1
|
Maliano MR, Yetming KD, Kalejta RF. Triple lysine and nucleosome-binding motifs of the viral IE19 protein are required for human cytomegalovirus S-phase infections. mBio 2024; 15:e0016224. [PMID: 38695580 PMCID: PMC11237493 DOI: 10.1128/mbio.00162-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 02/29/2024] [Indexed: 06/13/2024] Open
Abstract
Herpesvirus genomes are maintained as extrachromosomal plasmids within the nuclei of infected cells. Some herpesviruses persist within dividing cells, putting the viral genome at risk of being lost to the cytoplasm during mitosis because karyokinesis (nuclear division) requires nuclear envelope breakdown. Oncogenic herpesviruses (and papillomaviruses) avoid genome loss during mitosis by tethering their genomes to cellular chromosomes, thereby ensuring viral genome uptake into newly formed nuclei. These viruses use viral proteins with DNA- and chromatin-binding capabilities to physically link viral and cellular genomes together in a process called tethering. The known viral tethering proteins of human papillomavirus (E2), Epstein-Barr virus (EBNA1), and Kaposi's sarcoma-associated herpesvirus (LANA) each contain two independent domains required for genome tethering, one that binds sequence specifically to the viral genome and another that binds to cellular chromatin. This latter domain is called a chromatin tethering domain (CTD). The human cytomegalovirus UL123 gene encodes a CTD that is required for the virus to productively infect dividing fibroblast cells within the S phase of the cell cycle, presumably by tethering the viral genome to cellular chromosomes during mitosis. The CTD-containing UL123 gene product that supports S-phase infections is the IE19 protein. Here, we define two motifs in IE19 required for S-phase infections: an N-terminal triple lysine motif and a C-terminal nucleosome-binding motif within the CTD.IMPORTANCEThe IE19 protein encoded by human cytomegalovirus (HCMV) is required for S-phase infection of dividing cells, likely because it tethers the viral genome to cellular chromosomes, thereby allowing them to survive mitosis. The mechanism through which IE19 tethers viral genomes to cellular chromosomes is not understood. For human papillomavirus, Epstein-Barr virus, and Kaposi's sarcoma-associated herpesvirus, viral genome tethering is required for persistence (latency) and pathogenesis (oncogenesis). Like these viruses, HCMV also achieves latency, and it modulates the properties of glioblastoma multiforme tumors. Therefore, defining the mechanism through which IE19 tethers viral genomes to cellular chromosomes may help us understand, and ultimately combat or control, HCMV latency and oncomodulation.
Collapse
Affiliation(s)
- Minor R. Maliano
- Institute for Molecular Virology, University of Wisconsin–Madison, Madison, Wisconsin, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Kristen D. Yetming
- Institute for Molecular Virology, University of Wisconsin–Madison, Madison, Wisconsin, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Molecular Biology, Charles River Laboratories, Wayne, Pennsylvania, USA
| | - Robert F. Kalejta
- Institute for Molecular Virology, University of Wisconsin–Madison, Madison, Wisconsin, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, Wisconsin, USA
| |
Collapse
|
2
|
Chakraborty D, Mondal B, Thirumalai D. Brewing COFFEE: A Sequence-Specific Coarse-Grained Energy Function for Simulations of DNA-Protein Complexes. J Chem Theory Comput 2024; 20:1398-1413. [PMID: 38241144 DOI: 10.1021/acs.jctc.3c00833] [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: 01/21/2024]
Abstract
DNA-protein interactions are pervasive in a number of biophysical processes ranging from transcription and gene expression to chromosome folding. To describe the structural and dynamic properties underlying these processes accurately, it is important to create transferable computational models. Toward this end, we introduce Coarse-grained Force Field for Energy Estimation, COFFEE, a robust framework for simulating DNA-protein complexes. To brew COFFEE, we integrated the energy function in the self-organized polymer model with side-chains for proteins and the three interaction site model for DNA in a modular fashion, without recalibrating any of the parameters in the original force-fields. A unique feature of COFFEE is that it describes sequence-specific DNA-protein interactions using a statistical potential (SP) derived from a data set of high-resolution crystal structures. The only parameter in COFFEE is the strength (λDNAPRO) of the DNA-protein contact potential. For an optimal choice of λDNAPRO, the crystallographic B-factors for DNA-protein complexes with varying sizes and topologies are quantitatively reproduced. Without any further readjustments to the force-field parameters, COFFEE predicts scattering profiles that are in quantitative agreement with small-angle X-ray scattering experiments, as well as chemical shifts that are consistent with NMR. We also show that COFFEE accurately describes the salt-induced unraveling of nucleosomes. Strikingly, our nucleosome simulations explain the destabilization effect of ARG to LYS mutations, which do not alter the balance of electrostatic interactions but affect chemical interactions in subtle ways. The range of applications attests to the transferability of COFFEE, and we anticipate that it would be a promising framework for simulating DNA-protein complexes at the molecular length-scale.
