1
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Hasecke L, Mata RA. Optimization of Quantum Nuclei Positions with the Adaptive Nuclear-Electronic Orbital Approach. J Phys Chem A 2024; 128:3205-3211. [PMID: 38619054 PMCID: PMC11056972 DOI: 10.1021/acs.jpca.4c00096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/08/2024] [Accepted: 03/08/2024] [Indexed: 04/16/2024]
Abstract
The use of multicomponent methods has become increasingly popular over the last years. Under this framework, nuclei (commonly protons) are treated quantum mechanically on the same footing as the electronic structure problem. Under the use of atomic-centered orbitals, this can lead to some complications as the ideal location of the nuclear basis centers must be optimized. In this contribution, we propose a straightforward approach to determine the position of such centers within the self-consistent cycle of a multicomponent calculation, making use of individual proton charge centroids. We test the method on model systems including the water dimer, a protonated water tetramer, and a porphine system. Comparing to numerical gradient calculations, the adaptive nuclear-electronic orbital (NEO) procedure is able to converge the basis centers to within a few cents of an Ångström and with less than 0.1 kcal/mol differences in absolute energies. This is achieved in one single calculation and with a small added computational effort of up to 80% compared to a regular NEO- self-consistent field run. An example application for the human transketolase proton wire is also provided.
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Affiliation(s)
- Lukas Hasecke
- Institute of Physical Chemistry, University
of Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
| | - Ricardo A. Mata
- Institute of Physical Chemistry, University
of Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
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2
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Tsujimura M, Saito K, Ishikita H. Stretching vibrational frequencies and pK a differences in H-bond networks of protein environments. Biophys J 2023; 122:4336-4347. [PMID: 37838831 PMCID: PMC10722396 DOI: 10.1016/j.bpj.2023.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 08/22/2023] [Accepted: 10/12/2023] [Indexed: 10/16/2023] Open
Abstract
The experimentally measured stretching vibrational frequencies of O-D [νO-D(donor)] and C=O [νC=O(donor)] H-bond donor groups can provide valuable information about the H-bonds in proteins. Here, using a quantum mechanical/molecular mechanical approach, the relationship between these vibrational frequencies and the difference in pKa values between H-bond donor and acceptor groups [ΔpKa(donor … acceptor)] in bacteriorhodopsin and photoactive yellow protein environments was investigated. The results show that νO-D(donor) is correlated with ΔpKa(donor … acceptor), regardless of the specific protein environment. νC=O(donor) is also correlated with ΔpKa(donor … acceptor), although the correlation is weak because the C=O bond does not have a proton. Importantly, the shifts in νO-D(donor) and νC=O(donor) are not caused by changes in pKa(donor) alone, but rather by changes in ΔpKa(donor … acceptor). Specifically, a decrease in ΔpKa(donor … acceptor) can lead to proton release from the H-bond donor group toward the acceptor group, resulting in shifts in the vibrational frequencies of the protein environment. These findings suggest that changes in the stretching vibrational frequencies, in particular νO-D(donor), can be used to monitor proton transfer in protein environments.
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Affiliation(s)
- Masaki Tsujimura
- Department of Advanced Interdisciplinary Studies, The University of Tokyo, Meguro-ku, Tokyo, Japan.
| | - Keisuke Saito
- Department of Applied Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Hiroshi Ishikita
- Department of Applied Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo, Japan.
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3
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Villot C, Lao KU. Electronic structure theory on modeling short-range noncovalent interactions between amino acids. J Chem Phys 2023; 158:094301. [PMID: 36889981 DOI: 10.1063/5.0138032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
While short-range noncovalent interactions (NCIs) are proving to be of importance in many chemical and biological systems, these atypical bindings happen within the so-called van der Waals envelope and pose an enormous challenge for current computational methods. We introduce SNCIAA, a database of 723 benchmark interaction energies of short-range noncovalent interactions between neutral/charged amino acids originated from protein x-ray crystal structures at the "gold standard" coupled-cluster with singles, doubles, and perturbative triples/complete basis set [CCSD(T)/CBS] level of theory with a mean absolute binding uncertainty less than 0.1 kcal/mol. Subsequently, a systematic assessment of commonly used computational methods, such as the second-order Møller-Plesset theory (MP2), density functional theory (DFT), symmetry-adapted perturbation theory (SAPT), composite electronic-structure methods, semiempirical approaches, and the physical-based potentials with machine learning (IPML) on SNCIAA is carried out. It is shown that the inclusion of dispersion corrections is essential even though these dimers are dominated by electrostatics, such as hydrogen bondings and salt bridges. Overall, MP2, ωB97M-V, and B3LYP+D4 turned out to be the most reliable methods for the description of short-range NCIs even in strongly attractive/repulsive complexes. SAPT is also recommended in describing short-range NCIs only if the δMP2 correction has been included. The good performance of IPML for dimers at close-equilibrium and long-range conditions is not transferable to the short-range. We expect that SNCIAA will assist the development/improvement/validation of computational methods, such as DFT, force-fields, and ML models, in describing NCIs across entire potential energy surfaces (short-, intermediate-, and long-range NCIs) on the same footing.
