. Nature uses predominantly chemical energy stored in thermodynamically activated, but kinetically stable, molecules. These high-energy molecules are exploited for the synthesis of other biomolecules, for the activation of biological machinery such as pumps and motors, and for the maintenance of structural order. Knowledge of how chemical energy is transferred to biochemical processes is essential for the development of artificial systems with life-like processes. Here, we discuss how chemical energy can be used to control the structural organization of organic molecules. Four different strategies have been identified according to a distinguishable physical-organic basis. For each class, one example from biology and one from chemistry are discussed in detail to illustrate the practical implementation of each concept and the distinct opportunities they offer. Specific attention is paid to the discussion of chemically fueled non-equilibrium self-assembly. We discuss the meaning of non-equilibrium self-assembly, its kinetic origin, and strategies to develop synthetic non-equilibrium systems.
Collapse
Affiliation(s)
- Krishnendu Das
- Department of Chemical Sciences|University of PadovaVia Marzolo 135131PadovaItaly
| | - Luca Gabrielli
- Department of Chemical Sciences|University of PadovaVia Marzolo 135131PadovaItaly
| | - Leonard J. Prins
- Department of Chemical Sciences|University of PadovaVia Marzolo 135131PadovaItaly
| |
Collapse
|
13
|
Das K, Gabrielli L, Prins LJ. Chemically Fueled Self‐Assembly in Biology and Chemistry. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100274] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Krishnendu Das
- Department of Chemical Sciences
- University of Padova Via Marzolo 1 35131 Padova Italy
| | - Luca Gabrielli
- Department of Chemical Sciences
- University of Padova Via Marzolo 1 35131 Padova Italy
| | - Leonard J. Prins
- Department of Chemical Sciences
- University of Padova Via Marzolo 1 35131 Padova Italy
| |
Collapse
|
14
|
Wallnöfer EA, Thurner GC, Kremser C, Talasz H, Stollenwerk MM, Helbok A, Klammsteiner N, Albrecht-Schgoer K, Dietrich H, Jaschke W, Debbage P. Albumin-based nanoparticles as contrast medium for MRI: vascular imaging, tissue and cell interactions, and pharmacokinetics of second-generation nanoparticles. Histochem Cell Biol 2020; 155:19-73. [PMID: 33040183 DOI: 10.1007/s00418-020-01919-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2020] [Indexed: 12/14/2022]
Abstract
This multidisciplinary study examined the pharmacokinetics of nanoparticles based on albumin-DTPA-gadolinium chelates, testing the hypothesis that these nanoparticles create a stronger vessel signal than conventional gadolinium-based contrast agents and exploring if they are safe for clinical use. Nanoparticles based on human serum albumin, bearing gadolinium and designed for use in magnetic resonance imaging, were used to generate magnet resonance images (MRI) of the vascular system in rats ("blood pool imaging"). At the low nanoparticle doses used for radionuclide imaging, nanoparticle-associated metals were cleared from the blood into the liver during the first 4 h after nanoparticle application. At the higher doses required for MRI, the liver became saturated and kidney and spleen acted as additional sinks for the metals, and accounted for most processing of the nanoparticles. The multiple components of the nanoparticles were cleared independently of one another. Albumin was detected in liver, spleen, and kidneys for up to 2 days after intravenous injection. Gadolinium was retained in the liver, kidneys, and spleen in significant concentrations for much longer. Gadolinium was present as significant fractions of initial dose for longer than 2 weeks after application, and gadolinium clearance was only complete after 6 weeks. Our analysis could not account quantitatively for the full dose of gadolinium that was applied, but numerous organs were found to contain gadolinium in the collagen of their connective tissues. Multiple lines of evidence indicated intracellular processing opening the DTPA chelates and leading to gadolinium long-term storage, in particular inside lysosomes. Turnover of the stored gadolinium was found to occur in soluble form in the kidneys, the liver, and the colon for up to 3 weeks after application. Gadolinium overload poses a significant hazard due to the high toxicity of free gadolinium ions. We discuss the relevance of our findings to gadolinium-deposition diseases.
Collapse
Affiliation(s)
- E A Wallnöfer
- Department of Radiology, Medical University of Innsbruck, Anichstrasse 35, 6020, Innsbruck, Austria
| | - G C Thurner
- Department of Radiology, Medical University of Innsbruck, Anichstrasse 35, 6020, Innsbruck, Austria
- Division of Histology and Embryology, Department of Anatomy, Histology and Embryology, Medical University of Innsbruck, Müllerstrasse 59, 6020, Innsbruck, Austria
| | - C Kremser
- Department of Radiology, Medical University of Innsbruck, Anichstrasse 35, 6020, Innsbruck, Austria
| | - H Talasz
- Division of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - M M Stollenwerk
- Faculty of Health and Society, Biomedical Laboratory Science, University Hospital MAS, Malmö University, 205 06, Malmö, Sweden
- Division of Histology and Embryology, Department of Anatomy, Histology and Embryology, Medical University of Innsbruck, Müllerstrasse 59, 6020, Innsbruck, Austria
| | - A Helbok
- Department of Nuclear Medicine, Innsbruck Medical University, Anichstrasse 35, 6020, Innsbruck, Austria
| | - N Klammsteiner
- Division of Histology and Embryology, Department of Anatomy, Histology and Embryology, Medical University of Innsbruck, Müllerstrasse 59, 6020, Innsbruck, Austria
| | - K Albrecht-Schgoer
- Department of Pharmaceutical Technology, Institute of Pharmacy, Leopold-Franzens-University Innsbruck, Innrain 80-82/IV, 6020, Innsbruck, Austria
- Institute of Cell Genetics, Department for Pharmacology and Genetics, Medical University of Innsbruck, Peter-Mayr-Strasse 1a, 6020, Innsbruck, Austria
| | - H Dietrich
- Central Laboratory Animal Facilities, Innsbruck Medical University, Peter-Mayr-Strasse 4a, 6020, Innsbruck, Austria
| | - W Jaschke
- Department of Radiology, Medical University of Innsbruck, Anichstrasse 35, 6020, Innsbruck, Austria
| | - P Debbage
- Division of Histology and Embryology, Department of Anatomy, Histology and Embryology, Medical University of Innsbruck, Müllerstrasse 59, 6020, Innsbruck, Austria.