Collapse
Affiliation(s)
- Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, 105 E 24th Street, Stop A5300, Austin 78712, Texas, United States
| | - Balaka Mondal
- Department of Chemistry, The University of Texas at Austin, 105 E 24th Street, Stop A5300, Austin 78712, Texas, United States
| | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin, 105 E 24th Street, Stop A5300, Austin 78712, Texas, United States
- Department of Physics, The University of Texas at Austin, 2515 Speedway, Austin 78712, Texas, United States
| |
Collapse
|
3
|
Chakraborty D, Mondal B, Thirumalai D. Brewing COFFEE: A sequence-specific coarse-grained energy function for simulations of DNA-protein complexes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.544064. [PMID: 37333386 PMCID: PMC10274755 DOI: 10.1101/2023.06.07.544064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
DNA-protein interactions are pervasive in a number of biophysical processes ranging from transcription, gene expression, to chromosome folding. To describe the structural and dynamic properties underlying these processes accurately, it is important to create transferable computational models. Toward this end, we introduce Coarse grained force field for energy estimation, COFFEE, a robust framework for simulating DNA-protein complexes. To brew COFFEE, we integrated the energy function in the Self-Organized Polymer model with Side Chains for proteins and the Three Interaction Site model for DNA in a modular fashion, without re-calibrating any of the parameters in the original force-fields. A unique feature of COFFEE is that it describes sequence-specific DNA-protein interactions using a statistical potential (SP) derived from a dataset of high-resolution crystal structures. The only parameter in COFFEE is the strength (λ D N A P R O ) of the DNA-protein contact potential. For an optimal choice of λ D N A P R O , the crystallographic B-factors for DNA-protein complexes, with varying sizes and topologies, are quantitatively reproduced. Without any further readjustments to the force-field parameters, COFFEE predicts the scattering profiles that are in quantitative agreement with SAXS experiments as well as chemical shifts that are consistent with NMR. We also show that COFFEE accurately describes the salt-induced unraveling of nucleosomes. Strikingly, our nucleosome simulations explain the destabilization effect of ARG to LYS mutations, which does not alter the balance of electrostatic interactions, but affects chemical interactions in subtle ways. The range of applications attests to the transferability of COFFEE, and we anticipate that it would be a promising framework for simulating DNA-protein complexes at the molecular length-scale.