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Affiliation(s)
- Corentin Villot
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, USA
| | - Ka Un Lao
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, USA
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4
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Absorption wavelength along chromophore low-barrier hydrogen bonds. iScience 2022; 25:104247. [PMID: 35521532 PMCID: PMC9062252 DOI: 10.1016/j.isci.2022.104247] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 03/18/2022] [Accepted: 04/07/2022] [Indexed: 11/22/2022] Open
Abstract
In low-barrier hydrogen bonds (H-bonds), the pKa values for the H-bond donor and acceptor moieties are nearly equal, whereas the redox potential values depend on the H+ position. Spectroscopic details of low-barrier H-bonds remain unclear. Here, we report the absorption wavelength along low-barrier H-bonds in protein environments, using a quantum mechanical/molecular mechanical approach. Low-barrier H-bonds form between Glu46 and p-coumaric acid (pCA) in the intermediate pRCW state of photoactive yellow protein and between Asp116 and the retinal Schiff base in the intermediate M-state of the sodium-pumping rhodopsin KR2. The H+ displacement of only ∼0.4 Å, which does not easily occur without low-barrier H-bonds, is responsible for the ∼50 nm-shift in the absorption wavelength. This may be a basis of how photoreceptor proteins have evolved to proceed photocycles using abundant protons. The low-barrier H-bond formation is a prerequisite for proton transfer How the absorption wavelength changes as H+ moves is an open question The H+ displacement of ∼0.4 Å leads to the absorption wavelength shift of ∼50 nm The localization of the molecular orbitals plays a key role in the wavelength shift
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5
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Kemp MT, Nichols DA, Zhang X, Defrees K, Na I, Renslo AR, Chen Y. Mutation of the conserved Asp-Asp pair impairs the structure, function, and inhibition of CTX-M Class A β-lactamase. FEBS Lett 2021; 595:2981-2994. [PMID: 34704263 DOI: 10.1002/1873-3468.14215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/07/2021] [Accepted: 10/21/2021] [Indexed: 11/07/2022]
Abstract
The Asp233-Asp246 pair is highly conserved in Class A β-lactamases, which hydrolyze β-lactam antibiotics. Here, we characterize its function using CTX-M-14 β-lactamase. The D233N mutant displayed decreased activity that is substrate-dependent, with reductions in kcat /Km ranging from 20% for nitrocefin to 6-fold for cefotaxime. In comparison, the mutation reduced the binding of a known reversible inhibitor by 10-fold. The mutant structures showed movement of the 213-219 loop and the loss of the Thr216-Thr235 hydrogen bond, which was restored by inhibitor binding. Mutagenesis of Thr216 further highlighted its contribution to CTX-M activity. These results demonstrate the importance of the aspartate pair to CTX-M hydrolysis of substrates with bulky side chains, while suggesting increased protein flexibility as a means to evolve drug resistance.