| |
Collapse
|
15
|
Ding X, Sun C, Cui H, Chen S, Gao Y, Yang Y, Wang J, He X, Iuga D, Tian F, Watts A, Zhao X. Functional roles of tyrosine 185 during the bacteriorhodopsin photocycle as revealed by in situ spectroscopic studies. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:1006-1014. [PMID: 29800547 DOI: 10.1016/j.bbabio.2018.05.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 04/15/2018] [Accepted: 05/20/2018] [Indexed: 01/22/2023]
Abstract
Tyrosine 185 (Y185), one of the aromatic residues within the retinal (Ret) chromophore binding pocket in helix F of bacteriorhodopsin (bR), is highly conserved among the microbial rhodopsin family proteins. Many studies have investigated the functions of Y185, but its underlying mechanism during the bR photocycle remains unclear. To address this research gap, in situ two-dimensional (2D) magic-angle spinning (MAS) solid-state NMR (ssNMR) of specifically labelled bR, combined with light-induced transient absorption change measurements, dynamic light scattering (DLS) measurements, titration analysis and site-directed mutagenesis, was used to elucidate the functional roles of Y185 during the bR photocycle in the native membrane environment. Different interaction modes were identified between Y185 and the Ret chromophore in the dark-adapted (inactive) state and M (active) state, indicating that Y185 may serve as a rotamer switch maintaining the protein dynamics, and plays an important role in the efficient proton-pumping mechanism in the bR purple membrane.
Collapse
Affiliation(s)
- Xiaoyan Ding
- Shanghai Key Laboratory of Magnetic Resonance, School of Physics and Materials Science, East China Normal University, Shanghai 200062, PR China; Department of Biochemistry and Molecular Biology, Penn State College of Medicine, PA 17033-0850, USA
| | - Chao Sun
- Shanghai Key Laboratory of Magnetic Resonance, School of Physics and Materials Science, East China Normal University, Shanghai 200062, PR China
| | - Haolin Cui
- Shanghai Key Laboratory of Magnetic Resonance, School of Physics and Materials Science, East China Normal University, Shanghai 200062, PR China
| | - Sijin Chen
- Shanghai Key Laboratory of Magnetic Resonance, School of Physics and Materials Science, East China Normal University, Shanghai 200062, PR China
| | - Yujiao Gao
- Shanghai Key Laboratory of Magnetic Resonance, School of Physics and Materials Science, East China Normal University, Shanghai 200062, PR China
| | - Yanan Yang
- Shanghai Key Laboratory of Magnetic Resonance, School of Physics and Materials Science, East China Normal University, Shanghai 200062, PR China
| | - Juan Wang
- Shanghai Key Laboratory of Magnetic Resonance, School of Physics and Materials Science, East China Normal University, Shanghai 200062, PR China
| | - Xiao He
- Shang Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, PR China
| | - Dinu Iuga
- The UK 850 MHz Solid-State NMR Facility, Department of Physics, University of Warwick, Coventry CV4 7AL, UK
| | - Fang Tian
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, PA 17033-0850, USA.
| | - Anthony Watts
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| | - Xin Zhao
- Shanghai Key Laboratory of Magnetic Resonance, School of Physics and Materials Science, East China Normal University, Shanghai 200062, PR China.
| |
Collapse
|
16
|
pH-sensitive vibrational probe reveals a cytoplasmic protonated cluster in bacteriorhodopsin. Proc Natl Acad Sci U S A 2017; 114:E10909-E10918. [PMID: 29203649 DOI: 10.1073/pnas.1707993114] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Infrared spectroscopy has been used in the past to probe the dynamics of internal proton transfer reactions taking place during the functional mechanism of proteins but has remained mostly silent to protonation changes in the aqueous medium. Here, by selectively monitoring vibrational changes of buffer molecules with a temporal resolution of 6 µs, we have traced proton release and uptake events in the light-driven proton-pump bacteriorhodopsin and correlate these to other molecular processes within the protein. We demonstrate that two distinct chemical entities contribute to the temporal evolution and spectral shape of the continuum band, an unusually broad band extending from 2,300 to well below 1,700 cm-1 The first contribution corresponds to deprotonation of the proton release complex (PRC), a complex in the extracellular domain of bacteriorhodopsin where an excess proton is shared by a cluster of internal water molecules and/or ionic E194/E204 carboxylic groups. We assign the second component of the continuum band to the proton uptake complex, a cluster with an excess proton reminiscent to the PRC but located in the cytoplasmic domain and possibly stabilized by D38. Our findings refine the current interpretation of the continuum band and call for a reevaluation of the last proton transfer steps in bacteriorhodopsin.
Collapse
|
17
|
Garni M, Thamboo S, Schoenenberger CA, Palivan CG. Biopores/membrane proteins in synthetic polymer membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1859:619-638. [PMID: 27984019 DOI: 10.1016/j.bbamem.2016.10.015] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/20/2016] [Accepted: 10/25/2016] [Indexed: 12/14/2022]
Abstract
BACKGROUND Mimicking cell membranes by simple models based on the reconstitution of membrane proteins in lipid bilayers represents a straightforward approach to understand biological function of these proteins. This biomimetic strategy has been extended to synthetic membranes that have advantages in terms of chemical and mechanical stability, thus providing more robust hybrid membranes. SCOPE OF THE REVIEW We present here how membrane proteins and biopores have been inserted both in the membrane of nanosized and microsized compartments, and in planar membranes under various conditions. Such bio-hybrid membranes have new properties (as for example, permeability to ions/molecules), and functionality depending on the specificity of the inserted biomolecules. Interestingly, membrane proteins can be functionally inserted in synthetic membranes provided these have appropriate properties to overcome the high hydrophobic mismatch between the size of the biomolecule and the membrane thickness. MAJOR CONCLUSION Functional insertion of membrane proteins and biopores in synthetic membranes of compartments or in planar membranes is possible by an appropriate selection of the amphiphilic copolymers, and conditions of the self-assembly process. These hybrid membranes have new properties and functionality based on the specificity of the biomolecules and the nature of the synthetic membranes. GENERAL SIGNIFICANCE Bio-hybrid membranes represent new solutions for the development of nanoreactors, artificial organelles or active surfaces/membranes that, by further gaining in complexity and functionality, will promote translational applications. This article is part of a Special Issue entitled: Lipid order/lipid defects and lipid-control of protein activity edited by Dirk Schneider.