Collapse
Affiliation(s)
- Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Stop A5300, Austin TX 78712, USA
| | - Balaka Mondal
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Stop A5300, Austin TX 78712, USA
| | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Stop A5300, Austin TX 78712, USA
- Department of Physics, The University of Texas at Austin, 2515 Speedway,Austin TX 78712, USA
| |
Collapse
|
4
|
Remodeling of algal photosystem I through phosphorylation. Biosci Rep 2023; 43:232211. [PMID: 36477263 PMCID: PMC9874419 DOI: 10.1042/bsr20220369] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/29/2022] [Accepted: 12/07/2022] [Indexed: 12/12/2022] Open
Abstract
Photosystem I (PSI) with its associated light-harvesting system is the most important generator of reducing power in photosynthesis. The PSI core complex is highly conserved, whereas peripheral subunits as well as light-harvesting proteins (LHCI) reveal a dynamic plasticity. Moreover, in green alga, PSI-LHCI complexes are found as monomers, dimers, and state transition complexes, where two LHCII trimers are associated. Herein, we show light-dependent phosphorylation of PSI subunits PsaG and PsaH as well as Lhca6. Potential consequences of the dynamic phosphorylation of PsaG and PsaH are structurally analyzed and discussed in regard to the formation of the monomeric, dimeric, and LHCII-associated PSI-LHCI complexes.
Collapse
|
5
|
Cardoso S, Sousa F, Pessoa Filho PA, R Azzoni A. Understanding the adsorption of plasmid DNA and RNA molecules onto arginine-agarose chromatographic resin. Mol Biol Rep 2022; 49:3893-3901. [PMID: 35178684 PMCID: PMC8853897 DOI: 10.1007/s11033-022-07239-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 02/08/2022] [Indexed: 11/29/2022]
Abstract
Background The production of nucleic acids (plasmid DNA or mRNA) in response to the development of new advanced vaccine platforms has greatly increased recently, mostly resulting from the pandemic situation. Due to the intended pharmaceutical use, nucleic acids preparations must fulfill all the required specifications in terms of purity and quality. Chromatography is a standard operation used to isolate these molecules from impurities, playing a central role in the manufacturing processes. However, the mechanism of nucleic acid adsorption in chromatographic resins is poorly understood, often leading to low adsorption capacities and a lack of specificity. Methods and results Here we investigated the adsorption of plasmid DNA and RNA molecules onto arginine-agarose, a resin with potential for large-scale application. Equilibrium batch studies were performed through pre-purified samples, using arginine-based ligands by varying the adsorption conditions in the pH value range from 6.0 to 9.0. Langmuir and Freundlich isotherm models were used to describe the adsorption equilibrium. The best fit for both nucleic acids was achieved using the Freundlich model. The correct choice of pH showed critical for controlling the efficacy of arginine-nucleic acid interaction, due to its influence on the nucleic acid structures. This type of analysis is necessary for the improvement of the selectivity and binding capacities of the resins used for plasmid DNA or mRNA purification. Conclusions The results presented here indicate that adsorption conditions can be tuned to enhance separation between pDNA and RNA, an important feature in the purification of nucleic acids for vaccine production.
Collapse
Affiliation(s)
- Sara Cardoso
- Departamento de Engenharia Química, Escola Politécnica da Universidade de São Paulo, Av. Prof. Luciano Gualberto, Trav. 3, Nº 380, São Paulo, SP, CEP 05508-900, Brazil
| | - Fani Sousa
- CICS-UBI - Centro de Investigação de Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506, Covilhã, Portugal
| | - Pedro A Pessoa Filho
- Departamento de Engenharia Química, Escola Politécnica da Universidade de São Paulo, Av. Prof. Luciano Gualberto, Trav. 3, Nº 380, São Paulo, SP, CEP 05508-900, Brazil
| | - Adriano R Azzoni
- Departamento de Engenharia Química, Escola Politécnica da Universidade de São Paulo, Av. Prof. Luciano Gualberto, Trav. 3, Nº 380, São Paulo, SP, CEP 05508-900, Brazil.
