1
|
Jiang Y, Chiu TP, Mitra R, Rohs R. Probing the role of the protonation state of a minor groove-linker histidine in Exd-Hox-DNA binding. Biophys J 2024; 123:248-259. [PMID: 38130056 PMCID: PMC10808038 DOI: 10.1016/j.bpj.2023.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 09/22/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023] Open
Abstract
DNA recognition and targeting by transcription factors (TFs) through specific binding are fundamental in biological processes. Furthermore, the histidine protonation state at the TF-DNA binding interface can significantly influence the binding mechanism of TF-DNA complexes. Nevertheless, the role of histidine in TF-DNA complexes remains underexplored. Here, we employed all-atom molecular dynamics simulations using AlphaFold2-modeled complexes based on previously solved co-crystal structures to probe the role of the His-12 residue in the Extradenticle (Exd)-Sex combs reduced (Scr)-DNA complex when binding to Scr and Ultrabithorax (Ubx) target sites. Our results demonstrate that the protonation state of histidine notably affected the DNA minor-groove width profile and binding free energy. Examining flanking sequences of various binding affinities derived from SELEX-seq experiments, we analyzed the relationship between binding affinity and specificity. We uncovered how histidine protonation leads to increased binding affinity but can lower specificity. Our findings provide new mechanistic insights into the role of histidine in modulating TF-DNA binding.
Collapse
Affiliation(s)
- Yibei Jiang
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California
| | - Tsu-Pei Chiu
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California
| | - Raktim Mitra
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California
| | - Remo Rohs
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California; Department of Chemistry, University of Southern California, Los Angeles, California; Department of Physics and Astronomy, University of Southern California, Los Angeles, California; Thomas Lord Department of Computer Science, University of Southern California, Los Angeles, California.
| |
Collapse
|
2
|
Ballin JD, Prevas JP, Ross CR, Toth EA, Wilson GM, Record MT. Contributions of the histidine side chain and the N-terminal alpha-amino group to the binding thermodynamics of oligopeptides to nucleic acids as a function of pH. Biochemistry 2010; 49:2018-30. [PMID: 20108951 DOI: 10.1021/bi902027z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Interactions of histidine with nucleic acid phosphates and histidine pK(a) shifts make important contributions to many protein-nucleic acid binding processes. To characterize these phenomena in simplified systems, we quantified binding of a histidine-containing model peptide HWKK ((+)NH(3)-His-Trp-Lys-Lys-NH(2)) and its lysine analogue KWKK ((+)NH(3)-Lys-Trp-Lys-Lys-NH(2)) to a single-stranded RNA model, polyuridylate (polyU), by changes in tryptophan fluorescence as a function of salt concentration and pH. For both HWKK and KWKK, equilibrium binding constants, K(obs), and magnitudes of log-log salt derivatives, SK(obs) identical with (partial differential logK(obs)/partial differential log[Na(+)]), decreased with increasing pH in the manner expected for a titration curve model in which deprotonation of the histidine and alpha-amino groups weakens binding and reduces its salt-dependence. Fully protonated HWKK and KWKK exhibit the same K(obs) and SK(obs) within uncertainty, and these SK(obs) values are consistent with limiting-law polyelectrolyte theory for +4 cationic oligopeptides binding to single-stranded nucleic acids. The pH-dependence of HWKK binding to polyU provides no evidence for pK(a) shifts nor any requirement for histidine protonation, in stark contrast to the thermodynamics of coupled protonation often seen for these cationic residues in the context of native protein structure where histidine protonation satisfies specific interactions (e.g., salt-bridge formation) within highly complementary binding interfaces. The absence of pK(a) shifts in our studies indicates that additional Coulombic interactions across the nonspecific-binding interface between RNA and protonated histidine or the alpha-amino group are not sufficient to promote proton uptake for these oligopeptides. We present our findings in the context of hydration models for specific vs nonspecific nucleic acid binding.
Collapse
Affiliation(s)
- Jeff D Ballin
- Department of Biochemistry and Molecular Biology and Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.