Collapse
Affiliation(s)
- Martina Garni
- Chemistry Department, University of Basel, Klingelbergstrasse 80, Switzerland
| | - Sagana Thamboo
- Chemistry Department, University of Basel, Klingelbergstrasse 80, Switzerland
| | | | - Cornelia G Palivan
- Chemistry Department, University of Basel, Klingelbergstrasse 80, Switzerland.
| |
Collapse
|
18
|
High production of bacteriorhodopsin from wild type Halobacterium salinarum. Extremophiles 2015; 19:1021-8. [DOI: 10.1007/s00792-015-0778-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 07/23/2015] [Indexed: 11/26/2022]
|
19
|
Wei C, Pohorille A. M2 proton channel: toward a model of a primitive proton pump. ORIGINS LIFE EVOL B 2015; 45:241-8. [PMID: 25777465 DOI: 10.1007/s11084-015-9421-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 11/06/2014] [Indexed: 01/23/2023]
Abstract
Transmembrane proton transfer was essential to early cellular systems in order to transduce energy for metabolic functions. The reliable, efficient and controlled generation of proton gradients became possible only with the emergence of active proton pumps. On the basis of features shared by most modern proton pumps we identify the essential mechanistic steps in active proton transport. Further, we discuss the mechanism of action of a small, transmembrane M2 proton channel from influenza A virus as a model for proton transport in protocells. The M2 channel is a 94-residue long, α-helical tetramer that is activated at low pH and exhibits high selectivity and directionality. A shorter construct, built of transmembrane fragments that are only 24 amino acids in length, exhibits very similar proton transport properties. Molecular dynamics simulations on the microsecond time-scale carried out for the M2 channel provided atomic level details on the activation of the channel in response to protonation of the histidine residue, His37. The pathway of proton conduction is mediated by His37, which accepts and donates protons at different interconverting conformation states when pH is lower than 6.5. The Val27 and Trp41 gates and the salt bridge between Asp44 and Arg45 further enhance the directionality of proton transport. It is argued that the architecture and the mechanism of action similar to that found in the M2 channel might have been the perfect starting point for evolution towards the earliest proton pumps, indicating that active proton transport could have readily emerged from simple, passive proton channels.
Collapse
Affiliation(s)
- Chenyu Wei
- NASA Ames Research Center, Mail Stop 239-4, Moffett Field, CA, 94035, USA
| | | |
Collapse
|
20
|
A Wilson M, Wei C, Pohorille A. Towards co-evolution of membrane proteins and metabolism. ORIGINS LIFE EVOL B 2014; 44:357-61. [PMID: 25614291 DOI: 10.1007/s11084-014-9393-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 10/31/2014] [Indexed: 11/25/2022]
Abstract
Primordial metabolism co-evolved with the earliest membrane peptides to produce more environmentally fit progeny. Here, we map a continuous, evolutionary path that connects nascent biochemistry with simple, membrane-bound oligopeptides, ion channels and, further, membrane proteins capable of energy transduction and utilization of energy for active transport.
Collapse
Affiliation(s)
- Michael A Wilson
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | | | | |
Collapse
|
21
|
Hara KY, Suzuki R, Suzuki T, Yoshida M, Kino K. ATP photosynthetic vesicles for light-driven bioprocesses. Biotechnol Lett 2011; 33:1133-8. [PMID: 21287230 DOI: 10.1007/s10529-011-0544-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Accepted: 01/21/2011] [Indexed: 10/18/2022]
Abstract
We prepared ATP photosynthetic vesicles from inside-out membranes of Escherichia coli cells that express delta-rhodopsin (a novel light-driven H(+) transporter) and TF(0)F(1)-ATP synthase (a thermo-stable ATP synthase). These vesicles showed light-dependent ATP synthesis. Furthermore, coupling the ATP photosynthetic vesicles with an ATP-hydrolyzing hexokinase enabled light-dependent glucose consumption. The ATP photosynthetic vesicles indicate their potential to applied to light-driven ATP-regenerating bioprocess for various ATP-hydrolyzing bioproductions.
Collapse
Affiliation(s)
- Kiyotaka Y Hara
- Organization of Advanced Science and Technology, Kobe University, Nada, Kobe, Japan
| | | | | | | | | |
Collapse
|
22
|
Xu J, Sigworth FJ, LaVan DA. Synthetic protocells to mimic and test cell function. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2010; 22:120-7. [PMID: 20217710 PMCID: PMC2845179 DOI: 10.1002/adma.200901945] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Synthetic protocells provide a new means to probe, mimic and deconstruct cell behavior; they are a powerful tool to quantify cell behavior and a useful platform to explore nanomedicine. Protocells are not simple particles; they mimic cell design and typically consist of a stabilized lipid bilayer with membrane proteins. With a finite number of well characterized components, protocells can be designed to maximize useful outputs. Energy conversion in cells is an intriguing output; many natural cells convert transmembrane ion gradients into electricity by membrane-protein regulated ion transport. Here, a synthetic cell system comprising two droplets separated by a lipid bilayer is described that functions as a biological battery. The factors that affect its electrogenic performance are explained and predicted by coupling equations of the electrodes, transport proteins and membrane behavior. We show that the output of such biological batteries can reach an energy density of 6.9 x 10(6) J m(-3), which is approximately 5% of the volumetric energy density of a lead-acid battery. The configuration with maximum power density has an energy conversion efficiency of 10%.
