Better understanding the biophysical basis of the biological process to transfer a viral genome to infect a cell is important to many disease related fields. Predicting the thermodynamic pressures and forces including the osmotic pressure necessary to confine DNA-a highly-negatively charged, elastic polymer-into capsids (over a 250-fold compaction) is a problem with implications not only relevant to infectious disease mechanism but in phage therapy or phage antibiotics(1) and therapeutic delivery(2). Experimental measurements of phage DNA confinement include osmotic pressure ejection-inhibition experiments(3) and single-molecule loading force measurements that provide force or pressure data for validation of theoretical models.(4, 5) Structural insight into DNA packaging is aided by cryo-electron microscopy asymmetric reconstructions done in the NCMI with our collaborator Chiu.(6, 7) Most current models of phage packing assume DNA behaves as a linearly elastic polymer that bends uniformly under stress, like the 'inverse spool'model.(8) The assumption of such spooled conformations is based primarily on interpretations of cryo-EM density maps, obtained by averaging thousands of structures(9), which show density rings, especially near the capsid surface. Recent evidence shows that during translocation packing, the DNA helix is rotated in a left-handed direction thus under twisting it.(10, 11) It Is known tha under twisting reduces persistence length by 2 orders of magnitude when strand separation occurs in sequence specific places.(12) Our hypothesis is that DNA kinking induced disorder can have a strong effect on packing and pressures. How DNA overcomes the unfavorable thermodynamic barrier to enter and pack inside a capsid depends on many different intermolecular interactions. Because phage genomes are around ten kilo-basepairs long, we will employ a multi scale technique to model the structure and consequent thermodynamics. We will refine a coarse-grained model of DNA from our previous work.(13) Preliminary simulations of unconnected DNA coarse grained polymer beads in capsid-like confinement already show ringed density distributions consistent with cryo-EM data. Connected polymer paths will be constructed consistent with data. We will produce an ensemble of entropically-driven, low free energy conformations of DNA in confinement. Ultimately, we will test hypotheses related to the amount of disorder, ion screening and the contribution of DNA-protein confinement interactions.

Public Health Relevance

Understanding the biophysical basis of the biological process which transfers a viral genome to infect a cell is important to many disease related fields. Predicting the thermodynamic pressures including the osmotic pressure necessary to confine DNA in phage capsids (over a 250-fold compaction) is a problem with implications in infection, phage therapies and therapeutic delivery. We will resolve questions of the thermodynamic mechanism of DNA ejection by phages.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM066813-11
Application #
8593300
Study Section
Macromolecular Structure and Function D Study Section (MSFD)
Program Officer
Preusch, Peter C
Project Start
2004-04-01
Project End
2016-12-31
Budget Start
2014-01-01
Budget End
2014-12-31
Support Year
11
Fiscal Year
2014
Total Cost
$240,975
Indirect Cost
$83,475
Name
University of Texas Medical Br Galveston
Department
Biochemistry
Type
Schools of Medicine
DUNS #
800771149
City
Galveston
State
TX
Country
United States
Zip Code
77555
Wang, Qian; Pettitt, B Montgomery (2014) Modeling DNA thermodynamics under torsional stress. Biophys J 106:1182-93
Myers, Christopher G; Pettitt, B Montgomery (2013) Communication: Origin of the contributions to DNA structure in phages. J Chem Phys 138:071103
Theruvathu, Jacob A; Yin, Y Whitney; Pettitt, B Montgomery et al. (2013) Comparison of the structural and dynamic effects of 5-methylcytosine and 5-chlorocytosine in a CpG dinucleotide sequence. Biochemistry 52:8590-8
Howard, Jesse J; Lynch, Gillian C; Pettitt, B Montgomery (2011) Ion and solvent density distributions around canonical B-DNA from integral equations. J Phys Chem B 115:547-56
Ambia-Garrido, J; Vainrub, Arnold; Montgomery Pettitt, B (2011) Free energy considerations for nucleic acids with dangling ends near a surface: a coarse grained approach. J Phys Condens Matter 23:325101
Vainrub, Arnold; Pettitt, B Montgomery (2011) Accurate prediction of binding thermodynamics for DNA on surfaces. J Phys Chem B 115:13300-3
Chen, Chuanying; Pettitt, B Montgomery (2011) The binding process of a nonspecific enzyme with DNA. Biophys J 101:1139-47
Ambia-Garrido, J; Vainrub, Arnold; Pettitt, B Montgomery (2010) A model for Structure and Thermodynamics of ssDNA and dsDNA Near a Surface: a Coarse Grained Approach. Comput Phys Commun 181:2001-2007
Howard, Jesse J; Perkyns, John S; Pettitt, B Montgomery (2010) The behavior of ions near a charged wall-dependence on ion size, concentration, and surface charge. J Phys Chem B 114:6074-83
Feng, Jun; Wong, Ka-Yiu; Lynch, Gillian C et al. (2009) Salt effects on surface-tethered peptides in solution. J Phys Chem B 113:9472-8

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