1
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Parker KA, Beratan DN. Undulating Free Energy Landscapes Buffer Redox Chains from Environmental Fluctuations. J Phys Chem B 2024. [PMID: 39244677 DOI: 10.1021/acs.jpcb.4c04637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2024]
Abstract
Roller-coaster or undulating free energy landscapes, with alternating high and low potential cofactors, occur frequently in biological redox chains. Yet, there is little understanding of the possible advantages created by these landscapes. We examined the tetraheme subunit associated with Blastochloris viridis reaction centers, comparing the dynamics of the native protein and of hypothetical (in silico) mutants. We computed the variation in the total number of electrons in wild type (WT) and mutant tetrahemes connected to an electron reservoir in the presence of a time-varying potential, as a model for a fluctuating redox environment. We found that roller-coaster free energy landscapes buffer the redox cofactor populations from these fluctuations. The WT roller-coaster landscape slows forward and backward electron transfer in the face of fluctuations, and may offer the advantage of sustaining the reduction of essential cofactors, such as the chlorophyll special pair in photosynthesis, even though an undulating landscape introduces thermodynamically uphill steps in multistep redox chains.
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Affiliation(s)
- Kelsey A Parker
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - David N Beratan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States
- Department of Physics, Duke University, Durham, North Carolina 27708, United States
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2
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Roy RR, Ullmann GM. Virtual Model Compound Approach for Calculating Redox Potentials of [Fe 2S 2]-Cys 4 Centers in Proteins - Structure Quality Matters. J Chem Theory Comput 2023; 19:8930-8941. [PMID: 37974307 DOI: 10.1021/acs.jctc.3c00779] [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: 11/19/2023]
Abstract
The midpoint potential of the [Fe2S2]-Cys4-cluster in proteins is known to vary between -200 and -450 mV. This variation is caused by the different electrostatic environment of the cluster in the respective proteins. Continuum electrostatics can quantify the impact of the protein environment on the redox potential. Thus, if the redox potential of a [Fe2S2]-Cys4-cluster model compound in aqueous solution would be known, then redox potentials in various protein complexes could be calculated. However, [Fe2S2]-Cys4-cluster models are not water-soluble, and thus, their redox potential can not be measured in aqueous solution. To overcome this problem, we introduce a method that we call Virtual Model Compound Approach (VMCA) to extrapolate the model redox potential from known redox potentials of proteins. We carefully selected high-resolution structures for our analysis and divide them into a fit set, for fitting the model redox potential, and an independent test set, to check the validity of the model redox potential. However, from our analysis, we realized that the some structures can not be used as downloaded from the PDB but had to be re-refined in order to calculate reliable redox potentials. Because of the re-refinement, we were able to significantly reduce the standard deviation of our derived model redox potential for the [Fe2S2]-Cys4-cluster from 31 mV to 10 mV. As the model redox potential, we obtained -184 mV. This model redox potential can be used to analyze the redox behavior of [Fe2S2]-Cys4-clusters in larger protein complexes.
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Affiliation(s)
- Rajeev Ranjan Roy
- Computational Biochemistry, Universitätsstr. 30, NWI, University of Bayreuth, Bayreuth, 95440, Germany
| | - G Matthias Ullmann
- Computational Biochemistry, Universitätsstr. 30, NWI, University of Bayreuth, Bayreuth, 95440, Germany
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3
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Chen Z, Kang XW, Zhou Y, Zhou Z, Tang S, Zou S, Wang K, Huang J, Ding B, Zhong D. Dissecting the Ultrafast Stepwise Bidirectional Proton Relay in a Blue-Light Photoreceptor. J Am Chem Soc 2023; 145:3394-3400. [PMID: 36722850 DOI: 10.1021/jacs.2c10206] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Proton relays through H-bond networks are essential in realizing the functionality of protein machines such as in photosynthesis and photoreceptors. It has been challenging to dissect the rates and energetics of individual proton-transfer steps during the proton relay. Here, we have designed a proton rocking blue light using a flavin (BLUF) domain with the flavin mononucleotide (FMN)-glutamic acid (E)-tryptophan (W) triad and have resolved the four individual proton-transfer steps kinetically using ultrafast spectroscopy. We have found that after the photo-induced charge separation forming FMN·-/E-COOH/WH·+, the proton first rapidly jumps from the bridging E-COOH to FMN- (τfPT2 = 3.8 ps; KIE = 1.0), followed by a second proton transfer from WH·+ to E-COO- (τfPT1 = 336 ps; KIE = 2.6) which immediately rocks back to W· (τrPT1 = 85 ps; KIE = 6.7), followed by a proton return from FMNH· to E-COO- (τrPT2 = 34 ps; KIE = 3.3) with the final charge recombination between FMN·- and WH·+ to close the reaction cycle. Our results revisited the Grotthuss mechanism on the ultrafast timescale using the BLUF domain as a paradigm protein.