| |
Collapse
|
6
|
A Germline-Encoded Structural Arginine Trap Underlies the Anti-DNA Reactivity of a Murine V Gene Segment. Int J Mol Sci 2021; 22:ijms22094541. [PMID: 33926148 PMCID: PMC8123574 DOI: 10.3390/ijms22094541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 11/30/2022] Open
Abstract
Autoimmunity may have its origins of early repertoire selection in developmental B cells. Such a primary repertoire is probably shaped by selecting B cells that can efficiently perform productive signaling, stimulated by self-antigens in the bone marrow, such as DNA. In support of that idea, we previously found a V segment from VH10 family that can form antibodies that bind to DNA independent of CDR3 usage. In this paper we designed four antibody fragments in a novel single-chain pre-BCR (scpre-BCR) format containing germinal V gene segments from families known to bind DNA (VH10) or not (VH4) connected to a murine surrogate light chain (SLC), lacking the highly charged unique region (UR), by a hydrophilic peptide linker. We also tested the influence of CDR2 on DNA reactivity by shuffling the CDR2 loop. The scpre-BCRs were expressed in bacteria. VH10 bearing scpre-BCR could bind DNA, while scpre-BCR carrying the VH4 segment did not. The CDR2 loop shuffling hampered VH10 reactivity while displaying a gain-of-function in the nonbinding VH4 germline. We modeled the binding sites demonstrating the conservation of a positivity charged pocket in the VH10 CDR2 as the possible cross-reactive structural element. We presented evidence of DNA reactivity hardwired in a V gene, suggesting a structural mechanism for innate autoreactivity. Therefore, while autoreactivity to DNA can lead to autoimmunity, efficiently signaling for B cell development is likely a trade-off mechanism leading to the selection of potentially autoreactive repertoires.
Collapse
|
7
|
Lenton S, Hervø-Hansen S, Popov AM, Tully MD, Lund M, Skepö M. Impact of Arginine-Phosphate Interactions on the Reentrant Condensation of Disordered Proteins. Biomacromolecules 2021; 22:1532-1544. [PMID: 33730849 PMCID: PMC8045028 DOI: 10.1021/acs.biomac.0c01765] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Re-entrant condensation results in the formation of a condensed protein regime between two critical ion concentrations. The process is driven by neutralization and inversion of the protein charge by oppositely charged ions. Re-entrant condensation of cationic proteins by the polyvalent anions, pyrophosphate and tripolyphosphate, has previously been observed, but not for citrate, which has similar charge and size compared to the polyphosphates. Therefore, besides electrostatic interactions, other specific interactions between the polyphosphate ions and proteins must contribute. Here, we show that additional attractive interactions between arginine and tripolyphosphate determine the re-entrant condensation and decondensation boundaries of the cationic, intrinsically disordered saliva protein, histatin 5. Furthermore, we show by small-angle X-ray scattering (SAXS) that polyvalent anions cause compaction of histatin 5, as would be expected based solely on electrostatic interactions. Hence, we conclude that arginine-phosphate-specific interactions not only regulate solution properties but also influence the conformational ensemble of histatin 5, which is shown to vary with the number of arginine residues. Together, the results presented here provide further insight into an organizational mechanism that can be used to tune protein interactions in solution of both naturally occurring and synthetic proteins.
Collapse
Affiliation(s)
- Samuel Lenton
- Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Stefan Hervø-Hansen
- Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Anton M Popov
- BM29 BIOSAXS, European Synchroton Radiation Facility, 71 avenue des Martyrs, Grenoble, Isère 38043, France
| | - Mark D Tully
- BM29 BIOSAXS, European Synchroton Radiation Facility, 71 avenue des Martyrs, Grenoble, Isère 38043, France
| | - Mikael Lund
- Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden.,LINXS-Lund Institute of Advanced Neutron and X-ray Science, Scheelevägen 19, SE-223 70 Lund, Sweden
| | - Marie Skepö
- Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden.,LINXS-Lund Institute of Advanced Neutron and X-ray Science, Scheelevägen 19, SE-223 70 Lund, Sweden
| |
Collapse
|
8
|
Tissue-Specific Delivery of CRISPR Therapeutics: Strategies and Mechanisms of Non-Viral Vectors. Int J Mol Sci 2020; 21:ijms21197353. [PMID: 33027946 PMCID: PMC7583726 DOI: 10.3390/ijms21197353] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 09/24/2020] [Accepted: 09/27/2020] [Indexed: 02/07/2023] Open
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) genome editing system has been the focus of intense research in the last decade due to its superior ability to desirably target and edit DNA sequences. The applicability of the CRISPR-Cas system to in vivo genome editing has acquired substantial credit for a future in vivo gene-based therapeutic. Challenges such as targeting the wrong tissue, undesirable genetic mutations, or immunogenic responses, need to be tackled before CRISPR-Cas systems can be translated for clinical use. Hence, there is an evident gap in the field for a strategy to enhance the specificity of delivery of CRISPR-Cas gene editing systems for in vivo applications. Current approaches using viral vectors do not address these main challenges and, therefore, strategies to develop non-viral delivery systems are being explored. Peptide-based systems represent an attractive approach to developing gene-based therapeutics due to their specificity of targeting, scale-up potential, lack of an immunogenic response and resistance to proteolysis. In this review, we discuss the most recent efforts towards novel non-viral delivery systems, focusing on strategies and mechanisms of peptide-based delivery systems, that can specifically deliver CRISPR components to different cell types for therapeutic and research purposes.