Collapse
Affiliation(s)
- Jian Xu
- School of Engineering and Applied Science, Yale University, New Haven, CT 06511 (USA)
| | - Fred J. Sigworth
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT 06520 (USA)
| | - David A. LaVan
- Ceramics Division, Materials Science and Engineering Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899 (USA)
| |
Collapse
|
23
|
Zhou P, Xu XW, Wu M, Huang WD, Oren A. Isolation and functional expression of the bop gene from Halobiforma lacisalsi. Microbiol Res 2009; 164:553-9. [PMID: 17689228 DOI: 10.1016/j.micres.2007.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2006] [Revised: 05/05/2007] [Accepted: 06/13/2007] [Indexed: 11/16/2022]
Abstract
A novel bop gene was described from Halobiforma lacisalsi strain AJ5(T), an extremely halophilic archaeon isolated from Ayakekum Lake, China. Following six rounds of PCR amplification based on the conserved fragment of the bop gene, the complete sequence of the bop gene, including the 5' and 3' flanking regions of the conserved fragment, was obtained by the ligation-mediated PCR amplification (LPA) approach. The data presented provide us with further insight into the distribution of bop-like genes in the family Halobacteriaceae. This is the first example of a bop-like gene in halophiles found in the high-pH environment. Alignment and hydropathy analysis of the deduced amino acid sequence identified the conserved functional sites as well as some variations compared with other bacterio-opsins. Molecular phylogenetic analysis revealed the position of the bacterio-opsin of strain AJ5, which is closest to that of Haloterrigena sp. arg-4 with 85% identity. In the presence of all-trans retinal, recombinant Escherichia coli cells expressing the gene turned dark purple. The purple membrane from the recombinant E. coli showed maximal absorption at 540 nm.
Collapse
Affiliation(s)
- Peng Zhou
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
| | | | | | | | | |
Collapse
|
24
|
Lórenz-Fonfría VA, Kandori H. Spectroscopic and Kinetic Evidence on How Bacteriorhodopsin Accomplishes Vectorial Proton Transport under Functional Conditions. J Am Chem Soc 2009; 131:5891-901. [DOI: 10.1021/ja900334c] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Víctor A. Lórenz-Fonfría
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| |
Collapse
|
25
|
Summers DP, Noveron J, Basa RCB. Energy transduction inside of amphiphilic vesicles: encapsulation of photochemically active semiconducting particles. ORIGINS LIFE EVOL B 2009; 39:127-40. [PMID: 19259781 DOI: 10.1007/s11084-009-9160-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Accepted: 12/14/2008] [Indexed: 10/21/2022]
Abstract
Amphiphilic bilayer membrane structures (vesicles) have been postulated to have been abiotically formed and spontaneously assemble on the prebiotic Earth, providing compartmentalization for the origin of life. These vesicles are similar to modern cellular membranes and can serve to contain water-soluble species, concentrate species, and have the potential to catalyze reactions. The origin of the use of photochemical energy in metabolism (i.e. energy transduction) is one of the central issues in the origin of life. This includes such questions as how energy transduction may have occurred before complex enzymatic systems, such as required by contemporary photosynthesis, had developed and how simple a photochemical system is possible. It has been postulated that vesicle structures developed the ability to capture and transduce light, providing energy for reactions. It has also been shown that pH gradients across the membrane surface can be photochemically created, but coupling these to drive chemical reactions has been difficult. Colloidal semiconducting mineral particles are known to photochemically drive redox chemistry. We propose that encapsulation of these particles has the potential to provide a source of energy transduction inside vesicles, and thereby drive protocellular chemistry, and represents a model system for early photosynthesis. In our experiments we show that TiO2 particles, in the approximately 20 nm size range, can be incorporated into vesicles and retain their photoactivity through the dehydration/rehydration cycles that have been shown to concentrate species inside a vesicle.
Collapse
Affiliation(s)
- David P Summers
- Carl Sagan Center for the Study of Life in the Universe, SETI Institute, Mountain View, USA.
| | | | | |
Collapse
|
26
|
|
27
|
Hughes GA. Nanostructure-mediated drug delivery. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2007; 1:22-30. [PMID: 17292054 DOI: 10.1016/j.nano.2004.11.009] [Citation(s) in RCA: 301] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2004] [Accepted: 11/30/2004] [Indexed: 11/17/2022]
Abstract
Nanotechnology is expected to have an impact on all industries including semiconductors, manufacturing, and biotechnology. Tools that provide the capability to characterize and manipulate materials at the nanoscale level further elucidate nanoscale phenomena and equip researchers and developers with the ability to fabricate novel materials and structures. One of the most promising societal impacts of nanotechnology is in the area of nanomedicine. Personalized health care, rational drug design, and targeted drug delivery are some of the benefits of a nanomedicine-based approach to therapy. This review will focus on the development of nanoscale drug delivery mechanisms. Nanostructured drug carriers allow for the delivery of not only small-molecule drugs but also the delivery of nucleic acids and proteins. Delivery of these molecules to specific areas within the body can be achieved, which will reduce systemic side effects and allow for more efficient use of the drug.
Collapse
|
28
|
Bondar AN, Suhai S, Fischer S, Smith JC, Elstner M. Suppression of the back proton-transfer from Asp85 to the retinal Schiff base in bacteriorhodopsin: A theoretical analysis of structural elements. J Struct Biol 2007; 157:454-69. [PMID: 17189704 DOI: 10.1016/j.jsb.2006.10.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2006] [Revised: 09/26/2006] [Accepted: 10/03/2006] [Indexed: 11/15/2022]
Abstract
The transfer of a proton from the retinal Schiff base to the nearby Asp85 protein group is an essential step in the directional proton-pumping by bacteriorhodopsin. To avoid the wasteful back reprotonation of the Schiff base from Asp85, the protein must ensure that, following Schiff base deprotonation, the energy barrier for back proton-transfer from Asp85 to the Schiff base is larger than that for proton-transfer from the Schiff base to Asp85. Here, three structural elements that may contribute to suppressing the back proton-transfer from Asp85 to the Schiff base are investigated: (i) retinal twisting; (ii) hydrogen-bonding distances in the active site; and (iii) the number and location of internal water molecules. The impact of the pattern of bond twisting on the retinal deprotonation energy is dissected by performing an extensive set of quantum-mechanical calculations. Structural rearrangements in the active site, such as changes of the Thr89:Asp85 distance and relocation of water molecules hydrogen-bonding to the Asp85 acceptor group, may participate in the mechanism which ensures that following the transfer of the Schiff base proton to Asp85 the protein proceeds with the subsequent photocycle steps, and not with back proton transfer from Asp85 to the Schiff base.
