Molecular basis of the structural stability of a Top7-based scaffold at extreme pH and temperature conditions

Soares, Thereza A.; Boschek, Curt B.; Apiyo, David; Baird, Cheryl L.; Straatsma, T. P.

doi:10.1016/j.jmgm.2010.01.013

Cited by 14 publications

(14 citation statements)

References 90 publications

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“…Remarkably, the sequence identity of the most aggressive design (TOP7_full) is only 28%, and using the BLOSUM62 based scoring system, we observe that most of the TOP7_full residues were actually favorable, obtaining positive scores. This low conservation is especially relevant considering that intensive studies on TOP7 have revealed the importance of beta-sheet conservation in order to keep its foldability [22, 50, 51]. Sequence folding prediction experiments showed that TOP7_full has a similar folding propensity to TOP7 and docking simulations also show lower binding energies as compared to the native peptide-antibody complex, reinforcing the experimental results obtained (S5B Fig),…”

Section: Resultssupporting

confidence: 76%

Rosetta FunFolDes – A general framework for the computational design of functional proteins

et al. 2018

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The robust computational design of functional proteins has the potential to deeply impact translational research and broaden our understanding of the determinants of protein function and stability. The low success rates of computational design protocols and the extensive in vitro optimization often required, highlight the challenge of designing proteins that perform essential biochemical functions, such as binding or catalysis. One of the most simplistic approaches for the design of function is to adopt functional motifs in naturally occurring proteins and transplant them to computationally designed proteins. The structural complexity of the functional motif largely determines how readily one can find host protein structures that are “designable”, meaning that are likely to present the functional motif in the desired conformation. One promising route to enhance the “designability” of protein structures is to allow backbone flexibility. Here, we present a computational approach that couples conformational folding with sequence design to embed functional motifs into heterologous proteins—Rosetta Functional Folding and Design (FunFolDes). We performed extensive computational benchmarks, where we observed that the enforcement of functional requirements resulted in designs distant from the global energetic minimum of the protein. An observation consistent with several experimental studies that have revealed function-stability tradeoffs. To test the design capabilities of FunFolDes we transplanted two viral epitopes into distant structural templates including one de novo “functionless” fold, which represent two typical challenges where the designability problem arises. The designed proteins were experimentally characterized showing high binding affinities to monoclonal antibodies, making them valuable candidates for vaccine design endeavors. Overall, we present an accessible strategy to repurpose old protein folds for new functions. This may lead to important improvements on the computational design of proteins, with structurally complex functional sites, that can perform elaborate biochemical functions related to binding and catalysis.

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Section: Resultssupporting

confidence: 76%

Rosetta FunFolDes – A general framework for the computational design of functional proteins

et al. 2018

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“…Such increased flexibility suggests that R2HB stability may be compromised since the β‐sheet core of Top7 has been identified as responsible for its stability . In fact, this finding corroborates with the observed inability of this chimeric protein to discriminate between HIV‐1 positive from negative patient sera …”

Section: Resultssupporting

confidence: 71%

“…The latter has been used for structure prediction and protein engineering to design and tune protein interactions with reliable results for short sequences . It has been widely applied to design better catalysts and proteins of immunological interest such as epitopes and antibodies . This is achieved by developing or modifying a protein structure to obtain a desired function or to improve its stability …”

Section: Introductionmentioning

confidence: 99%

Assessing protein conformational sampling and structural stability via de novo design and molecular dynamics simulations

et al. 2015

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Molecular dynamics and de novo techniques, associated to quality parameter sets, have excelled at determining the structure of small proteins with high accuracy. To achieve a detailed description of protein conformations, these methods must critically assess the thermodynamic features of the molecular ensembles. Here, a comparison of the conformational ensemble generated by molecular dynamics and de novo techniques were carried out for six Top7-based proteins carrying gp41 HIV-1 epitopes. The native Top7, a highly stable computationally designed protein, was used as benchmark. Structural stability, flexibility, and secondary structure content were assessed. The consistency of the latter was compared to experimental circular dichroism spectra for all proteins. While both methods are capable to identify the stable from unstable chimeric proteins, the sampled conformational space and flexibility differ significantly in both methods. Molecular dynamics simulations seem to better describe secondary structure content and identify regions responsible for conformational instability. The de novo method, as implemented in Rosetta-a prime tool for protein design, overestimates secondary structure content. On the other hand, its empirical energy function is capable to predict the threshold for protein stability.

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“…This finding is consistent with the previous observation that the b-sheet in Top7 comprises a stable core, which is responsible for its stability when it is subjected to changes in pH and temperature. 28,29 The average number of hydrogen bonds does not change significantly, except for Top7_R5L, Top7_R8A and Top7_R8B where there is a decrease of ca. 8% or more in these values.…”

Section: Structural Dynamics and Stabilitymentioning

confidence: 95%

De novo design of immunoreactive conformation-specific HIV-1 epitopes based on Top7 scaffold

et al. 2013

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Molecular basis of the structural stability of a Top7-based scaffold at extreme pH and temperature conditions

Cited by 14 publications

References 90 publications

Rosetta FunFolDes – A general framework for the computational design of functional proteins

Rosetta FunFolDes – A general framework for the computational design of functional proteins

Assessing protein conformational sampling and structural stability via de novo design and molecular dynamics simulations

De novo design of immunoreactive conformation-specific HIV-1 epitopes based on Top7 scaffold

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