Collapse
|
9
|
Nucleosome movement analysis based on second-order information entropy and density functional theory. Biophys Chem 2020; 265:106436. [PMID: 32731086 DOI: 10.1016/j.bpc.2020.106436] [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: 04/15/2020] [Revised: 07/14/2020] [Accepted: 07/14/2020] [Indexed: 10/23/2022]
Abstract
Dynamics of +1 and -1 nucleosomes near TSS of yeast chromosome 2 were analyzed by using second-order information entropy and density functional theory method. Second-order information entropy can measure the interaction intensity between nucleosome sequences and nucleosome histones based on the intensity of base association. In addition, density functional theory method can be used to obtain the global interaction intensity between nucleosome sequences and nucleosome histones based on energy state size and active or non-active state of binucleoside pairs. Our results showed asymmetry of interaction intensity on both sides of the nucleosome central site, and that +1 nucleosomes tend to move toward the 5'-end and -1 nucleosomes tend to move toward the 3'-end. Under the dynamic balance of nucleosome movement, in roder to shut down gene transcription, +1 and -1 nucleosomes will cover TSS. If the dynamic balance is destroyed, +1 and -1 nucleosomes stay away from each other to expose TSS to restart gene transcription. The movement trend of +1 and -1 nucleosomes coincides with the biological mechanism of gene transcription and non-transcription, and the nucleosome sequences contain the dynamic information of nucleosome movement, which provides effective technical support for the study of gene transcription regulation mechanism.
Collapse
|
10
|
Bozorgmehr JH. The origin of chromosomal histones in a 30S ribosomal protein. Gene 2020; 726:144155. [PMID: 31629821 DOI: 10.1016/j.gene.2019.144155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 10/01/2019] [Accepted: 10/03/2019] [Indexed: 11/18/2022]
Abstract
Histones are genes that regulate chromatin structure. They are present in both eukaryotes and archaea, and form nucleosomes with DNA, but their exact evolutionary origins have hitherto remained a mystery. A longstanding hypothesis is that they have precursors in ribosomal proteins with whom they share much in common in terms of size and chemistry. By examining the proteome of the Asgard archaeon, Lokiarchaeum, the most conserved of all the histones, H4, is found to plausibly be homologous with one of its 30S ribosomal proteins, RPS6. This is based on both sequence identity and statistical analysis. The N-terminal tail, containing key sites involved in post-translational modifications, is notably present in the precursor gene. Although other archaeal groups possess similar homologs, these are not as close to H4 as the one found in Lokiarchaeum. The other core histones, H2A, H2B and H3, appear to have also evolved from the same ribosomal protein. Parts of H4 are also similar to another ribosomal protein, namely RPS15, suggesting that the ancestral precursor could have resembled both. Eukaryotic histones, in addition, appear to have an independent origin to that of their archaeal counterparts that evolved from similar, but still different, 30S subunit proteins, some of which are much more like histones in terms of their physical structure. The nucleosome may, therefore, be not only of archaeal but also of ribosomal origin.