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Affiliation(s)
- Zijing Chen
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai200240, China
| | - Xiu-Wen Kang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai200240, China
| | - Yalin Zhou
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai200240, China
| | - Zhongneng Zhou
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai200240, China
| | - Siwei Tang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai200240, China
| | - Shuhua Zou
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai200240, China
| | - Kailin Wang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai200240, China
| | - Jiulong Huang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai200240, China
| | - Bei Ding
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai200240, China
| | - Dongping Zhong
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai200240, China.,Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, Ohio43210, United States.,School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai200240, China
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4
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Song X, Fu Q, Bu Y. Nonlinear Migration Dynamics of Excess Electrons along Linear Oligopeptides Controlled by an Applied Electric Field. Chemphyschem 2019; 20:1497-1507. [PMID: 30912277 DOI: 10.1002/cphc.201900149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/16/2019] [Indexed: 11/06/2022]
Abstract
Migration of an excess electron along linear oligopeptides governed by the external electric field (Eex ) which is against the inner dipole electric field is theoretically investigated, including the effects of Eex on the structural and electronic properties of electron migration. Two structural properties including electron-binding ability and the dipole moment of linear oligopeptides are sensitive to the Eex values and can be largely modulated by Eex due to the competition of Eex and the inner electric field and electron transfer caused by Eex . In the case of low Eex values, two structural properties decrease slightly, while for high Eex values, the electron-binding ability continually increases strongly, with dipole moments firstly increasing significantly and then increasing more slowly at higher Eex . Additionally, linear oligopeptides of different chain lengths influence the modulation extent of Eex and the longer the chain length is, the more sensitive modulation of Eex is. In addition, electronic properties represented by electron spin densities and singly occupied molecular orbital distributions vary with Eex intensities, leading to an unusual electron migration behavior. As Eex increases, an excess electron transfers from the N-terminus to the C-terminus and jumps over a neighboring dipole unit of two termini to other units, respectively, instead of transferring by means of a one-by-one dipole unit hopping mechanism. These findings not only promote a deeper understanding of the connection between Eex and structural and electronic properties of electron transfer behavior in peptides, but also provide a new insight into the modulation of electron migration along the oligopeptides.
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Affiliation(s)
- Xiufang Song
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, People's Republic of China
| | - Qiang Fu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, People's Republic of China
| | - Yuxiang Bu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, People's Republic of China.,School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, 273165, People's Republic of China
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5
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Culka M, Gisdon FJ, Ullmann GM. Computational Biochemistry-Enzyme Mechanisms Explored. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 109:77-112. [PMID: 28683923 DOI: 10.1016/bs.apcsb.2017.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Understanding enzyme mechanisms is a major task to achieve in order to comprehend how living cells work. Recent advances in biomolecular research provide huge amount of data on enzyme kinetics and structure. The analysis of diverse experimental results and their combination into an overall picture is, however, often challenging. Microscopic details of the enzymatic processes are often anticipated based on several hints from macroscopic experimental data. Computational biochemistry aims at creation of a computational model of an enzyme in order to explain microscopic details of the catalytic process and reproduce or predict macroscopic experimental findings. Results of such computations are in part complementary to experimental data and provide an explanation of a biochemical process at the microscopic level. In order to evaluate the mechanism of an enzyme, a structural model is constructed which can be analyzed by several theoretical approaches. Several simulation methods can and should be combined to get a reliable picture of the process of interest. Furthermore, abstract models of biological systems can be constructed combining computational and experimental data. In this review, we discuss structural computational models of enzymatic systems. We first discuss various models to simulate enzyme catalysis. Furthermore, we review various approaches how to characterize the enzyme mechanism both qualitatively and quantitatively using different modeling approaches.
