Optimal design of thermally stable proteins

Motivation: For many biotechnological purposes, it is desirable to redesign proteins to be more structurally and functionally stable at higher temperatures. For example, chemical reactions are intrinsically faster at higher temperatures, so using enzymes that are stable at higher temperatures would lead to more efficient industrial processes. We describe an innovative and computationally efficient method called Improved Configurational Entropy (ICE), which can be used to redesign a protein to be more thermally stable (i.e. stable at high temperatures). This can be accomplished by systematically modifying the amino acid sequence via local structural entropy (LSE) minimization. The minimization problem is modeled as a shortest path problem in an acyclic graph with nonnegative weights and is solved efficiently using Dijkstra's method

Capillary HPLC Separation of Selected Neuropeptides

Neuropeptides play a pivotal role in brain and peripheral nervous system function. As high performance liquid chromatography (HPLC) becomes the central tool in the separation and characterization of peptide and protein samples, its selectivity optimization has attracted increasing attention. This research program aims to develop useful, quantitative analysis methods for neuropeptides and their hydrolysis fragments by capillary HPLC. Related peptide pairs are successfully separated, such as leu-enkephalin and [Des-Tyr1] leu-enkephalin, dynorphin A and dynorphin B, galanin and its fragment Gal1-16. The hydrolysis of leu-enkephalin to [Des-Tyr1] leu-enkephalin by organotypic hippocampal slice cultures (OHSCs) can be monitored by the same HPLC system. The separation of seven hippocampal neuropeptides with similar hydrophobicity, Bj-PRO-5a, [Des-Tyr1] leu-enkephalin, leu-enkephalin, pentagastrin, Antho-RW-amide I, dynorphin A 1-6 and angiotensin II, is accomplished by thermally tuned tandem capillary columns (T3C). The chromatographic selectivity is continuously, systematically and significantly optimized by individual adjustment of each column’s temperature. The T3C concept is applied for the first time with capillary columns, which is an important step towards optimization of selectivity for separations of small samples by liquid chromatography

Band-edge Bilayer Plasmonic Nanostructure for Surface Enhanced Raman Spectroscopy

Spectroscopic analysis of large biomolecules is critical in a number of applications, including medical diagnostics and label-free biosensing. Recently, it has been shown that Raman spectroscopy of proteins can be used to diagnose some diseases, including a few types of cancer. These experiments have however been performed using traditional Raman spectroscopy and the development of the Surface enhanced Raman spectroscopy (SERS) assays suitable for large biomolecules could lead to a substantial decrease in the amount of specimen necessary for these experiments. We present a new method to achieve high local field enhancement in surface enhanced Raman spectroscopy through the simultaneous adjustment of the lattice plasmons and localized surface plasmon polaritons, in a periodic bilayer nanoantenna array resulting in a high enhancement factor over the sensing area, with relatively high uniformity. The proposed plasmonic nanostructure is comprised of two interacting nanoantenna layers, providing a sharp band-edge lattice plasmon mode and a wide-band localized surface plasmon for the separate enhancement of the pump and emitted Raman signals. We demonstrate the application of the proposed nanostructure for the spectral analysis of large biomolecules by binding a protein (streptavidin) selectively on the hot-spots between the two stacked layers, using a low concentration solution (100 nM) and we successfully acquire its SERS spectrum

Multiple Folding Pathways of the SH3 domain

Experimental observations suggest that proteins follow different pathways under different environmental conditions. We perform molecular dynamics simulations of a model of the SH3 domain over a broad range of temperatures, and identify distinct pathways in the folding transition. We determine the kinetic partition temperature --the temperature for which the SH3 domain undergoes a rapid folding transition with minimal kinetic barriers-- and observe that below this temperature the model protein may undergo a folding transition via multiple folding pathways. The folding kinetics is characterized by slow and fast pathways and the presence of only one or two intermediates. Our findings suggest the hypothesis that the SH3 domain, a protein for which only two-state folding kinetics was observed in previous experiments, may exhibit intermediates states under extreme experimental conditions, such as very low temperatures. A very recent report (Viguera et al., Proc. Natl. Acad. Sci. USA, 100:5730--5735, 2003) of an intermediate in the folding transition of the Bergerac mutant of the alpha-spectrin SH3 domain protein supports this hypothesis.Comment: 16 pages, 4 figures To be published in the "Journal of Molecular Biology