Collapse
|
11
|
The influence of monovalent and divalent metal cations on the stability of the DNA-protein interaction in the nucleosome core particle. ADVANCES IN QUANTUM CHEMISTRY 2020. [DOI: 10.1016/bs.aiq.2020.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
12
|
Huang SY, Qian M, Pierre VC. A Combination of Factors: Tuning the Affinity of Europium Receptors for Phosphate in Water. Inorg Chem 2019; 58:16087-16099. [PMID: 31738520 DOI: 10.1021/acs.inorgchem.9b02650] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Although recognition of hard anions by hard metal ions is primarily achieved via direct coordination, electrostatic and hydrogen-bonding interactions also play essential roles in tuning the affinity of such supramolecular receptors for their target. In the case of EuIII hydroxypyridinone-based complexes, the addition of a single charged group (-NH3+, -CO2-, or -SO3-) or neutral hydrogen-bonding moiety (-OH) peripheral to the open coordination site substantially affects the affinity of the metal receptor for phosphate in water at neutral pH. A single primary ammonium increases the first association constant for phosphate in neutral water by 2 orders of magnitude over its neutral analogue. The addition of a peripheral alcohol group also increases the affinity of the receptor but to a lesser degree (21-fold). On the other hand, negatively charged complexes bearing either a carboxylate or sulfate moiety have negligible affinity for phosphate. Interestingly, the peripheral group also influences the stoichiometry of the lanthanide receptor for phosphate. While the complex bearing a -NH3+ group binds phosphate in a 1:2 ratio, those with -OH and H (control) both form 1:3 complexes. Although the positively charged EuIII-Lys-HOPO has the highest Ka1 for phosphate, a greater increase in luminescence intensity (36-fold) is observed with the neutral EuIII-Ser-HOPO complex. Notably, whereas the affinity of the EuIII complexes for phosphate is substantially influenced by the presence of a single charged group or hydrogen-bond donor, their selectivity for phosphate over competing anions remains unaffected by the addition of the peripheral groups.
Collapse
Affiliation(s)
- Sheng-Yin Huang
- Department of Chemistry , University of Minnesota , Pleasant St. SE , Minneapolis , Minnesota 55455 , United States
| | - Michelle Qian
- Department of Chemistry , University of Minnesota , Pleasant St. SE , Minneapolis , Minnesota 55455 , United States
| | - Valerie C Pierre
- Department of Chemistry , University of Minnesota , Pleasant St. SE , Minneapolis , Minnesota 55455 , United States
| |
Collapse
|
13
|
Bhayani JA, Hill BL, Sharma A, Iglesias AA, Olsen KW, Ballicora MA. Mapping of a Regulatory Site of the Escherichia coli ADP-Glucose Pyrophosphorylase. Front Mol Biosci 2019; 6:89. [PMID: 31608288 PMCID: PMC6773804 DOI: 10.3389/fmolb.2019.00089] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 09/06/2019] [Indexed: 11/13/2022] Open
Abstract
The enzyme ADP-glucose pyrophosphorylase (ADP-Glc PPase) controls the biosynthesis of glycogen in bacteria and starch in plants. It is regulated by various activators in different organisms according to their metabolic characteristics. In Escherichia coli, the major allosteric activator is fructose 1,6-bisphosphate (FBP). Other potent activator analogs include 1,6-hexanediol bisphosphate (HBP) and pyridoxal 5'-phosphate (PLP). Recently, a crystal structure with FBP bound was reported (PDB ID: 5L6S). However, it is possible that the FBP site found is not directly responsible for the activation of the enzyme. We hypothesized FBP activates by binding one of its phosphate groups to another site ("P1") in which a sulfate molecule was observed. In the E. coli enzyme, Arg40, Arg52, and Arg386 are part of this "P1" pocket and tightly complex this sulfate, which is also present in the crystal structures of ADP-Glc PPases from Agrobacterium tumefaciens and Solanum tuberosum. To test this hypothesis, we modeled alternative binding conformations of FBP, HBP, and PLP into "P1." In addition, we performed a scanning mutagenesis of Arg residues near potential phosphate binding sites ("P1," "P2," "P3"). We found that Arg40 and Arg52 are essential for FBP and PLP binding and activation. In addition, mutation of Arg386 to Ala decreased the apparent affinity for the activators more than 35-fold. We propose that the activator binds at this "P1" pocket, as well as "P2." Arg40 and Arg52 are highly conserved residues and they may be a common feature to complex the phosphate moiety of different sugar phosphate activators in the ADP-Glc PPase family.
