Phase separation in amino acid mixtures is governed by composition

Macromolecular phase separation has recently come to immense prominence as it is central to the formation of membraneless organelles, leading to a new paradigm of cellular organization. This type of phase transition, often termed liquid-liquid phase separation (LLPS), is mediated by molecular interactions between biomolecules, including nucleic acids and both ordered and disordered proteins. In the latter case, the separation between protein-dense and -dilute phases is often interpreted using models adapted from polymer theory. Specifically, the “stickers and spacers” model proposes that the formation of condensate-spanning networks in protein solutions originates from the interplay between two classes of residues and that the main determinants for phase separation are multivalency and sequence patterning. The duality of roles of stickers (aromatics like Phe and Tyr) and spacers (Gly and polar residues) may apply more broadly in protein-like mixtures, and the presence of these two types of components alone may suffice for LLPS to take place. In order to explore this hypothesis, we use atomistic molecular dynamics simulations of capped amino acid residues as a minimal model system. We study the behavior of pure amino acids in water for three types of residues corresponding to the spacer and sticker categories and of their multicomponent mixtures. In agreement with previous observations, we find that the spacer-type amino acids fail to phase separate on their own, while the sticker is prone to aggregation. However, ternary amino acid mixtures involving both types of amino acids phase separate into two phases that retain intermediate degrees of compaction and greater fluidity than sticker-only condensates. Our results suggest that LLPS is an emergent property of amino acid mixtures determined by composition.Financial support to D.D.S. comes from Eusko Jaurlaritza (Basque Government) through the project IT1254-19 and the Spanish Government through grants RYC-2016-19590 and PID2021-127907NB-I00 (MCIN/AEI/10.13039/501100011033/FEDER, UE). The author thanks Xabier López for useful discussions and Athi N. Naganathan and Robert B. Best for their comments on the manuscript. The author also acknowledges the staff at the DIPC Supercomputing Center for technical support

MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations

Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible to obtain long-timescale behavior of small to intermediate biomolecules and complexes. To model the interactions of many molecules at large lengthscales, particle-based reaction-diffusion (RD) simulations are more suitable but lack molecular detail. Thus, coupling MSMs and RD simulations (MSM/RD) would be highly desirable, as they could efficiently produce simulations at large time- and lengthscales, while still conserving the characteristic features of the interactions observed at atomic detail. While such a coupling seems straightforward, fundamental questions are still open: Which definition of MSM states is suitable? Which protocol to merge and split RD particles in an association/dissociation reaction will conserve the correct bimolecular kinetics and thermodynamics? In this paper, we make the first step towards MSM/RD by laying out a general theory of coupling and proposing a first implementation for association/dissociation of a protein with a small ligand (A + B C). Applications on a toy model and CO diffusion into the heme cavity of myoglobin are reported

Influence of the nonprotein amino acid mimosine in peptide conformational propensities from novel amber force field parameters

Mimosine is a nonprotein amino acid derived from plantsknown for its ability to bind to divalent and trivalent metal cations suchas Zn2+, Ni2+, Fe2+, orAl3+. This results in interesting antimicrobial andanticancer properties, which make mimosine a promising candidate fortherapeutic applications. One possibility is to incorporate mimosine intosynthetic short peptide drugs. However, how this amino acid affects thepeptide structure is not well understood, reducing our ability to designeffective therapeutic compounds. In this work, we used computersimulations to understand this question. Wefirst built parameters for themimosine residue to be used in combination with two classical forcefields of the Amber family. Then, we used atomistic molecular dynamicssimulations with the resulting parameter sets to evaluate the influence ofmimosine in the structural propensities for this amino acid. We comparedthe results of these simulations with homologous peptides, wheremimosine is replaced by either phenylalanine or tyrosine. We found that the strong dipole in mimosine induces a preference forconformations where the amino acid rings are stacked over more extended conformations. We validated our results using quantummechanical calculations, which provide a robust foundation for the outcome of our classical simulation

The response of Greek key proteins to changes in connectivity depends on the nature of their secondary structure.