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Affiliation(s)
- M Trent Kemp
- Department of Molecular Medicine, University of South Florida College of Medicine, Tampa, FL, USA
| | - Derek A Nichols
- Department of Molecular Medicine, University of South Florida College of Medicine, Tampa, FL, USA
| | - Xiujun Zhang
- Department of Molecular Medicine, University of South Florida College of Medicine, Tampa, FL, USA
| | - Kyle Defrees
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Insung Na
- Department of Molecular Medicine, University of South Florida College of Medicine, Tampa, FL, USA
| | - Adam R Renslo
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Yu Chen
- Department of Molecular Medicine, University of South Florida College of Medicine, Tampa, FL, USA
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6
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Koeppe B, Tolstoy PM, Guo J, Denisov GS, Limbach HH. Combined NMR and UV-Vis Spectroscopic Studies of Models for the Hydrogen Bond System in the Active Site of Photoactive Yellow Protein: H-Bond Cooperativity and Medium Effects. J Phys Chem B 2021; 125:5874-5884. [PMID: 34060830 DOI: 10.1021/acs.jpcb.0c09923] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Intramolecular hydrogen bonds in aprotic media were studied by combined (simultaneous) NMR and UV-vis spectroscopy. The species under investigation were anionic and featured single or coupled H-bonds between, for example, carboxylic groups and phenolic oxygen atoms (COO···H···OC)-, among phenolic oxygen atoms (CO···H···OC)-, and hydrogen bond chains between a carboxylic group and two phenolic oxygen atoms (COO···H···(OC)···H···OC)-. The last anion may be regarded as a small molecule model for the hydrogen bond system in the active site of wild-type photoactive yellow protein (PYP) while the others mimic the corresponding H-bonds in site-selective mutants. Proton positions in isolated hydrogen bonds and hydrogen bond chains were assessed by calculations for vacuum conditions and spectroscopically for the two media, CD2Cl2 and the liquefied gas mixture CDClF2/CDF3 at low temperatures. NMR parameters allow for the estimation of time-averaged H-bond geometries, and optical spectra give additional information about geometry distributions. Comparison of the results from the various systems revealed the effects of the formation of hydrogen bond chains and changes of medium conditions on the geometry of individual H-bonds. In particular, the proton in a hydrogen bond to a carboxylic group shifts from the phenolic oxygen atom in the system COO-···H-OC to the carboxylic group in COO-H···(OC)-···H-OC as a result of hydrogen bond formation to the additional phenolic donor. Increase in medium polarity may, however, induce the conversion of a structure of a type COO-H···(OC)-···H-OC to the type COO-···H-(OC)···H-OC. Application of these results obtained from the model systems to PYP suggests that both cooperative effects within the hydrogen bond chain and a low-polarity protein environment are prerequisites for the stabilization of negative charge on the cofactor and hence for the spectral tuning of the photoreceptor.
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Affiliation(s)
- Benjamin Koeppe
- J. Heyrovský Institute of Physical Chemistry, Dolejškova 2155/3, 182 23 Prague 8, Czech Republic
| | - Peter M Tolstoy
- Institute of Chemistry, St. Petersburg State University, Universitetskij pr. 26, 198504 St. Petersburg, Russia
| | - Jing Guo
- Department of Radiology, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Gleb S Denisov
- Department of Physics, St. Petersburg State University, 198504 St. Petersburg, Russian Federation
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7
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Protonation Equilibrium in the Active Site of the Photoactive Yellow Protein. Molecules 2021; 26:molecules26072025. [PMID: 33918211 PMCID: PMC8037372 DOI: 10.3390/molecules26072025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/30/2021] [Accepted: 03/30/2021] [Indexed: 11/17/2022] Open
Abstract
The role and existence of low-barrier hydrogen bonds (LBHBs) in enzymatic and protein activity has been largely debated. An interesting case is that of the photoactive yellow protein (PYP). In this protein, two short HBs adjacent to the chromophore, p-coumaric acid (pCA), have been identified by X-ray and neutron diffraction experiments. However, there is a lack of agreement on the chemical nature of these H-bond interactions. Additionally, no consensus has been reached on the presence of LBHBs in the active site of the protein, despite various experimental and theoretical studies having been carried out to investigate this issue. In this work, we perform a computational study that combines classical and density functional theory (DFT)-based quantum mechanical/molecular mechanical (QM/MM) simulations to shed light onto this controversy. Furthermore, we aim to deepen our understanding of the chemical nature and dynamics of the protons involved in the two short hydrogen bonds that, in the dark state of PYP, connect pCA with the two binding pocket residues (E46 and Y42). Our results support the existence of a strong LBHB between pCA and E46, with the H fully delocalized and shared between both the carboxylic oxygen of E46 and the phenolic oxygen of pCA. Additionally, our findings suggest that the pCA interaction with Y42 can be suitably described as a typical short ionic H-bond of moderate strength that is fully localized on the phenolic oxygen of Y42.