Collapse
Affiliation(s)
- Ana-Nicoleta Bondar
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
| | | | | | | | | |
Collapse
|
29
|
Ferreira AM, Bashford D. Model for Proton Transport Coupled to Protein Conformational Change: Application to Proton Pumping in the Bacteriorhodopsin Photocycle. J Am Chem Soc 2006; 128:16778-90. [PMID: 17177428 DOI: 10.1021/ja060742d] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A modeling method is presented for protein systems in which proton transport is coupled to conformational change, as in proton pumps and in motors driven by the proton-motive force. Previously developed methods for calculating pKa values in proteins using a macroscopic dielectric model are extended beyond the equilibrium case to a master-equation model for the time evolution of the system through states defined by ionization microstate and a discrete set of conformers. The macroscopic dielectric model supplies free energy changes for changes of protonation microstate, while the method for obtaining the energetics of conformational change and the relaxation rates, the other ingredients needed for the master equation, are system dependent. The method is applied to the photoactivated proton pump, bacteriorhodopsin, using conformational free energy differences from experiment and treating relaxation rates through three adjustable parameters. The model is found to pump protons with an efficiency relatively insensitive to parameter choice over a wide range of parameter values, and most of the main features of the known photocycle from very early M to the return to the resting state are reproduced. The boundaries of these parameter ranges are such that short-range proton transfers are faster than longer-range ones, which in turn are faster than conformational changes. No relaxation rates depend on conformation. The results suggest that an "accessibility switch", while not ruled out, is not required and that vectorial proton transport can be achieved through the coupling of the energetics of ionization and conformational states.
Collapse
Affiliation(s)
- Antonio M Ferreira
- Department of Molecular Biotechnology, Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, 332 North Lauderdale Street, Memphis, TN 38105, USA
| | | |
Collapse
|
30
|
Lanyi JK. Proton transfers in the bacteriorhodopsin photocycle. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1757:1012-8. [PMID: 16376293 DOI: 10.1016/j.bbabio.2005.11.003] [Citation(s) in RCA: 156] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2005] [Revised: 11/08/2005] [Accepted: 11/10/2005] [Indexed: 11/23/2022]
Abstract
The steps in the mechanism of proton transport in bacteriorhodopsin include examples for most kinds of proton transfer reactions that might occur in a transmembrane pump: proton transfer via a bridging water molecule, coupled protonation/deprotonation of two buried groups separated by a considerable distance, long-range proton migration over a hydrogen-bonded aqueous chain, and capture as well as release of protons at the membrane-water interface. The conceptual and technical advantages of this system have allowed close examination of many of these model reactions, some at an atomic level.
Collapse
Affiliation(s)
- Janos K Lanyi
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA.
| |
Collapse
|
31
|
Robust hybrid thin films that incorporate lamellar phospholipid bilayer assemblies and transmembrane proteins. Biointerphases 2006; 1:6. [DOI: 10.1116/1.2185654] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
|
32
|
|
33
|
Xu XW, Wu M, Huang WD. Isolation and characterization of a novel strain of Natrinema containing a bop gene. J Zhejiang Univ Sci B 2005; 6:142-6. [PMID: 15633251 PMCID: PMC1389630 DOI: 10.1631/jzus.2005.b0142] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A novel member of extremely halophilic archaea, strain AJ2, was isolated from Ayakekum Lake located in Altun Mountain National Nature Reserve of Xinjiang Uygur Autonomous Region in China. The strain AJ2 requires at least 10% (w/v) NaCl and grows 10% to 30% (optimum at 20%). Phylogenetic analysis based on 16S rDNA sequence comparison revealed that strain AJ2 clustered to three Natrinema species with less than 97.7% sequence similarities, suggesting AJ2 is a novel member of Natrinema. A bacteriorhodopsin-encoding (bop) gene was subsequently detected in the AJ2 genome using the polymerase chain reaction technique. The cloning and sequencing of a 401 base pairs fragment indicated the deduced amino acid sequence of bop from AJ2 is different from that reported for bacteriorhodopsins. This is the first reported detection of a bop gene in Natrinema.
Collapse
Affiliation(s)
- Xue-wei Xu
- School of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Min Wu
- School of Life Sciences, Zhejiang University, Hangzhou 310027, China
- †E-mail:
| | - Wei-da Huang
- School of Life Sciences, Fudan University, Shanghai 200433, China
| |
Collapse
|
34
|
Abstract
Photosynthetic proteins are a source of biological material well-suited to technological applications. They exhibit light-induced electron transfer across lipid membranes that can be exploited for the construction of photo-optical electrical devices. The structure and function of photosynthetic proteins differ across the photosynthetic evolutionary scale, allowing for their application in a range of technologies. Here we provide a general description of the basic and technical research in this sector and an overview of biochips and biosensors based on photochemical activity that have been developed for the bioassay of pollutants.
Collapse
Affiliation(s)
- Maria Teresa Giardi
- Institute of Crystallography, National Council of Research, Department of Molecular Design and Nanotechnology, Area of Research of Rome, Via Salaria Km 29.300, 00016 Monterotondo scalo Rome, Italy
| | | |
Collapse
|
35
|
Pohorille A, Schweighofer K, Wilson MA. The origin and early evolution of membrane channels. ASTROBIOLOGY 2005; 5:1-17. [PMID: 15711166 DOI: 10.1089/ast.2005.5.1] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The origin and early evolution of ion channels are considered from the point of view that the transmembrane segments of membrane proteins are structurally quite simple and do not require specific sequences to fold. We argue that the transport of solute species, especially ions, required an early evolution of efficient transport mechanisms, and that the emergence of simple ion channels was protobiologically plausible. We also argue that, despite their simple structure, such channels could possess properties that, at the first sight, appear to require markedly greater complexity. These properties can be subtly modulated by local modifications to the sequence rather than global changes in molecular architecture. In order to address the evolution and development of ion channels, we focus on identifying those protein domains that are commonly associated with ion channel proteins and are conserved throughout the three main domains of life (Eukarya, Bacteria, and Archaea). We discuss the potassium-sodium-calcium superfamily of voltage-gated ion channels, mechanosensitive channels, porins, and ABC-transporters and argue that these families of membrane channels have sufficiently universal architectures that they can readily adapt to the diverse functional demands arising during evolution.