What governs the balance between connectivity and topology in regulating the mechanism of protein folding? We use circular permutation to vary the order of the helices in the all-α Greek key protein FADD (Fas-associated death domain) to investigate this question. Unlike all-β Greek key proteins, where changes in the order of secondary structure cause a shift in the folding nucleus, the position of the nucleus in FADD is unchanged, even when permutation reduces the complexity significantly. We suggest that this is because local helical contacts are so dominant that permutation has little effect on the entropic cost of forming the folding nucleus whereas, in all-β Greek key proteins, all interactions in the nucleus are long range. Thus, the type of secondary structure modulates the sensitivity of proteins to changes in connectivity.This work was supported by the Wellcome Trust (WT095195) (J.C), Engineering and Physical Sciences Research Council (UK) Grant EP/J016764/1 (D.D.S.) and an Engineering and Physical Sciences Research Council (UK) studentship (K.R.K.). J.C. is a Wellcome Trust Senior Research fellow.This is the final published version. It first appeared at http://www.sciencedirect.com/science/article/pii/S0022283615002168#

Evaluación de potenciales de plegamento de proteínas con algoritmos genéticos

Para el estudio del proceso de plegamiento de proteínas, por el cual una proteína alcanza su estructura tridimensional funcional o conformación nativa, un problema esencial es el diseño de potenciales de interacción. En la bibliografía puede encontrarse una gran variedad de modelos para las interacciones elaborados por distintos grupos de investigación. El propósito de esta tesis doctoral es la evaluación detallada e independiente de algunos de estos potenciales. Para ello, partimos de la premisa de que la conformación nativa de una proteína corresponde a su mínimo de energía libre. Por tanto, un requisito para un modelo que trate de reproducir fielmente las interacciones en proteínas será que sea capaz de definir el mínimo global en la conformación nativa. El espacio conformacional accesible para una proteína es muy amplio, debido al elevado número de grados de libertad de una cadena polipeptídica. Habitualmente, los métodos utilizados para estudiar el proceso de plegamiento son el de Monte Cario y la dinámica molecular, pero ninguno de ells permite evaluar sistemáticamente potenciales de interacción. En cambio, los algoritmos genéticos pueden resultar muy útiles en esta tarea. Los algoritmos genéticos, y más en general, los algoritmos evolutivos, se valen de los métodos de la evolución natural para tratar de alcanzar soluciones óptimas para problemas de búsqueda complicados. En esta Tesis Doctoral hemos desarrollado un algoritmo evolutivo para la minimización de la energía que utiliza una representación reducida de la estructura de las proteínas. En primer lugar hemos puesto a prueba distintos aspectos de nuestra metodología utilizando un tipo de potencial que permite comprobar su eficacia en espacios de búsqueda complicados, un potencial de tipo Gó. A continuación, hemos llevado a cabo la evaluación de una serie de potenciales hidrofóbicos tomados de la bibliografía. Estos potenciales dan cuenta de la interacción que se produce entre las cadenas laterales de los residuos de las proteínas. El siguiente paso ha sido la evaluación de distintos modelos para el enlace de hidrógeno del esqueleto polipeptídico, que estabiliza los distintos tipos de estructura secundaria de proteínas. Finalmente, estudiamos el resultado de la suma de las dos contribuciones estudiadas: enlaces de hidrógeno e Interacción hidrófoba, con los potenciales que han ofrecido mejores resultados en las etapas anteriores

