More Like this

1. The Analytical Flory Random Coil Is a Simple-to-Use Reference Model for Unfolded and Disordered Proteins

   https://doi.org/10.1021/acs.jpcb.3c01619  

   Alston, Jhullian J.; Ginell, Garrett M.; Soranno, Andrea; Holehouse, Alex S. (May 2023, The Journal of Physical Chemistry B)

   Denatured, unfolded, and intrinsically disordered proteins (collectively referred to here as unfolded proteins) can be described using analytical polymer models. These models capture various polymeric properties and can be fit to simulation results or experimental data. However, the model parameters commonly require users’ decisions, making them useful for data interpretation but less clearly applicable as stand-alone reference models. Here we use all-atom simulations of polypeptides in conjunction with polymer scaling theory to parameterize an analytical model of unfolded polypeptides that behave as ideal chains (ν = 0.50). The model, which we call the analytical Flory random coil (AFRC), requires only the amino acid sequence as input and provides direct access to probability distributions of global and local conformational order parameters. The model defines a specific reference state to which experimental and computational results can be compared and normalized. As a proof-of-concept, we use the AFRC to identify sequence-specific intramolecular interactions in simulations of disordered proteins. We also use the AFRC to contextualize a curated set of 145 different radii of gyration obtained from previously published small-angle X-ray scattering experiments of disordered proteins. The AFRC is implemented as a stand-alone software package and is also available via a Google Colab notebook. In summary, the AFRC provides a simple-to-use reference polymer model that can guide intuition and aid in interpreting experimental or simulation results. 

   more » « less
2. Generation of unfolded outer membrane protein ensembles defined by hydrodynamic properties

   https://doi.org/10.1007/s00249-023-01639-y  

   Devlin, Taylor; Fleming, Patrick J.; Loza, Nicole; Fleming, Karen G. (March 2023, European Biophysics Journal)

   Outer membrane proteins (OMPs) must exist as an unfolded ensemble while interacting with a chaperone network in the periplasm of Gram-negative bacteria. Here, we developed a method to model unfolded OMP (uOMP) conformational ensembles using the experimental properties of two well-studied OMPs. The overall sizes and shapes of the unfolded ensembles in the absence of a denaturant were experimentally defined by measuring the sedimentation coefficient as a function of urea concentration. We used these data to model a full range of unfolded conformations by parameterizing a targeted coarse-grained simulation protocol. The ensemble members were further refined by short molecular dynamics simulations to reflect proper torsion angles. The final conformational ensembles have polymer properties different from unfolded soluble and intrinsically disordered proteins and reveal inherent differences in the unfolded states that necessitate further investigation. Building these uOMP ensembles advances the understanding of OMP biogenesis and provides essential information for interpreting structures of uOMP-chaperone complexes. 

   more » « less
3. Exploring Nearest Neighbor Interactions and Their Influence on the Gibbs Energy Landscape of Unfolded Proteins and Peptides

   https://doi.org/10.3390/ijms23105643  

   Schweitzer-Stenner, Reinhard (May 2022, International Journal of Molecular Sciences)

   The Flory isolated pair hypothesis (IPH) is one of the corner stones of the random coil model, which is generally invoked to describe the conformational dynamics of unfolded and intrinsically disordered proteins (IDPs). It stipulates, that individual residues sample the entire sterically allowed space of the Ramachandran plot without exhibiting any correlations with the conformational dynamics of its neighbors. However, multiple lines of computational, bioinformatic and experimental evidence suggest that nearest neighbors have a significant influence on the conformational sampling of amino acid residues. This implies that the conformational entropy of unfolded polypeptides and proteins is much less than one would expect based on the Ramachandran plots of individual residues. A further implication is that the Gibbs energies of residues in unfolded proteins or polypeptides are not additive. This review provides an overview of what is currently known and what has yet to be explored regarding nearest neighbor interactions in unfolded proteins. 

   more » « less
4. Tailoring the formation and stability of self-assembled structures from precisely engineered intrinsically disordered protein polymers: A comprehensive review

   https://doi.org/10.1016/j.giant.2023.100158  

   Doole, Fathima T.; Camp, Christopher P.; Kim, Minkyu (June 2023, Giant)

   Intrinsically disordered proteins (IDPs) are a class of proteins that lack stable three-dimensional structures. Despite their natural tendency to be disordered, precise modulations of molecular parameters (e.g., sequence, length) through biomolecular engineering tools and control of environmental conditions tailor the formation of dynamic self-assembled structures. In addition to designing structures that respond to external stimuli for specific biotechnological applications (e.g., biosensors), other applications require stable structures (e.g., engineered tissues, drug delivery vehicles) that resist unintended changes and disassembly across various environmental conditions, such as different concentrations and temperatures. This review provides a comprehensive understanding of the design and engineering principles that govern the self-assembly of biosynthetic IDPs and their stability. Specifically, elastin-like polypeptides (ELPs) are highlighted as a prominent example of biosynthetically designed, thermoresponsive IDPs. Examples include ELPs that form various self-assembled structures by themselves as ELP homopolymers or diblock copolymers, ELPs combined with other IDPs in diblock copolymers, and ELP-based polymer hybrids containing functional (bio)molecules. It is anticipated that the efforts to enhance the stability of self-assembled structures through the precise engineering of IDP-based polymers have expanded the potential for diverse biotechnological applications in tissue engineering, drug delivery, diagnostic assays, and biomedicine. 

   more » « less
5. Modeling pKas of unfolded proteins to probe structural models of unfolded state

   https://doi.org/10.1142/S0219633619500202  

   Tajielyato, Nayere; Alexov, Emil (June 2019, Journal of Theoretical and Computational Chemistry)

   null (Ed.)

   Modeling unfolded states of proteins has implications for protein folding and stability. Since in unfolded state proteins adopt multiple conformations, any experimentally measured quantity is ensemble averaged, therefore the computed quantity should be ensemble averaged as well. Here, we investigate the possibility that one can model an unfolded state ensemble with the coil model approach, algorithm such as “flexible-meccano” [Ozenne V et al., Flexible-meccano: A tool for the generation of explicit ensemle descriptions of intrinsically disordered proteins and their associated experimental observables, Bioinformatics 28:1463–1470, 2012], developed to generate structures for intrinsically disordered proteins. We probe such a possibility by using generated structures to calculate pKas of titratable groups and compare with experimental data. It is demonstrated that even with a small number of representative structures of unfolded state, the average calculated pKas are in very good agreement with experimentally measured pKas. Also, predictions are made for titratable groups for which there is no experimental data available. This suggests that the coil model approach is suitable for generating 3D structures of unfolded state of proteins. To make the approach suitable for large-scale modeling, which requires limited number of structures, we ranked the structures according to their solvent accessible surface area (SASA). It is shown that in the majority of cases, the top structures with smallest SASA are enough to represent unfolded state. 

   more » « less