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Affiliation(s)
- Martin Culka
- Computational Biochemistry, University of Bayreuth, Bayreuth, Germany
| | - Florian J Gisdon
- Computational Biochemistry, University of Bayreuth, Bayreuth, Germany
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6
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Feliks M, Field MJ. Pcetk: A pDynamo-based Toolkit for Protonation State Calculations in Proteins. J Chem Inf Model 2015; 55:2288-96. [DOI: 10.1021/acs.jcim.5b00262] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mikolaj Feliks
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Martin J. Field
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
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7
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Beyer SR, Müller L, Southall J, Cogdell RJ, Ullmann GM, Köhler J. The open, the closed, and the empty: time-resolved fluorescence spectroscopy and computational analysis of RC-LH1 complexes from Rhodopseudomonas palustris. J Phys Chem B 2015; 119:1362-73. [PMID: 25526393 DOI: 10.1021/jp510822k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We studied the time-resolved fluorescence of isolated RC-LH1 complexes from Rhodopseudomonas palustris as a function of the photon fluence and the repetition rate of the excitation laser. Both parameters were varied systematically over 3 orders of magnitude. On the basis of a microstate description we developed a quantitative model for RC-LH1 and obtained very good agreement between experiments and elaborate simulations based on a global master equation approach. The model allows us to predict the relative population of RC-LH1 complexes with the special pair in the neutral state or in the oxidized state P(+) and those complexes that lack a reaction center.
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Affiliation(s)
- Sebastian R Beyer
- Experimental Physics IV and Bayreuther Institut für Makromolekülforschung (BIMF), University of Bayreuth , 95440 Bayreuth, Germany
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8
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Bauß A, Koslowski T. Storage, transport, release: heme versatility in nitrite reductase electron transfer studied by molecular dynamics simulations. Phys Chem Chem Phys 2015; 17:4483-91. [DOI: 10.1039/c4cp04383a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Using molecular dynamics simulations of the thermodynamic integration type, we study the energetics and kinetics of electron transfer through the nitrite reductase enzyme of Sulfurospirillum deleyianum, Wolinella succinogenes and Campylobacter jejuni.
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Affiliation(s)
- Anna Bauß
- Institut für Physikalische Chemie
- Universität Freiburg
- D-79104 Freiburg im Breisgau
- Germany
| | - Thorsten Koslowski
- Institut für Physikalische Chemie
- Universität Freiburg
- D-79104 Freiburg im Breisgau
- Germany
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9
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Burggraf F, Koslowski T. Charge transfer through a cytochrome multiheme chain: Theory and simulation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:186-92. [DOI: 10.1016/j.bbabio.2013.09.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 08/22/2013] [Accepted: 09/10/2013] [Indexed: 10/26/2022]
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10
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Olson TL, Williams JC, Allen JP. Influence of protein interactions on oxidation/reduction midpoint potentials of cofactors in natural and de novo metalloproteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:914-22. [PMID: 23466333 DOI: 10.1016/j.bbabio.2013.02.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 02/13/2013] [Accepted: 02/23/2013] [Indexed: 01/14/2023]
Abstract
As discussed throughout this special issue, oxidation and reduction reactions play critical roles in the function of many organisms. In photosynthetic organisms, the conversion of light energy drives oxidation and reduction reactions through the transfer of electrons and protons in order to create energy-rich compounds. These reactions occur in proteins such as cytochrome c, a heme-containing water-soluble protein, the bacteriochlorophyll-containing reaction center, and photosystem II where water is oxidized at the manganese cluster. A critical measure describing the ability of cofactors in proteins to participate in such reactions is the oxidation/reduction midpoint potential. In this review, the basic concepts of oxidation/reduction reactions are reviewed with a summary of the experimental approaches used to measure the midpoint potential of metal cofactors. For cofactors in proteins, the midpoint potential not only depends upon the specific chemical characteristics of cofactors but also upon interactions with the surrounding protein, such as the nature of the coordinating ligands and protein environment. These interactions can be tailored to optimize an oxidation/reduction reaction carried out by the protein. As examples, the midpoint potentials of hemes in cytochromes, bacteriochlorophylls in reaction centers, and the manganese cluster of photosystem II are discussed with an emphasis on the influence that protein interactions have on these potentials. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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Affiliation(s)