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8
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Yodsin N, Sakagami H, Udagawa T, Ishimoto T, Jungsuttiwong S, Tachikawa M. Metal-doped carbon nanocones as highly efficient catalysts for hydrogen storage: Nuclear quantum effect on hydrogen spillover mechanism. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2021.111486] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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9
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Kumar P, Agarwal PK, Cuneo MJ. On the Case of the Misplaced Hydrogens. Chembiochem 2021; 22:288-297. [PMID: 32706524 PMCID: PMC7952024 DOI: 10.1002/cbic.202000376] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/21/2020] [Indexed: 12/30/2022]
Abstract
Few other elements play a more central role in biology than hydrogen. The interactions, bonding and movement of hydrogen atoms are central to biological catalysis, structure and function. Yet owing to the elusive nature of a single hydrogen atom few experimental and computational techniques can precisely determine its location. This is exemplified in short hydrogen bonds (SHBs) where the location of the hydrogen atom is indicative of the underlying strength of the bonds, which can vary from 1-5 kcal/mol in canonical hydrogen bonds, to an almost covalent nature in single-well hydrogen bonds. Owing to the often-times inferred position of hydrogen, the role of SHBs in biology has remained highly contested and debated. This has also led to discrepancies in computational, biochemical and structural studies of proteins thought to use SHBs in performing chemistry and stabilizing interactions. Herein, we discuss in detail two distinct examples, namely the conserved catalytic triad and the photoreceptor, photoactive yellow protein, where studies of these SHB-containing systems have permitted contextualization of the role these unique hydrogen bonds play in biology.
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Affiliation(s)
- Prashasti Kumar
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pratul K Agarwal
- Arium BioLabs LLC, Knoxville, TN, 37932, USA
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State University, Stillwater, OK 74078, USA
| | - Matthew J Cuneo
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38103, USA
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10
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Lin CY, Boxer SG. Unusual Spectroscopic and Electric Field Sensitivity of Chromophores with Short Hydrogen Bonds: GFP and PYP as Model Systems. J Phys Chem B 2020; 124:9513-9525. [DOI: 10.1021/acs.jpcb.0c07730] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Chi-Yun Lin
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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11
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Wang J. Visualization of H atoms in the X-ray crystal structure of photoactive yellow protein: Does it contain low-barrier hydrogen bonds? Protein Sci 2019; 28:1966-1972. [PMID: 31441173 DOI: 10.1002/pro.3716] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/15/2019] [Accepted: 08/19/2019] [Indexed: 11/07/2022]
Abstract
The hydrogen bond (HB) between 4-hydroxycinnamic acid (HC4) and glutamic acid E46 of photoactive yellow protein is exceptionally strong. In the 0.82-å resolution X-ray structure for this protein (PDB ID: 1NWZ), the OH…O distance is only 2.57 å. The position of the H atom between these two O atoms has not been determined in that structure, and in the absence of that information, it is impossible to determine whether or not this HB is a low-barrier HB (LBHB), as was proposed recently based on neutron structures of this protein (Yamaguchi et al., Proceedings of the National Academy of Sciences of the United States of America, 2009, 106: 440-444). Residual electron density maps computed using the 1NWZ data reveal that this H atom is 0.92 å from the Oε2 atom of E46 and 1.67 å from the O4 ' of HC4, and that the OH…O bond angle is 167°. These observations indicate that E46 is protonated, and HC4 is deprotonated, as was originally suggested, and that the HB in question is not an LBHB.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
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12
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Xu Z, Zhang Q, Shi J, Zhu W. Underestimated Noncovalent Interactions in Protein Data Bank. J Chem Inf Model 2019; 59:3389-3399. [PMID: 31294978 DOI: 10.1021/acs.jcim.9b00258] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Noncovalent interactions (NCIs) play essential roles in the structure and function of biomacromolecules. There are various NCIs, e.g., hydrogen bonds (HBs), cation-π and π-π interactions, and ionic bonds, among which HBs are the most widespread and well-studied. By utilizing the ratio of the observed HBs over pseudo HBs (1.0 Å longer than the HB distance criteria without angle constraints), we demonstrated that HBs in both protein-ligand and protein-protein interfaces are overlooked in structures deposited in PDB. After the QM/MM optimization of 12 protein-ligand complexes, we showed that the overlooked HBs could be recovered. With a systematic search in the PDB, we found that the HB number per residue (NHB/R) in proteins decreases as structural resolution becomes lower, implying that HBs are overlooked even today, regardless of the type of refinement approach used. Similarly, cation-π, π-π, and ionic interactions were found to be significantly lost, manifesting the universal underestimation of various NCIs. Considering the vital role of NCIs, it is important to recover the NCIs to facilitate drug design, to explore protein-protein interaction, and to study protein structure and function.