Collapse
Affiliation(s)
- Jaina A. Bhayani
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Benjamin L. Hill
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Anisha Sharma
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Alberto A. Iglesias
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (UNL-CONICET), CCT CONICET, Santa Fe, Argentina
| | - Kenneth W. Olsen
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Miguel A. Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| |
Collapse
|
14
|
Avilés-Moreno JR, Berden G, Oomens J, Martínez-Haya B. Insights into the Recognition of Phosphate Groups by Peptidic Arginine from Action Spectroscopy and Quantum Chemical Computations. J Phys Chem B 2019; 123:7528-7535. [PMID: 31449420 DOI: 10.1021/acs.jpcb.9b06201] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The side group of the amino acid arginine is typically in its guanidinium protonated form under physiological conditions and participates in a broad range of ligand binding and charge transfer processes of proteins. The recognition of phosphate moieties by guanidinium plays a particularly key role in the interactions of proteins with ATP and nucleic acids. Moreover, it has been recently identified as the driving force for the inhibition of kinase phosphorilation activity by guanidinium derivatives devised as potential anticancer agents. We report on a fundamental investigation of the interactions and coordination arrangements formed by guanidinium with phosphoric, phosphate, and pyrophosphate groups. Action vibrational spectroscopy and ab initio quantum chemical computations are employed to characterize the conformations of benchmark positively charged complexes isolated in an ion trap. The multidentate structure of guanidinium and of the phosphate groups gives rise to a rich conformational landscape with a particular relevance of tweezer-like configurations, where phosphate is effectively trapped by two guanidinium cations. The pyrophosphate complex incorporates a Na+ cation, which serves to compare the interactions associated with the localized versus diffuse charge distributions of the alkali cation and guanidinium, respectively, within a common supramolecular framework.
Collapse
Affiliation(s)
- Juan Ramón Avilés-Moreno
- Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - Bruno Martínez-Haya
- Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, 41013 Seville, Spain
| |
Collapse
|
15
|
Elbahnsi A, Retureau R, Baaden M, Hartmann B, Oguey C. Holding the Nucleosome Together: A Quantitative Description of the DNA–Histone Interface in Solution. J Chem Theory Comput 2018; 14:1045-1058. [DOI: 10.1021/acs.jctc.7b00936] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Ahmad Elbahnsi
- LBPA,
UMR 8113, ENS Paris-Saclay - CNRS, 61 avenue du Président Wilson, 94235 cedex Cachan, France
- LPTM,
UMR 8089, CNRS, Université de Cergy-Pontoise, 2 avenue Adolphe Chauvin, 95302 Cergy-Pontoise, France
| | - Romain Retureau
- LBPA,
UMR 8113, ENS Paris-Saclay - CNRS, 61 avenue du Président Wilson, 94235 cedex Cachan, France
| | - Marc Baaden
- Laboratoire
de Biochimie Théorique, CNRS, UPR9080, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Brigitte Hartmann
- LBPA,
UMR 8113, ENS Paris-Saclay - CNRS, 61 avenue du Président Wilson, 94235 cedex Cachan, France
| | - Christophe Oguey
- LPTM,
UMR 8089, CNRS, Université de Cergy-Pontoise, 2 avenue Adolphe Chauvin, 95302 Cergy-Pontoise, France
| |
Collapse
|
16
|
Parcon PA, Balasubramaniam M, Ayyadevara S, Jones RA, Liu L, Shmookler Reis RJ, Barger SW, Mrak RE, Griffin WST. Apolipoprotein E4 inhibits autophagy gene products through direct, specific binding to CLEAR motifs. Alzheimers Dement 2017; 14:230-242. [PMID: 28945989 PMCID: PMC6613789 DOI: 10.1016/j.jalz.2017.07.754] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Revised: 05/11/2017] [Accepted: 07/05/2017] [Indexed: 02/08/2023]