Collapse
Affiliation(s)
- Andrew Pohorille
- NASA Ames Research Center, Moffett Field, California 94035, USA.
| | | | | |
Collapse
|
36
|
Ruiz-Mirazo K, Moreno A. Basic autonomy as a fundamental step in the synthesis of life. ARTIFICIAL LIFE 2004; 10:235-259. [PMID: 15245626 DOI: 10.1162/1064546041255584] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In the search for the primary roots of autonomy (a pivotal concept in Varela's comprehensive understanding of living beings), the theory of autopoiesis provided an explicit criterion to define minimal life in universal terms, and was taken as a guideline in the research program for the artificial synthesis of biological systems. Acknowledging the invaluable contribution of the autopoietic school to present biological thinking, we offer an alternative way of conceiving the most basic forms of autonomy. We give a bottom-up account of the origins of "self-production" (or self-construction, as we propose to call it), pointing out which are the minimal material and energetic requirements for the constitution of basic autonomous systems. This account is, indeed, committed to the project of developing a general theory of biology, but well grounded in the universal laws of physics and chemistry. We consider that the autopoietic theory was formulated in highly abstract terms and, in order to advance in the implementation of minimal autonomous systems (and, at the same time, make major progress in exploring the origins of life), a more specific characterization of minimal autonomous systems is required. Such a characterization will not be drawn from a review of the autopoietic criteria and terminology (à la Fleischaker) but demands a whole reformulation of the question: a proper naturalization of the concept of autonomy. Finally, we also discuss why basic autonomy, according to our account, is necessary but not sufficient for life, in contrast with Varela's idea that autopoiesis was a necessary and sufficient condition for it.
Collapse
|
37
|
Nath S. Molecular mechanisms of energy transduction in cells: engineering applications and biological implications. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2003; 85:125-80. [PMID: 12930095 DOI: 10.1007/3-540-36466-8_5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
The synthesis of ATP from ADP and inorganic phosphate by F1F0-ATP synthase, the universal enzyme in biological energy conversion, using the energy of a transmembrane gradient of ions, and the use of ATP by the myosin-actin system to cause muscular contraction are among the most fundamental processes in biology. Both the ATP synthase and the myosin-actin may be looked upon as molecular machines. A detailed analysis of the molecular mechanisms of energy transduction by these molecular machines has been carried out in order to understand the means by which living cells produce and consume energy. These mechanisms have been compared with each other and their biological implications have been discussed. The thermodynamics of energy coupling in the oxidative phosphorylation process has been developed and the consistency of the mechanisms with the thermodynamics has been explored. Novel engineering applications that can result have been discussed in detail and several directions for future work have been pointed out.
Collapse
Affiliation(s)
- Sunil Nath
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi 110 016, India.
| |
Collapse
|
38
|
Whitmire SE, Wolpert D, Markelz AG, Hillebrecht JR, Galan J, Birge RR. Protein flexibility and conformational state: a comparison of collective vibrational modes of wild-type and D96N bacteriorhodopsin. Biophys J 2003; 85:1269-77. [PMID: 12885670 PMCID: PMC1303244 DOI: 10.1016/s0006-3495(03)74562-7] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2002] [Accepted: 03/28/2003] [Indexed: 10/21/2022] Open
Abstract
Far infrared (FIR) spectral measurements of wild-type (WT) and D96N mutant bacteriorhodopsin thin films have been carried out using terahertz time domain spectroscopy as a function of hydration, temperature, and conformational state. The results are compared to calculated spectra generated via normal mode analyses using CHARMM. We find that the FIR absorbance is slowly increasing with frequency and without strong narrow features over the range of 2-60 cm(-1) and up to a resolution of 0.17 cm(-1). The broad absorption shifts in frequency with decreasing temperature as expected with a strongly anharmonic potential and in agreement with neutron inelastic scattering results. Decreasing hydration shifts the absorption to higher frequencies, possibly resulting from decreased coupling mediated by the interior water molecules. Ground-state FIR absorbances have nearly identical frequency dependence, with the mutant having less optical density than the WT. In the M state, the FIR absorbance of the WT increases whereas there is no change for D96N. These results represent the first measurement of FIR absorbance change as a function of conformational state.
Collapse
Affiliation(s)
- S E Whitmire
- Physics Department, University at Buffalo, State University of New York, Buffalo, New York, USA
| | | | | | | | | | | |
Collapse
|
39
|
Friedman R, Nachliel E, Gutman M. The role of small intraprotein cavities in the catalytic cycle of bacteriorhodopsin. Biophys J 2003; 85:886-96. [PMID: 12885636 PMCID: PMC1303210 DOI: 10.1016/s0006-3495(03)74528-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The last phase of the proton transfer cycle of bacteriorhodopsin calls for a passage of a proton from D38 to D96. This reaction utilizes a narrow shaft approximately 10-A long that connects the two carboxylates that cross through a very hydrophobic domain. As the shaft is too narrow to be permanently hydrated, there are two alternatives for the proton propagation into the channel. The proton may propagate through the shaft without solvation at the expense of a high electrostatic barrier; alternatively, the shaft will expand to accommodate some water molecules, thus lowering the Born energy for the insertion of the charge into the protein (B. Schätzler, N. A. Dencher, J. Tittor, D. Oesterhelt, S. Yaniv-Checover, E. Nachliel, and G. Gutman, 2003, BIOPHYS: J. 84:671-686). A comparative study of nine published crystal-structures of bacteriorhodopsin identified, next to the shaft, microcavities in the protein whose position and surrounding atoms are common to the reported structures. Some of the cavities either shrink or expand during the photocycle. It is argued that the plasticity of the cavities provides a working space needed for the transient solvation of the shaft, thus reducing the activation energy necessary for the solvation of the shaft. This suggestion is corroborated by the recent observations of Klink et al. (B. U. Klink, R. Winter, M. Engelhard, and I. Chizhov, 2002, BIOPHYS: J. 83:3490-3498) that the late phases of the photocycle (tau >/=1 ms) are strongly inhibited by external pressure.