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Affiliation(s)
- Zhijian Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China
| | - Qian Zhang
- Department of Computer Science and Technology , East China Normal University , Shanghai 200241 , China
| | - Jiye Shi
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China.,Open Studio for Druggability Research of Marine Natural Products , Pilot National Laboratory for Marine Science and Technology (Qingdao) , Qingdao 266237 , China
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13
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Thomson B, Both J, Wu Y, Parrish RM, Martínez TJ, Boxer SG. Perturbation of Short Hydrogen Bonds in Photoactive Yellow Protein via Noncanonical Amino Acid Incorporation. J Phys Chem B 2019; 123:4844-4849. [PMID: 31117606 PMCID: PMC7061054 DOI: 10.1021/acs.jpcb.9b01571] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photoactive yellow protein (PYP) is a small photoreceptor protein that has two unusually short hydrogen bonds between the deprotonated p-coumaric acid chromophore and two amino acids, a tyrosine and a glutamic acid. This has led to considerable debate as to whether the glutamic acid-chromophore hydrogen bond is a low barrier hydrogen bond, with conflicting results in the literature. We have modified the p Ka of the tyrosine by amber suppression and of the chromophore by chemical substitution. X-ray crystal structures of these modified proteins are nearly identical to the wild-type protein, so the heavy atom distance between proton donor and acceptor is maintained, even though these modifications change the relative proton affinity between donor and acceptor. Despite a considerable change in relative proton affinity, the NMR chemical shifts of the hydrogen-bonded protons are only moderately affected. QM/MM calculations were used to explore the protons' potential energy surface and connect the calculated proton position with empirically measured proton chemical shifts. The results are inconsistent with a low barrier hydrogen bond but in all cases are consistent with a localized proton, suggesting an ionic hydrogen bond rather than a low barrier hydrogen bond.
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Affiliation(s)
| | | | | | - Robert M. Parrish
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Todd J. Martínez
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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14
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Mix LT, Carroll EC, Morozov D, Pan J, Gordon WR, Philip A, Fuzell J, Kumauchi M, van Stokkum I, Groenhof G, Hoff WD, Larsen DS. Excitation-Wavelength-Dependent Photocycle Initiation Dynamics Resolve Heterogeneity in the Photoactive Yellow Protein from Halorhodospira halophila. Biochemistry 2018; 57:1733-1747. [PMID: 29465990 DOI: 10.1021/acs.biochem.7b01114] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Photoactive yellow proteins (PYPs) make up a diverse class of blue-light-absorbing bacterial photoreceptors. Electronic excitation of the p-coumaric acid chromophore covalently bound within PYP results in triphasic quenching kinetics; however, the molecular basis of this behavior remains unresolved. Here we explore this question by examining the excitation-wavelength dependence of the photodynamics of the PYP from Halorhodospira halophila via a combined experimental and computational approach. The fluorescence quantum yield, steady-state fluorescence emission maximum, and cryotrapping spectra are demonstrated to depend on excitation wavelength. We also compare the femtosecond photodynamics in PYP at two excitation wavelengths (435 and 475 nm) with a dual-excitation-wavelength-interleaved pump-probe technique. Multicompartment global analysis of these data demonstrates that the excited-state photochemistry of PYP depends subtly, but convincingly, on excitation wavelength with similar kinetics with distinctly different spectral features, including a shifted ground-state beach and altered stimulated emission oscillator strengths and peak positions. Three models involving multiple excited states, vibrationally enhanced barrier crossing, and inhomogeneity are proposed to interpret the observed excitation-wavelength dependence of the data. Conformational heterogeneity was identified as the most probable model, which was supported with molecular mechanics simulations that identified two levels of inhomogeneity involving the orientation of the R52 residue and different hydrogen bonding networks with the p-coumaric acid chromophore. Quantum calculations were used to confirm that these inhomogeneities track to altered spectral properties consistent with the experimental results.