Designability of lattice model heteropolymers

Protein folds are highly designable, in the sense that many sequences fold to the same conformation. In the present work we derive an expression for the designability in a 20 letter lattice model of proteins which, relying only on the Central Limit Theorem, has a generality which goes beyond the simple model used in its derivation. This expression displays an exponential dependence on the energy of the optimal sequence folding on the given conformation measured with respect to the lowest energy of the conformational dissimilar structures, energy difference which constitutes the only parameter controlling designability. Accordingly, the designability of a native conformation is intimately connected to the stability of the sequences folding to them.Comment: in press on Phys. Rev.

Dry and wet interfaces: Influence of solvent particles on molecular recognition

We present a coarse-grained lattice model to study the influence of water on the recognition process of two rigid proteins. The basic model is formulated in terms of the hydrophobic effect. We then investigate several modifications of our basic model showing that the selectivity of the recognition process can be enhanced by considering the explicit influence of single solvent particles. When the number of cavities at the interface of a protein-protein complex is fixed as an intrinsic geometric constraint, there typically exists a characteristic fraction that should be filled with water molecules such that the selectivity exhibits a maximum. In addition the optimum fraction depends on the hydrophobicity of the interface so that one has to distinguish between dry and wet interfaces.Comment: 11 pages, 7 figure

Emergence of stable and fast folding protein structures

The number of protein structures is far less than the number of sequences. By imposing simple generic features of proteins (low energy and compaction) on all possible sequences we show that the structure space is sparse compared to the sequence space. Even though the sequence space grows exponentially with N (the number of amino acids) we conjecture that the number of low energy compact structures only scales as ln N. This implies that many sequences must map onto countable number of basins in the structure space. The number of sequences for which a given fold emerges as a native structure is further reduced by the dual requirements of stability and kinetic accessibility. The factor that determines the dual requirement is related to the sequence dependent temperatures, T_\theta (collapse transition temperature) and T_F (folding transition temperature). Sequences, for which \sigma =(T_\theta-T_F)/T_\theta is small, typically fold fast by generically collapsing to the native-like structures and then rapidly assembling to the native state. Such sequences satisfy the dual requirements over a wide temperature range. We also suggest that the functional requirement may further reduce the number of sequences that are biologically competent. The scheme developed here for thinning of the sequence space that leads to foldable structures arises naturally using simple physical characteristics of proteins. The reduction in sequence space leading to the emergence of foldable structures is demonstrated using lattice models of proteins.Comment: latex, 18 pages, 8 figures, to be published in the conference proceedings "Stochastic Dynamics and Pattern Formation in Biological Systems

Trends in the design and use of elastin-like recombinamers as biomaterials

Producción CientíficaElastin-like recombinamers (ELRs), which derive from one of the repetitive domains found in natural elastin, have been intensively studied in the last few years from several points of view. In this mini review, we discuss all the recent works related to the investigation of ELRs, starting with those that define these polypeptides as model intrinsically disordered proteins or regions (IDPs or IDRs) and its relevance for some biomedical applications. Furthermore, we summarize the current knowledge on the development of drug, vaccine and gene delivery systems based on ELRs, while also emphasizing the use of ELR-based hydrogels in tissue engineering and regenerative medicine (TERM). Finally, we show different studies that explore applications in other fields, and several examples that describe biomaterial blends in which ELRs have a key role. This review aims to give an overview of the recent advances regarding ELRs and to encourage further investigation of their properties and applications.Comisión Europea (project NMP-2014-646075)Ministerio de Economía, Industria y Competitividad (projects PCIN-2015-010 / MAT2016-78903-R / BES-2014-069763)Junta de Castilla y León (project VA317P18