Collapse
Affiliation(s)
- Ran Friedman
- Laser Laboratory for Fast Reactions in Biology, Department of Biochemistry, Tel Aviv University, Tel Aviv 69978, Israel
| | | | | |
Collapse
|
40
|
Xu J, Stickrath AB, Bhattacharya P, Nees J, Váró G, Hillebrecht JR, Ren L, Birge RR. Direct measurement of the photoelectric response time of bacteriorhodopsin via electro-optic sampling. Biophys J 2003; 85:1128-34. [PMID: 12885657 PMCID: PMC1303231 DOI: 10.1016/s0006-3495(03)74549-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The photovoltaic signal associated with the primary photochemical event in an oriented bacteriorhodopsin film is measured by directly probing the electric field in the bacteriorhodopsin film using an ultrafast electro-optic sampling technique. The inherent response time is limited only by the laser pulse width of 500 fs, and permits a measurement of the photovoltage with a bandwidth of better than 350 GHz. All previous published studies have been carried out with bandwidths of 50 GHz or lower. We observe a charge buildup with an exponential formation time of 1.68 +/- 0.05 ps and an initial decay time of 31.7 ps. Deconvolution with a 500-fs Gaussian excitation pulse reduces the exponential formation time to 1.61 +/- 0.04 ps. The photovoltaic signal continues to rise for 4.5 ps after excitation, and the voltage profile corresponds well with the population dynamics of the K state. The origin of the fast photovoltage is assigned to the partial isomerization of the chromophore and the coupled motion of the Arg-82 residue during the primary event.
Collapse
Affiliation(s)
- J Xu
- Solid State Electronics Laboratory, Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan, USA
| | | | | | | | | | | | | | | |
Collapse
|
41
|
Pohorille A, Wilson MA, Chipot C. Membrane peptides and their role in protobiological evolution. ORIGINS LIFE EVOL B 2003; 33:173-97. [PMID: 12967266 DOI: 10.1023/a:1024627726231] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
How simple membrane peptides performed such essential protocellular functions as transport of ions and organic matter across membranes separating the interior of the cell from the environment, capture and utilization of energy, and transduction of environmental signals, is a key question in protobiological evolution. On the basis of detailed, molecular-level computer simulations we explain how these peptides fold at water-membrane interfaces, insert into membranes, self-assemble into higher-order structures and acquire functions. We have investigated the interfacial behavior and folding of several peptides built of leucine and glutamine residues and have demonstrated that many of them tend to adopt ordered structures. Further, we have studied the insertion of an alpha-helical peptide containing leucine (L) and serine (S) of the form (LSLLLSL)3 into a model membrane. The transmembrane state is metastable, and approximately 15 kcal mol(-1) is required to insert the peptide into the membrane. Investigations of dimers formed by (LSLLLSL)3 and glycophorin A demonstrate how the favorable free energy of helix association can offset the unfavorable free energy of insertion, leading to self-assembly of peptide helices in the membrane. An example of a self-assembled structure is the tetrameric transmembrane pore of the influenza virus M2 protein, which is an efficient and selective voltage-gated proton channel. Our simulations explain the gating mechanism and provide guidelines how to re-engineer the channel to act as a simple proton pump. In general, emergence of integral membrane proteins appears to be quite feasible and may be easier to envision than the emergence of water-soluble proteins.
Collapse
Affiliation(s)
- Andrew Pohorille
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | | | | |
Collapse
|
42
|
Gillespie NB, Wise KJ, Ren L, Stuart JA, Marcy DL, Hillebrecht J, Li Q, Ramos L, Jordan K, Fyvie S, Birge RR. Characterization of the Branched-Photocycle Intermediates P and Q of Bacteriorhodopsin. J Phys Chem B 2002. [DOI: 10.1021/jp021221p] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nathan B. Gillespie
- Departments of Chemistry and of Molecular and Cell Biology, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, and W. M. Keck Center for Molecular Electronics and Department of Chemistry, Syracuse University, 111 College Place, Syracuse, New York 13244-4100
| | - Kevin J. Wise
- Departments of Chemistry and of Molecular and Cell Biology, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, and W. M. Keck Center for Molecular Electronics and Department of Chemistry, Syracuse University, 111 College Place, Syracuse, New York 13244-4100
| | - Lei Ren
- Departments of Chemistry and of Molecular and Cell Biology, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, and W. M. Keck Center for Molecular Electronics and Department of Chemistry, Syracuse University, 111 College Place, Syracuse, New York 13244-4100
| | - Jeffrey A. Stuart
- Departments of Chemistry and of Molecular and Cell Biology, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, and W. M. Keck Center for Molecular Electronics and Department of Chemistry, Syracuse University, 111 College Place, Syracuse, New York 13244-4100
| | - Duane L. Marcy
- Departments of Chemistry and of Molecular and Cell Biology, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, and W. M. Keck Center for Molecular Electronics and Department of Chemistry, Syracuse University, 111 College Place, Syracuse, New York 13244-4100
| | - Jason Hillebrecht
- Departments of Chemistry and of Molecular and Cell Biology, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, and W. M. Keck Center for Molecular Electronics and Department of Chemistry, Syracuse University, 111 College Place, Syracuse, New York 13244-4100
| | - Qun Li
- Departments of Chemistry and of Molecular and Cell Biology, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, and W. M. Keck Center for Molecular Electronics and Department of Chemistry, Syracuse University, 111 College Place, Syracuse, New York 13244-4100
| | - Lavoisier Ramos
- Departments of Chemistry and of Molecular and Cell Biology, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, and W. M. Keck Center for Molecular Electronics and Department of Chemistry, Syracuse University, 111 College Place, Syracuse, New York 13244-4100
| | - Kevin Jordan