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Affiliation(s)
- L Tyler Mix
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Elizabeth C Carroll
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Dmitry Morozov
- Department of Chemistry and NanoScience Center , University of Jyväskylä , P.O. Box 35, 40014 Jyväskylä , Finland
| | - Jie Pan
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | | | | | - Jack Fuzell
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Masato Kumauchi
- Department of Microbiology and Molecular Genetics , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
| | - Ivo van Stokkum
- Faculty of Sciences , Vrije Universiteit Amsterdam , De Boelelaan 1081 , 1081 HV Amsterdam , The Netherlands
| | - Gerrit Groenhof
- Department of Chemistry and NanoScience Center , University of Jyväskylä , P.O. Box 35, 40014 Jyväskylä , Finland
| | - Wouter D Hoff
- Department of Microbiology and Molecular Genetics , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
| | - Delmar S Larsen
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
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15
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Cao K, Li N, Wang H, Cao X, He J, Zhang B, He QY, Zhang G, Sun X. Two zinc-binding domains in the transporter AdcA from Streptococcus pyogenes facilitate high-affinity binding and fast transport of zinc. J Biol Chem 2018; 293:6075-6089. [PMID: 29491141 DOI: 10.1074/jbc.m117.818997] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 02/25/2018] [Indexed: 11/06/2022] Open
Abstract
Zinc is an essential metal in bacteria. One important bacterial zinc transporter is AdcA, and most bacteria possess AdcA homologs that are single-domain small proteins due to better efficiency of protein biogenesis. However, a double-domain AdcA with two zinc-binding sites is significantly overrepresented in Streptococcus species, many of which are major human pathogens. Using molecular simulation and experimental validations of AdcA from Streptococcus pyogenes, we found here that the two AdcA domains sequentially stabilize the structure upon zinc binding, indicating an organization required for both increased zinc affinity and transfer speed. This structural organization appears to endow Streptococcus species with distinct advantages in zinc-depleted environments, which would not be achieved by each single AdcA domain alone. This enhanced zinc transport mechanism sheds light on the significance of the evolution of the AdcA domain fusion, provides new insights into double-domain transporter proteins with two binding sites for the same ion, and indicates a potential target of antimicrobial drugs against pathogenic Streptococcus species.
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Affiliation(s)
- Kun Cao
- From the Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huang-Pu Avenue West, Guangzhou 510632, China
| | - Nan Li
- From the Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huang-Pu Avenue West, Guangzhou 510632, China
| | - Hongcui Wang
- From the Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huang-Pu Avenue West, Guangzhou 510632, China
| | - Xin Cao
- From the Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huang-Pu Avenue West, Guangzhou 510632, China
| | - Jiaojiao He
- From the Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huang-Pu Avenue West, Guangzhou 510632, China
| | - Bing Zhang
- From the Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huang-Pu Avenue West, Guangzhou 510632, China
| | - Qing-Yu He
- From the Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huang-Pu Avenue West, Guangzhou 510632, China
| | - Gong Zhang
- From the Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huang-Pu Avenue West, Guangzhou 510632, China
| | - Xuesong Sun
- From the Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huang-Pu Avenue West, Guangzhou 510632, China
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16
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Wei Y, Li Q, Scheiner S. The π-Tetrel Bond and its Influence on Hydrogen Bonding and Proton Transfer. Chemphyschem 2018; 19:736-743. [DOI: 10.1002/cphc.201701136] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 11/27/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Yuanxin Wei
- Laboratory of Theoretical and Computational Chemistry and School of Chemistry and Chemical Engineering; Yantai University; Yantai 264005 China), Fax: (+86) 535-6902063
| | - Qingzhong Li
- Laboratory of Theoretical and Computational Chemistry and School of Chemistry and Chemical Engineering; Yantai University; Yantai 264005 China), Fax: (+86) 535-6902063
| | - Steve Scheiner
- Department of Chemistry and Biochemistry; Utah State University; Logan UT 84322-0300 USA
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17
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Sugiura K, Tachikawa M, Udagawa T. Nuclear quantum effect and H/D isotope effect on Cl· + (H2O)n → HCl + OH·(H2O)n−1 (n = 1–3) reactions. RSC Adv 2018; 8:17191-17201. [PMID: 35539263 PMCID: PMC9080416 DOI: 10.1039/c8ra02679c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/03/2018] [Indexed: 11/26/2022] Open
