More Like this

1. High-Resolution Structure of the Nuclease Domain of the Human Parvovirus B19 Main Replication Protein NS1

   https://doi.org/10.1128/jvi.02164-21  

   Sanchez, Jonathan L.; Ghadirian, Niloofar; Horton, Nancy C. (May 2022, Journal of Virology)

   Frappier, Lori (Ed.)

   ABSTRACT Two new structures of the N-terminal domain of the main replication protein, NS1, of human parvovirus B19 (B19V) are presented here. This domain (NS1-nuc) plays an important role in the “rolling hairpin” replication of the single-stranded B19V DNA genome, recognizing origin of replication sequences in double-stranded DNA, and cleaving (i.e., nicking) single-stranded DNA at a nearby site known as the terminal resolution site (trs). The three-dimensional structure of NS1-nuc is well conserved between the two forms, as well as with a previously solved structure of a sequence variant of the same domain; however, it is shown here at a significantly higher resolution (2.4 Å). Using structures of NS1-nuc homologues bound to single- and double-stranded DNA, models for DNA recognition and nicking by B19V NS1-nuc are presented that predict residues important for DNA cleavage and for sequence-specific recognition at the viral origin of replication. IMPORTANCE The high-resolution structure of the DNA binding and cleavage domain of the main replicative protein, NS1, from the human-pathogenic virus human parvovirus B19 is presented here. Included also are predictions of how the protein recognizes important sequences in the viral DNA which are required for viral replication. These predictions can be used to further investigate the function of this protein, as well as to predict the effects on viral viability due to mutations in the viral protein and viral DNA sequences. Finally, the high-resolution structure facilitates structure-guided drug design efforts to develop antiviral compounds against this important human pathogen. 

   more » « less
2. Measuring interactions of DNA with nanoporous protein crystals by atomic force microscopy

   https://doi.org/10.1039/D1NR01703A  

   Wang, Dafu; Stuart, Julius D.; Jones, Alec A.; Snow, Christopher D.; Kipper, Matt J. (June 2021, Nanoscale)

   null (Ed.)

   Crosslinked porous protein crystals are a new biomaterial that can be engineered to encapsulate, stabilize, and organize guest molecules, nanoparticles, and biological moieties. In this study, for the first time, the combined interactions of DNA strands with porous protein crystals are quantitatively measured by high-resolution atomic force microscopy (AFM) and chemical force microscopy. The surface structure of protein crystals with unusually large pores was observed in liquid via high-resolution AFM. Force–distance ( F – D ) curves were also obtained using AFM tips modified to present or capture DNA. The modification of AFM tips allowed the tips to covalently bind DNA that was pre-loaded in the protein crystal nanopores. The modified tips enabled the interactions of DNA molecules with protein crystals to be quantitatively studied while revealing the morphology of the buffer-immersed protein crystal surface in detail, thereby preserving the structure and properties of protein crystals that could be disrupted or destroyed by drying. The hexagonal space group was manifest at the crystal surface, as were the strong interactions between DNA and the porous protein crystals in question. In sum, this study furthered our understanding of how a new protein-based biomaterial can be used to bind guest DNA assemblies. 

   more » « less
3. PDA-Pred: Predicting the binding affinity of protein-DNA complexes using machine learning techniques and structural features

   https://doi.org/10.1016/j.ymeth.2023.03.002  

   Harini, K.; Kihara, Daisuke; Michael Gromiha, M. (May 2023, Methods)

