A Kinematic Observation and Conjecture for Creating Stable Constructs of a Peptide Nanoparticle

Shahbazi, Zahra; Pimentel, Tais A. P. F.; Ilieş, Horea T.; Kazerounian, Kazem; Burkhard, Peter

doi:10.1007/978-90-481-9262-5_22

Cited by 3 publications

(3 citation statements)

References 10 publications

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“…The Protofold platform has since provided a kinematic testbed for subsequent research activities. Examples are predicting hydrogen bond connectivity sub-graphs [49], its application to the design of stable peptide nano-particles [50], the analysis of protein mobility (using the 'pebble game' algorithm) [51], the development of mechanical models for secondary structural elements [52], and nano-machanism synthesis from a 'link soup' of pre-specified structural elements [53,54].…”

Section: Related Workmentioning

confidence: 99%

Protofold II: Enhanced Model and Implementation for Kinetostatic Protein Folding1

Tavousi

Behandish

Ilieş

et al. 2015

Journal of Nanotechnology in Engineering and Medicine

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A reliable prediction of 3D protein structures from sequence data remains a big challenge due to both theoretical and computational difficulties. We have previously shown that our kinetostatic compliance method (KCM) implemented into the Protofold package can overcome some of the key difficulties faced by other de novo structure prediction methods, such as the very small time steps required by the molecular dynamics (MD) approaches or the very large number of samples needed by the Monte Carlo (MC) sampling techniques. In this article, we improve the free energy formulation used in Protofold by including the typically underrated entropic effects, imparted due to differences in hydrophobicity of the chemical groups, which dominate the folding of most water-soluble proteins. In addition to the model enhancement, we revisit the numerical implementation by redesigning the algorithms and introducing efficient data structures that reduce the expected complexity from quadratic to linear. Moreover, we develop and optimize parallel implementations of the algorithms on both central and graphics processing units (CPU/GPU) achieving speed-ups up to two orders of magnitude on the GPU. Our simulations are consistent with the general behavior observed in the folding process in aqueous solvent, confirming the effectiveness of model improvements. We report on the folding process at multiple levels; namely, the formation of secondary structural elements and tertiary interactions between secondary elements or across larger domains. We also observe significant enhancements in running times that make the folding simulation tractable for large molecules.

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Section: Related Workmentioning

confidence: 99%

Protofold II: Enhanced Model and Implementation for Kinetostatic Protein Folding1

Tavousi

Behandish

Ilieş

et al. 2015

Journal of Nanotechnology in Engineering and Medicine

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show abstract

“…Mobility reduction is observed when there is more rigidity due to the formation of hydrogen bonds. 41 Shahbazi et al studied the linker 2ic8 and found that there were many flexible segments, which can result in aggregation without icosahedral structural arrangement, as can be seen from the TEM data in Figure 4 .…”

Section: Discussionmentioning

confidence: 97%

“…The aggregation results reported ( Figure 4 ) can be understood in light of the work by Shahbazi et al on this particular linker region. 41 Predicting the formation of hydrogen bonds allows the expected mobility of protein chains to be estimated. Mobility reduction is observed when there is more rigidity due to the formation of hydrogen bonds.…”

Section: Discussionmentioning

confidence: 99%

Optimizing the design of protein nanoparticles as carriers for vaccine applications

Doll

Neef

Duong

et al. 2015

Nanomedicine: Nanotechnology, Biology and Medicine

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Successful vaccine development remains a huge challenge for infectious diseases such as malaria, HIV and influenza. As a novel way to present antigenic epitopes to the immune system, we have developed icosahedral self-assembling protein nanoparticles (SAPNs) to serve as a prototypical vaccine platform for infectious diseases. Here we examine some biophysical factors that affect the self-assembly of these nanoparticles, which have as basic building blocks coiled-coil oligomerization domains joined by a short linker region. Relying on in silico computer modeling predictions, we selected five different linker regions from the RCSB protein database that connect oligomerization domains, and then further studied the self-assembly and stability of in vitro produced nanoparticles through biophysical characterization of formed particles. One design in particular, T2i88, revealed excellent self-assembly and homogeneity thus paving the way towards a more optimized nanoparticle for vaccine applications.

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The Evolving Role of Robot Kinematics in Bio-Nanotechnology

Kazerounian,

Ilies

2024

Springer Proceedings in Advanced Robotics

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A Kinematic Observation and Conjecture for Creating Stable Constructs of a Peptide Nanoparticle

Cited by 3 publications

References 10 publications

Protofold II: Enhanced Model and Implementation for Kinetostatic Protein Folding1

Protofold II: Enhanced Model and Implementation for Kinetostatic Protein Folding1

Optimizing the design of protein nanoparticles as carriers for vaccine applications

The Evolving Role of Robot Kinematics in Bio-Nanotechnology

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