Structures of TraI in solution

Abstract

Bacterial conjugation, a DNA transfer mechanism involving transport of one plasmid strand from donor to recipient, is driven by plasmid-encoded proteins. The F TraI protein nicks one F plasmid strand, separates cut and uncut strands, and pilots the cut strand through a secretion pore into the recipient. TraI is a modular protein with identifiable nickase, ssDNA-binding, helicase and protein-protein interaction domains. While domain structures corresponding to roughly 1/3 of TraI have been determined, there has been no comprehensive structural study of the entire TraI molecule, nor an examination of structural changes to TraI upon binding DNA. Here, we combine solution studies using small-angle scattering and circular dichroism spectroscopy with molecular Monte Carlo and molecular dynamics simulations to assess solution behavior of individual and groups of domains. Despite having several long (>100 residues) apparently disordered or highly dynamic regions, TraI folds into a compact molecule. Based on the biophysical characterization, we have generated models of intact TraI. These data and the resulting models have provided clues to the regulation of TraI function.

Investigating Structure and Dynamics of Proteins in Amorphous Phases Using Neutron Scattering

“…SasCalc (golden vector method) [35] allows the computation of neutron scattering profiles from structures and it can be freely accessed from a website [36]. Examples of this methodology are published in the literature [29], [34], [37], [38], [39], [40]. In the absence of crystallographic data, there are tools to generate molecular shapes that fit the experimental data, such as DAMMIF [41].…”

Combined Monte Carlo/torsion-angle molecular dynamics for ensemble modeling of proteins, nucleic acids and carbohydrates

“…As shown in Figure 5, Figure S6). It should be noted that the TAMD simulation of TraI using all the implicit solvent models led to RGYR values less than that observed experimentally [34]. These observations reflect a fundamental limitation of the current implicit solvent models, which energetically favor and over-stabilize compact state of proteins [53].…”

“…An A-B system (first two domains of full-length HIV-1 Gag protein, residues 1-276) and an A-tail system (first domain with a flexible linker of full-length HIV-1 Gag protein, residues 1-143) were built from the full-length model. A fourth protein model taken from a fragment of TraI protein consisting of residues 381-858 was constructed as previously described [34]. This fragment contains three globular domains spanning residues 381-573, residues 577-789 and residues 804-849, respectively connected by regions of flexible amino-acids.…”

Searching for Aquamelt Behavior among Silklike Biomimetics during Fibrillation under Flow

“…As a result, the SAXS/WAXS patterns of the fibers are obtained. Previously, the SASSIE Web server has been applied to generate the all-atomic models of biomacromolecules − and to investigate the structuring in synthetic polymers, , including aquamelts of PEO . In our study, the SAXS/WAXS patterns of peptide fibers are compared with available experimental data. − …”