- T L Olson
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-1604, USA
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11
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Ullmann RT, Andrade SLA, Ullmann GM. Thermodynamics of transport through the ammonium transporter Amt-1 investigated with free energy calculations. J Phys Chem B 2012; 116:9690-703. [PMID: 22804733 DOI: 10.1021/jp305440f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Amt-1 from Archaeoglobus fulgidus (AfAmt-1) belongs to the Amt/Rh family of ammonium/ammonia transporting membrane proteins. The transport mode and the precise microscopic permeation mechanism utilized by these proteins are intensely debated. Open questions concern the identity of the transported substrate (ammonia and/or ammonium) and whether the transport is passive or active. To address these questions, we studied the overall thermodynamics of the different transport modes as a function of the environmental conditions. Then, we investigated the thermodynamics of the underlying microscopic transport mechanisms with free energy calculations within a continuum electrostatics model. The formalism developed for this purpose is of general utility in the calculation of binding free energies for ligands with multiple protonation forms or other binding forms. The results of our calculations are compared to the available experimental and theoretical data on Amt/Rh proteins and discussed in light of the current knowledge on the physiological conditions experienced by microorganisms and plants. We found that microscopic models of electroneutral and electrogenic transport modes are in principle thermodynamically viable. However, only the electrogenic variants have a net thermodynamic driving force under the physiological conditions experienced by microorganisms and plants. Thus, the transport mechanism of AfAmt-1 is most likely electrogenic.
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Affiliation(s)
- R Thomas Ullmann
- Structural Biology/Bioinformatics, University of Bayreuth, Universitätsstrasse 30, BGI, 95447 Bayreuth, Germany.
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12
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Feliks M, Ullmann GM. Glycerol Dehydratation by the B12-Independent Enzyme May Not Involve the Migration of a Hydroxyl Group: A Computational Study. J Phys Chem B 2012; 116:7076-87. [DOI: 10.1021/jp301165b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mikolaj Feliks
- Computational Biochemistry Group, University of Bayreuth, Universitätsstr. 30, BGI, 95447
Bayreuth, Germany
| | - G. Matthias Ullmann
- Computational Biochemistry Group, University of Bayreuth, Universitätsstr. 30, BGI, 95447
Bayreuth, Germany
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13
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Biedermann F, Scherman OA. Cucurbit[8]uril mediated donor-acceptor ternary complexes: a model system for studying charge-transfer interactions. J Phys Chem B 2012; 116:2842-9. [PMID: 22309573 DOI: 10.1021/jp2110067] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A supramolecular self-assembly approach is described which allows for the convenient preparation of a wide range of charge-transfer (CT) donor-acceptor complexes in aqueous solutions. When one equiv of the macrocyclic host cucurbit[8]uril (CB[8]) is added to an aqueous donor and acceptor solution, a heteroternary complex forms inside the host's cavity with a well-defined face-to-face π-π-stacking geometry of the donor and acceptor. This heteroternary, CB[8]-mediated complex offers the opportunity to study the CT phenomena at low concentrations and free from complications arising from any donor-donor and acceptor-acceptor interactions as a result of the large binding affinities and the very high selectivity over the formation of these homoternary complexes. Thus, this supramolocular self-assembly strategy is a practical donor-acceptor mix-and-match approach with synthetic advantages over much more cumbersome tethering schemes. While the characteristic UV/vis features of a few CB[8] ternary systems had been described as a CT band, we present for the first time systematic evidence for the existence of CT interactions between several donor-acceptor pairs that are mediated by the host CB[8]. Correlation of the experimentally obtained CT λ(max) to computed HOMO-LUMO energies demonstrated that the CT process in the host's cavity can be described by the Mulliken model. Furthermore, the literature claim of a "CT driving force" for the formation of CB[8] ternary complexes was scrutinized and evaluated by calorimetric (ITC) and ESI-MS measurements. The findings indicated that neither in the aqueous medium nor in the "gas-phase" is CT of energetic relevance to the Gibbs free binding energy. In contrast, electrostatic considerations combined with solvation effects are much better suited to rationalize the observed trends in binding affinities. Additionally, the CT λ(max) was found to be much more red-shifted (≥75 nm) inside the CB[8] cavity than in any polar organic solvents or water, indicating a significant stabilization of the CT excited state within the host cavity, further demonstrating the unique electrostatic, polar properties of the host cavity.