   Protein–DNA interactions play an important role in various biological processes such as gene expression, replication, and transcription. Understanding the important features that dictate the binding affinity of protein-DNA complexes and predicting their affinities is important for elucidating their recognition mechanisms. In this work, we have collected the experimental binding free energy (ΔG) for a set of 391 Protein-DNA complexes and derived several structure-based features such as interaction energy, contact potentials, volume and surface area of binding site residues, base step parameters of the DNA and contacts between different types of atoms. Our analysis on relationship between binding affinity and structural features revealed that the important factors mainly depend on the number of DNA strands as well as functional and structural classes of proteins. Specifically, binding site properties such as number of atom contacts between the DNA and protein, volume of protein binding sites and interaction-based features such as interaction energies and contact potentials are important to understand the binding affinity. Further, we developed multiple regression equations for predicting the binding affinity of protein-DNA complexes belonging to different structural and functional classes. Our method showed an average correlation and mean absolute error of 0.78 and 0.98 kcal/mol, respectively, between the experimental and predicted binding affinities on a jack-knife test. We have developed a webserver, PDA-PreD (Protein-DNA Binding affinity predictor), for predicting the affinity of protein-DNA complexes and it is freely available at https://web.iitm.ac.in/bioinfo2/pdapred/ 

   more » « less
4. ComparePD : Improving protein– DNA complex model comparison with hydrogen bond energy‐based metrics

   https://doi.org/10.1002/prot.26493  

   Malik, Fareeha Kanwal; Guo, Jun‐tao (March 2023, Proteins: Structure, Function, and Bioinformatics)

   Abstract Computational modeling of protein–DNA complex structures has important implications in biomedical applications such as structure‐based, computer aided drug design. A key step in developing methods for accurate modeling of protein–DNA complexes is similarity assessment between models and their reference complex structures. Existing methods primarily rely on distance‐based metrics and generally do not consider important functional features of the complexes, such as interface hydrogen bonds that are critical to specific protein–DNA interactions. Here, we present a new scoring function, ComparePD, which takes interface hydrogen bond energy and strength into account besides the distance‐based metrics for accurate similarity measure of protein–DNA complexes. ComparePD was tested on two datasets of computational models of protein–DNA complexes generated using docking (classified as easy, intermediate, and difficult cases) and homology modeling methods. The results were compared with PDDockQ, a modified version of DockQ tailored for protein–DNA complexes, as well as the metrics employed by the community‐wide experiment CAPRI (Critical Assessment of PRedicted Interactions). We demonstrated that ComparePD provides an improved similarity measure over PDDockQ and the CAPRI classification method by considering both conformational similarity and functional importance of the complex interface. ComparePD identified more meaningful models as compared to PDDockQ for all the cases having different top models between ComparePD and PDDockQ except for one intermediate docking case. 

   more » « less
5. A thermophilic phage uses a small terminase protein with a fixed helix–turn–helix geometry

   https://doi.org/10.1074/jbc.RA119.012224  

   Hayes, Janelle A.; Hilbert, Brendan J.; Gaubitz, Christl; Stone, Nicholas P.; Kelch, Brian A. (March 2020, Journal of Biological Chemistry)

   Tailed bacteriophages use a DNA-packaging motor to encapsulate their genome during viral particle assembly. The small terminase (TerS) component of this DNA-packaging machinery acts as a molecular matchmaker that recognizes both the viral genome and the main motor component, the large terminase (TerL). However, how TerS binds DNA and the TerL protein remains unclear. Here we identified gp83 of the thermophilic bacteriophage P74-26 as the TerS protein. We found that TerS P76-26 oligomerizes into a nonamer that binds DNA, stimulates TerL ATPase activity, and inhibits TerL nuclease activity. A cryo-EM structure of TerS P76-26 revealed that it forms a ring with a wide central pore and radially arrayed helix–turn–helix domains. The structure further showed that these helix–turn–helix domains, which are thought to bind DNA by wrapping the double helix around the ring, are rigidly held in an orientation distinct from that seen in other TerS proteins. This rigid arrangement of the putative DNA-binding domain imposed strong constraints on how TerS P76-26 can bind DNA. Finally, the TerS P76-26 structure lacked the conserved C-terminal β-barrel domain used by other TerS proteins for binding TerL. This suggests that a well-ordered C-terminal β-barrel domain is not required for TerS P76-26 to carry out its matchmaking function. Our work highlights a thermophilic system for studying the role of small terminase proteins in viral maturation and presents the structure of TerS P76-26 , revealing key differences between this thermophilic phage and its mesophilic counterparts. 

   more » « less