Abstract
Cl· + (H2O)n → HCl + OH·(H2O)n−1 (n = 1–3) reactions are fundamental and important ones in atmospheric chemistry. In this study, we focused on the nuclear quantum effect (NQE) of the hydrogen nucleus on these reactions with the aid of the multicomponent quantum mechanics (MC_QM) method, which can directly take account of NQE of light nuclei. Our study reveals that the NQE of the hydrogen nucleus lowers the activation barriers of the reactions and enhances the catalytic effects of second and third water molecules. In particular, we find that (i) the NQE of the proton removes the activation barrier of the reverse reaction of HCl + OH· → Cl· + H2O, and (ii) the catalytic effect of the third water molecule appears in only our MC_QM calculation. We also analyze the H/D isotope effects on these reactions by using the MC_QM method. Cl·+ (H2O)n → HCl + OH(H2O)n−1 (n = 1–3) reactions have been investigated using multicomponent quantum mechanics method, which can take account of the nuclear quantum effect of proton and deuteron.![]()
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Affiliation(s)
- Keita Sugiura
- Department of Chemistry and Biomolecular Science
- Faculty of Engineering
- Gifu University
- Gifu 501-1193
- Japan
| | - Masanori Tachikawa
- Quantum Chemistry Division
- Graduate School of NanoBioScience
- Yokohama City University
- Yokohama
- Japan
| | - Taro Udagawa
- Department of Chemistry and Biomolecular Science
- Faculty of Engineering
- Gifu University
- Gifu 501-1193
- Japan
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18
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Gozem S, Luk HL, Schapiro I, Olivucci M. Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores. Chem Rev 2017; 117:13502-13565. [DOI: 10.1021/acs.chemrev.7b00177] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Samer Gozem
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Hoi Ling Luk
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
| | - Igor Schapiro
- Fritz
Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Massimo Olivucci
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro
2, 53100 Siena, Italy
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19
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Lin J, Pozharski E, Wilson MA. Short Carboxylic Acid-Carboxylate Hydrogen Bonds Can Have Fully Localized Protons. Biochemistry 2017; 56:391-402. [PMID: 27989121 PMCID: PMC5805389 DOI: 10.1021/acs.biochem.6b00906] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Short hydrogen bonds (H-bonds) have been proposed to play key functional roles in several proteins. The location of the proton in short H-bonds is of central importance, as proton delocalization is a defining feature of low-barrier hydrogen bonds (LBHBs). Experimentally determining proton location in H-bonds is challenging. Here, bond length analysis of atomic (1.15-0.98 Å) resolution X-ray crystal structures of the human protein DJ-1 and its bacterial homologue, YajL, was used to determine the protonation states of H-bonded carboxylic acids. DJ-1 contains a buried, dimer-spanning 2.49 Å H-bond between Glu15 and Asp24 that satisfies standard donor-acceptor distance criteria for a LBHB. Bond length analysis indicates that the proton is localized on Asp24, excluding a LBHB at this location. However, similar analysis of the Escherichia coli homologue YajL shows both residues may be protonated at the H-bonded oxygen atoms, potentially consistent with a LBHB. A Protein Data Bank-wide screen identifies candidate carboxylic acid H-bonds in approximately 14% of proteins, which are typically short [⟨dO-O⟩ = 2.542(2) Å]. Chemically similar H-bonds between hydroxylated residues (Ser/Thr/Tyr) and carboxylates show a trend of lengthening O-O distance with increasing H-bond donor pKa. This trend suggests that conventional electronic effects provide an adequate explanation for short, charge-assisted carboxylic acid-carboxylate H-bonds in proteins, without the need to invoke LBHBs in general. This study demonstrates that bond length analysis of atomic resolution X-ray crystal structures provides a useful experimental test of certain candidate LBHBs.
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Affiliation(s)
- Jiusheng Lin
- Department of Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, NE, 68588
| | - Edwin Pozharski
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics, University of Maryland School of Medicine, Baltimore, MD, 21201,Institute for Bioscience and Biotechnology Research, Rockville, MD 20850,To whom correspondence can be addressed: Edwin Pozharski: or Mark A. Wilson:
| | - Mark A. Wilson
- Department of Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, NE, 68588,To whom correspondence can be addressed: Edwin Pozharski: or Mark A. Wilson:
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