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Affiliation(s)
- Frank Biedermann
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdon
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14
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Dumit VI, Cortez N, Matthias Ullmann G. Distinguishing two groups of flavin reductases by analyzing the protonation state of an active site carboxylic acid. Proteins 2011; 79:2076-85. [PMID: 21538544 DOI: 10.1002/prot.23027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Revised: 02/08/2011] [Accepted: 02/25/2011] [Indexed: 11/12/2022]
Abstract
Flavin-containing reductases are involved in a wide variety of physiological reactions such as photosynthesis, nitric oxide synthesis, and detoxification of foreign compounds, including therapeutic drugs. Ferredoxin-NADP(H)-reductase (FNR) is the prototypical enzyme of this family. The fold of this protein is highly conserved and occurs as one domain of several multidomain enzymes such as the members of the diflavin reductase family. The enzymes of this family have emerged as fusion of a FNR and a flavodoxin. Although the active sites of these enzymes are very similar, different enzymes function in opposite directions, that is, some reduce oxidized nicotinamide adenine dinucleotide phosphate (NADP(+)) and some oxidize reduced nicotinamide adenine dinucleotide phosphate (NADPH). In this work, we analyze the protonation behavior of titratable residues of these enzymes through electrostatic calculations. We find that a highly conserved carboxylic acid in the active site shows a different titration behavior in different flavin reductases. This residue is deprotonated in flavin reductases present in plastids, but protonated in bacterial counterparts and in diflavin reductases. The protonation state of the carboxylic acid may also influence substrate binding. The physiological substrate for plastidic enzymes is NADP(+), but it is NADPH for the other mentioned reductases. In this article, we discuss the relevance of the environment of this residue for its protonation and its importance in catalysis. Our results allow to reinterpret and explain experimental data.
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Affiliation(s)
- Verónica I Dumit
- Structural Biology/Bioinformatics, University of Bayreuth, 95447 Bayreuth, Germany
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15
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Abstract
Fundamental research into bioinorganic catalysis of the kind presented at this Faraday Discussion has the potential to turn inspiration drawn from impressive natural energy and chemical transformations into artificial catalyst constructions useful to mankind. Creating bio-inspired artificial constructions requires a level of understanding well beyond simple description of structures and mechanisms of natural enzymes. To be useful, such description must be augmented by a practical sense of structural and energetic engineering tolerances of the mechanism. Significant barriers to achieving an engineering understanding of enzyme mechanisms arise from natural protein complexity. In certain cases we can surmount these barriers to understanding, such as natural electron tunneling, coupling of electron tunneling to light capture and proton exchange as well as simpler bond breaking redox catalysis. Hope for similar solutions of more complex bioinorganic enzymes is indicated in several papers presented in this Discussion. Armed with an engineering understanding of mechanism, the current serious frustrations to successful creation of functional artificial proteins that are rooted in protein complexity can fall away. Here we discuss the genetic and biological roots of protein complexity and show how to dodge and minimize the effects of complexity. In the best-understood cases, artificial enzymes can be designed from scratch using the simplest of protein scaffolds.
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Affiliation(s)
- P Leslie Dutton
- Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA.
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