| | | | | | | | | | | |
Collapse
|
3
|
Eliseo T, Sánchez IE, Nadra AD, Dellarole M, Paci M, de Prat Gay G, Cicero DO. Indirect DNA Readout on the Protein Side: Coupling between Histidine Protonation, Global Structural Cooperativity, Dynamics, and DNA Binding of the Human Papillomavirus Type 16 E2C Domain. J Mol Biol 2009; 388:327-44. [PMID: 19285507 DOI: 10.1016/j.jmb.2009.03.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Revised: 03/06/2009] [Accepted: 03/06/2009] [Indexed: 11/26/2022]
|
4
|
Fradet-Turcotte A, Vincent C, Joubert S, Bullock PA, Archambault J. Quantitative analysis of the binding of simian virus 40 large T antigen to DNA. J Virol 2007; 81:9162-74. [PMID: 17596312 PMCID: PMC1951407 DOI: 10.1128/jvi.00384-07] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
SV40 large T antigen (T-ag) is a multifunctional protein that successively binds to 5'-GAGGC-3' sequences in the viral origin of replication, melts the origin, unwinds DNA ahead of the replication fork, and interacts with host DNA replication factors to promote replication of the simian virus 40 genome. The transition of T-ag from a sequence-specific binding protein to a nonspecific helicase involves its assembly into a double hexamer whose formation is likely dictated by the propensity of T-ag to oligomerize and its relative affinities for the origin as well as for nonspecific double- and single-stranded DNA. In this study, we used a sensitive assay based on fluorescence anisotropy to measure the affinities of wild-type and mutant forms of the T-ag origin-binding domain (OBD), and of a larger fragment containing the N-terminal domain (N260), for different DNA substrates. We report that the N-terminal domain does not contribute to binding affinity but reduces the propensity of the OBD to self-associate. We found that the OBD binds with different affinities to its four sites in the origin and determined a consensus binding site by systematic mutagenesis of the 5'-GAGGC-3' sequence and of the residue downstream of it, which also contributes to affinity. Interestingly, the OBD also binds to single-stranded DNA with an approximately 10-fold higher affinity than to nonspecific duplex DNA and in a mutually exclusive manner. Finally, we provide evidence that the sequence specificity of full-length T-ag is lower than that of the OBD. These results provide a quantitative basis onto which to anchor our understanding of the interaction of T-ag with the origin and its assembly into a double hexamer.
Collapse
Affiliation(s)
- Amélie Fradet-Turcotte
- Laboratory of Molecular Virology, Institut de Recherches Cliniques de Montréal (IRCM), 110 Pine Avenue West, Montreal, Quebec, Canada
| | | | | | | | | |
Collapse
|
5
|
Meinke G, Phelan P, Moine S, Bochkareva E, Bochkarev A, Bullock PA, Bohm A. The crystal structure of the SV40 T-antigen origin binding domain in complex with DNA. PLoS Biol 2007; 5:e23. [PMID: 17253903 PMCID: PMC1779811 DOI: 10.1371/journal.pbio.0050023] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2006] [Accepted: 11/17/2006] [Indexed: 01/07/2023] Open
Abstract
DNA replication is initiated upon binding of "initiators" to origins of replication. In simian virus 40 (SV40), the core origin contains four pentanucleotide binding sites organized as pairs of inverted repeats. Here we describe the crystal structures of the origin binding domain (obd) of the SV40 large T-antigen (T-ag) both with and without a subfragment of origin-containing DNA. In the co-structure, two T-ag obds are oriented in a head-to-head fashion on the same face of the DNA, and each T-ag obd engages the major groove. Although the obds are very close to each other when bound to this DNA target, they do not contact one another. These data provide a high-resolution structural model that explains site-specific binding to the origin and suggests how these interactions help direct the oligomerization events that culminate in assembly of the helicase-active dodecameric complex of T-ag.
Collapse
Affiliation(s)
- Gretchen Meinke
- Department of Biochemistry, School of Medicine, and the Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
| | - Paul Phelan
- Department of Biochemistry, School of Medicine, and the Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
| | - Stephanie Moine
- Department of Biochemistry, School of Medicine, and the Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
| | - Elena Bochkareva
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
| | - Alexey Bochkarev
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
| | - Peter A Bullock
- Department of Biochemistry, School of Medicine, and the Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
| | - Andrew Bohm
- Department of Biochemistry, School of Medicine, and the Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
- * To whom correspondence should be addressed. E-mail:
| |
Collapse
|
6
|
Reese DK, Meinke G, Kumar A, Moine S, Chen K, Sudmeier JL, Bachovchin W, Bohm A, Bullock PA. Analyses of the interaction between the origin binding domain from simian virus 40 T antigen and single-stranded DNA provide insights into DNA unwinding and initiation of DNA replication. J Virol 2006; 80:12248-59. [PMID: 17005644 PMCID: PMC1676264 DOI: 10.1128/jvi.01201-06] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
DNA helicases are essential for DNA metabolism; however, at the molecular level little is known about how they assemble or function. Therefore, as a model for a eukaryotic helicase, we are analyzing T antigen (T-ag) the helicase encoded by simian virus 40. In this study, nuclear magnetic resonance (NMR) methods were used to investigate the transit of single-stranded DNA (ssDNA) through the T-ag origin-binding domain (T-ag OBD). When the residues that interact with ssDNA are viewed in terms of the structure of a hexamer of the T-ag OBD, comprised of residues 131 to 260, they indicate that ssDNA passes over one face of the T-ag OBD and then transits through a gap in the open ring structure. The NMR-based conclusions are supported by an analysis of previously described mutations that disrupt critical steps during the initiation of DNA replication. These and related observations are discussed in terms of the threading of DNA through T-ag hexamers and the initiation of viral DNA replication.