- Departments of Chemistry and of Molecular and Cell Biology, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, and W. M. Keck Center for Molecular Electronics and Department of Chemistry, Syracuse University, 111 College Place, Syracuse, New York 13244-4100
| | - Sean Fyvie
- Departments of Chemistry and of Molecular and Cell Biology, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, and W. M. Keck Center for Molecular Electronics and Department of Chemistry, Syracuse University, 111 College Place, Syracuse, New York 13244-4100
| | - Robert R. Birge
- Departments of Chemistry and of Molecular and Cell Biology, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, and W. M. Keck Center for Molecular Electronics and Department of Chemistry, Syracuse University, 111 College Place, Syracuse, New York 13244-4100
| |
Collapse
|
43
|
Wise KJ, Gillespie NB, Stuart JA, Krebs MP, Birge RR. Optimization of bacteriorhodopsin for bioelectronic devices. Trends Biotechnol 2002; 20:387-94. [PMID: 12175770 DOI: 10.1016/s0167-7799(02)02023-1] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Bacteriorhodopsin (BR) is the photoactive proton pump found in the purple membrane of the salt marsh archaeon Halobacterium salinarum. Evolution has optimized this protein for high photochemical efficiency, thermal stability and cyclicity, as the organism must be able to function in a hot, stagnant and resource-limited environment. Photonic materials generated via organic chemistry have yet to surpass the native protein in terms of quantum efficiency or cyclicity. However, the native protein still lacks the overall efficiency necessary for commercial viability and virtually all successful photonic devices using bacteriorhodopsin are based on chemical or genetic variants of the native protein. We show that genetic engineering can provide significant improvement in the device capabilities of proteins and, in the case of bacteriorhodopsin, a 700-fold improvement has been realized in volumetric data storage. We conclude that semi-random mutagenesis and directed evolution will play a prominent role in future efforts in bioelectronic optimization.
Collapse
Affiliation(s)
- Kevin J Wise
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
| | | | | | | | | |
Collapse
|
44
|
Nachliel E, Gutman M, Tittor J, Oesterhelt D. Proton transfer dynamics on the surface of the late M state of bacteriorhodopsin. Biophys J 2002; 83:416-26. [PMID: 12080130 PMCID: PMC1302157 DOI: 10.1016/s0006-3495(02)75179-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The cytoplasmic surface of the BR (initial) state of bacteriorhodopsin is characterized by a cluster of three carboxylates that function as a proton-collecting antenna. Systematic replacement of most of the surface carboxylates indicated that the cluster is made of D104, E161, and E234 (Checover, S., Y. Marantz, E. Nachliel, M. Gutman, M. Pfeiffer, J. Tittor, D. Oesterhelt, and N. Dencher. 2001. Biochemistry. 40:4281-4292), yet the BR state is a resting configuration; thus, its proton-collecting antenna can only indicate the presence of its role in the photo-intermediates where the protein is re-protonated by protons coming from the cytoplasmic matrix. In the present study we used the D96N and the triple (D96G/F171C/F219L) mutant for monitoring the proton-collecting properties of the protein in its late M state. The protein was maintained in a steady M state by continuous illumination and subjected to reversible pulse protonation caused by repeated excitation of pyranine present in the reaction mixture. The re-protonation dynamics of the pyranine anion was subjected to kinetic analysis, and the rate constants of the reaction of free protons with the surface groups and the proton exchange reactions between them were calculated. The reconstruction of the experimental signal indicated that the late M state of bacteriorhodopsin exhibits an efficient mechanism of proton delivery to the unoccupied-most basic-residue on its cytoplasmic surface (D38), which exceeds that of the BR configuration of the protein. The kinetic analysis was carried out in conjunction with the published structure of the M state (Sass, H., G. Büldt, R. Gessenich, D. Hehn, D. Neff, R. Schlesinger, J. Berendzen, and P. Ormos. 2000. Nature. 406:649-653), the model that resolves most of the cytoplasmic surface. The combination of the kinetic analysis and the structural information led to identification of two proton-conducting tracks on the protein's surface that are funneling protons to D38. One track is made of the carboxylate moieties of residues D36 and E237, while the other is made of D102 and E232. In the late M state the carboxylates of both tracks are closer to D38 than in the BR (initial) state, accounting for a more efficient proton equilibration between the bulk and the protein's proton entrance channel. The triple mutant resembles in the kinetic properties of its proton conducting surface more the BR-M state than the initial state confirming structural similarities with the BR-M state and differences to the BR initial state.
Collapse
Affiliation(s)
- Esther Nachliel
- Laser Laboratory for Fast Reactions in Biology, Department of Biochemistry, Tel Aviv University, Tel Aviv 69978, Israel
| | | | | | | |
Collapse
|
45
|
Abstract
A variety of techniques can now be used to alter the genome of a cell. Although these techniques are very powerful, they have limitations related to cost and efficiency of scale. Artificial cells designed for specific applications combine properties of biological systems such as nanoscale efficiency, self-organization and adaptability at relatively low cost. Individual components needed for such structures have already been developed, and now the main challenge is to integrate them in functional microscopic compartments. It will then become possible to design and construct communities of artificial cells that can perform different tasks related to therapeutic and diagnostic applications.
Collapse
Affiliation(s)
- Andrew Pohorille
- Exobiology Branch, NASA-Ames Research Center, MS 239-4, 94035, Moffett Field, CA, USA.
| | | |
Collapse
|
46
|
|
47
|
|
48
|
Niemeyer CM. Nanoparticles, Proteins, and Nucleic Acids: Biotechnology Meets Materials Science. Angew Chem Int Ed Engl 2001; 40:4128-4158. [DOI: 10.1002/1521-3773(20011119)40:22<4128::aid-anie4128>3.0.co;2-s] [Citation(s) in RCA: 2006] [Impact Index Per Article: 87.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2001] [Indexed: 01/04/2023]
|