Abstract
Introduction: Alzheimer apolipoprotein E (APOE) ε4/ε4 carriers have earlier disease onset and more protein aggregates than patients with other APOE genotypes. Autophagy opposes aggregation, and important autophagy genes are coordinately regulated by transcription factor EB (TFEB) binding to “coordinated lysosomal expression and regulation” (CLEAR) DNA motifs. Methods: Autophagic gene expression was assessed in brains of controls and Alzheimer’s disease (AD) patients parsed by APOE genotype and in a glioblastoma cell line expressing either apoE3 or apoE4. Computational modeling assessed interactions between apoE and mutated apoE with CLEAR or modified DNA. Results: Three TFEB-regulated mRNA transcripts—SQSTM, MAP1LC3B, and LAMP2—were lower in AD ε4/ε4 than in AD ε3/ε3 brains. Computational modeling predicted avid specific binding of apoE4 to CLEAR motifs. ApoE was found in cellular nuclei, and in vitro binding assays suggest competition between apoE4 and TFEB at CLEAR sites. Conclusion: ApoE4-CLEAR interactions may account for suppressed autophagy in APOE ε4/ε4 carriers and, in this way, contribute to earlier AD onset.
Collapse
Affiliation(s)
- Paul A Parcon
- Donald W. Reynolds Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Meenakshisundaram Balasubramaniam
- Donald W. Reynolds Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR, USA; Geriatric Research Education and Clinical Center, Central Arkansas Veterans Healthcare System, Little Rock, AR, USA
| | - Srinivas Ayyadevara
- Donald W. Reynolds Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR, USA; Geriatric Research Education and Clinical Center, Central Arkansas Veterans Healthcare System, Little Rock, AR, USA
| | - Richard A Jones
- Donald W. Reynolds Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR, USA; Geriatric Research Education and Clinical Center, Central Arkansas Veterans Healthcare System, Little Rock, AR, USA
| | - Ling Liu
- Donald W. Reynolds Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Robert J Shmookler Reis
- Donald W. Reynolds Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR, USA; Geriatric Research Education and Clinical Center, Central Arkansas Veterans Healthcare System, Little Rock, AR, USA
| | - Steven W Barger
- Donald W. Reynolds Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR, USA; Geriatric Research Education and Clinical Center, Central Arkansas Veterans Healthcare System, Little Rock, AR, USA
| | - Robert E Mrak
- Department of Pathology, University of Toledo Health Sciences Campus, Toledo, OH, USA
| | - W Sue T Griffin
- Donald W. Reynolds Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR, USA; Geriatric Research Education and Clinical Center, Central Arkansas Veterans Healthcare System, Little Rock, AR, USA.
| |
Collapse
|
17
|
A theoretical model of the interaction between phosphates in the ATP molecule and guanidinium systems. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-2012-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
18
|
Kalel R, Mora AK, Ghosh R, Dhavale DD, Palit DK, Nath S. Interaction of a Julolidine-Based Neutral Ultrafast Molecular Rotor with Natural DNA: Spectroscopic and Molecular Docking Studies. J Phys Chem B 2016; 120:9843-53. [DOI: 10.1021/acs.jpcb.6b04811] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rahul Kalel
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
- Department
of Chemistry, Savitribai Phule Pune University, Pune 411007, India
| | - Aruna K. Mora
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Rajib Ghosh
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Dilip D. Dhavale
- Department
of Chemistry, Savitribai Phule Pune University, Pune 411007, India
| | - Dipak K. Palit
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Sukhendu Nath
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| |
Collapse
|