Collapse
Affiliation(s)
- Danielle K Reese
- Department of Biochemistry A703, Tufts University School of Medicine, 136 Harrison Ave., Boston, MA 02111, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Iyer LM, Koonin EV, Leipe DD, Aravind L. Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members. Nucleic Acids Res 2005; 33:3875-96. [PMID: 16027112 PMCID: PMC1176014 DOI: 10.1093/nar/gki702] [Citation(s) in RCA: 219] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We report an in-depth computational study of the protein sequences and structures of the superfamily of archaeo-eukaryotic primases (AEPs). This analysis greatly expands the range of diversity of the AEPs and reveals the unique active site shared by all members of this superfamily. In particular, it is shown that eukaryotic nucleo-cytoplasmic large DNA viruses, including poxviruses, asfarviruses, iridoviruses, phycodnaviruses and the mimivirus, encode AEPs of a distinct family, which also includes the herpesvirus primases whose relationship to AEPs has not been recognized previously. Many eukaryotic genomes, including chordates and plants, encode previously uncharacterized homologs of these predicted viral primases, which might be involved in novel DNA repair pathways. At a deeper level of evolutionary connections, structural comparisons indicate that AEPs, the nucleases involved in the initiation of rolling circle replication in plasmids and viruses, and origin-binding domains of papilloma and polyoma viruses evolved from a common ancestral protein that might have been involved in a protein-priming mechanism of initiation of DNA replication. Contextual analysis of multidomain protein architectures and gene neighborhoods in prokaryotes and viruses reveals remarkable parallels between AEPs and the unrelated DnaG-type primases, in particular, tight associations with the same repertoire of helicases. These observations point to a functional equivalence of the two classes of primases, which seem to have repeatedly displaced each other in various extrachromosomal replicons.
Collapse
Affiliation(s)
| | | | | | - L. Aravind
- To whom correspondence should be addressed. Tel: +1 301 594 2445; Fax: +1 301 480 9241;
| |
Collapse
|
8
|
Arunkumar AI, Klimovich V, Jiang X, Ott RD, Mizoue L, Fanning E, Chazin WJ. Insights into hRPA32 C-terminal domain--mediated assembly of the simian virus 40 replisome. Nat Struct Mol Biol 2005; 12:332-9. [PMID: 15793585 PMCID: PMC2600586 DOI: 10.1038/nsmb916] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2004] [Accepted: 03/04/2005] [Indexed: 11/09/2022]
Abstract
Simian virus 40 (SV40) provides a model system for the study of eukaryotic DNA replication, in which the viral protein, large T antigen (Tag), marshals human proteins to replicate the viral minichromosome. SV40 replication requires interaction of Tag with the host single-stranded DNA-binding protein, replication protein A (hRPA). The C-terminal domain of the hRPA32 subunit (RPA32C) facilitates initiation of replication, but whether it interacts with Tag is not known. Affinity chromatography and NMR revealed physical interaction between hRPA32C and the Tag origin DNA-binding domain, and a structural model of the complex was determined. Point mutations were then designed to reverse charges in the binding sites, resulting in substantially reduced binding affinity. Corresponding mutations introduced into intact hRPA impaired initiation of replication and primosome activity, implying that this interaction has a critical role in assembly and progression of the SV40 replisome.
Collapse
Affiliation(s)
- Alphonse I Arunkumar
- Department of Biochemistry, Vanderbilt University, Nashville Tennessee 37232-8725 USA
| | | | | | | | | | | | | |
Collapse
|
9
|
Stillman B. Origin recognition and the chromosome cycle. FEBS Lett 2005; 579:877-84. [PMID: 15680967 DOI: 10.1016/j.febslet.2004.12.011] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2004] [Revised: 12/10/2004] [Accepted: 12/10/2004] [Indexed: 11/29/2022]
Abstract
Prior to the initiation of DNA replication, chromosomes must establish a biochemical mark that permits the recruitment in S phase of the DNA replication machinery that copies DNA. The process of chromosome replication in eukaryotes also must be coordinated with segregation of the duplicated chromosomes to daughter cells during mitosis. Protein complexes that utilize ATP coordinate events at origins of DNA replication and later they participate in the initiation of DNA replication. In eukaryotes, some of these proteins also play a part in later processes that ensure accurate inheritance of chromosomes in mitosis, including spindle attachment of chromosomes, accurate duplication of centrosomes and cytokinesis. A perspective of how ATP-dependent proteins accomplish this task in eukaryotes is discussed.
Collapse
Affiliation(s)
- Bruce Stillman
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
| |
Collapse
|