Atomistic molecular simulations of Aβ-Zn conformational ensembles

The amyloid-forming Aβ peptide is able to interact with metal cations to form very stable complexes that influence fibril formation and contribute to the onset of Alzheimer's disease. Multiple structures of peptides derived from Aβ in complex with different metals have been resolved experimentally to provide an atomic-level description of the metal-protein interactions. However, Aβ is intrinsically disordered, and hence more amenable to an ensemble description. Molecular dynamics simulations can now reach the timescales needed to generate ensembles for these type of complexes. However, this requires accurate force fields both for the protein and the protein-metal interactions. Here we use state-of-the-art methods to generate force field parameters for the Zn(II) cations in a set of complexes formed by different Aβ variants and combine them with the Amber99SB*-ILDN optimized force field. Upon comparison of NMR experiments with the simulation results, further optimized with a Bayesian/Maximum entropy approach, we provide an accurate description of the molecular ensembles for most Aβ-metal complexes. We find that the resulting conformational ensembles are more heterogeneous than the NMR models deposited in the Protein Data Bank.Financial support comes from Eusko Jaurlaritza (Basque Government) through the project IT1584-22 and from the Spanish Ministry of Science and Universities through the Office of Science Research (MINECO/FEDER) through grant PID2021-127907NB-I00. DDS acknowledges the Spanish Ministry of Science and Universities for a Ramón y Cajal contract (Grant RYC-2016-19590)

Geomorphological significance of lichen colonization in a present snow hollow: Hoya del Cuchillar de las Navajas, Sierra de Gredos (Spain)

18 páginas, 12 figuras y 1 tablaThis paper discusses the results of a lichenometrical and geomorphological study of one of the few remaining active snow hollows in the central region of the Iberian Peninsula. The study area, located on a glacial shoulder, is called Hoya del Cuchillar de las Navajas. A protalus rampart occurs at the base of the hollow. Our studies, conducted between 1992 and 1998, were designed to determine the geomorphological characteristics of Hoya, the mobility of the deposits, and the characteristics of the snow cover. These data formed the basis for a study of the lichen colonization on the blocks and on the wall surrounding the snow hollow. All of the lichen species found were analyzed according to their abundance, distribution and the extent of their surface cover. Measurements of the diameter of the thalli of the species Rhizocarpon geographicum were also obtained. Thalli of this species were found to require a mean snow-free growing season of at least 95 days 13.5 weeks per year. Maximum mean thallus diameters indicate that the protalus rampart was formed during the Little Ice Age and became inactive 130 years ago.The staff of the Refugio Jose Antonio Elola (Laguna Grande de Gredos) is thanked for its cooperation and hospitality. We are indebted to Alicia Ferrero for her careful revision of the English manuscript. Financial support was provided by the Proyecto de Investigacion Multidisciplinar PR218 / 94-5653 (Universidad Complutense de Madrid)Peer reviewe

Rules governing metal coordination in Aβ–Zn(ii) complex models from quantum mechanical calculations

Transition metals directly contribute to the neurotoxicity of the aggregates of the amyloid-forming Aβ peptide. The understanding and rationalization of the coordination modes of metals to Aβ amyloid is, therefore, of paramount importance to understand the capacity of a given metal to promote peptide aggregation. Experimentally, multiple Aβ–metal structures have been resolved, which exhibit different modes of coordination in both the monomeric and oligomeric forms of Aβ. Although Zn(II) metalloproteins are very abundant and often involve cysteine residues in the first coordination shell, in the case of Aβ–Zn(II), though, Zn(II) is coordinated by glutamic/aspartic acid and/or histidine residues exclusively, making for an interesting case study. Here we present a systematic analysis of the underlying chemistry on Aβ–Zn(II) coordination, where relative stabilities of different coordination arrangements indicate that a mixture of Glu/Asp and His residues is favored. A detailed comparison between different coordination shell geometries shows that tetrahedral coordination is generally favored in the aqueous phase. Our calculations show an interplay between dative covalent interactions and electrostatics which explains the observed trends. Multiple structures deposited in the Protein Data Bank support our findings, suggesting that the trends found in our work may be transferable to other Zn(II) metalloproteins with this type of coordination.The authors gratefully acknowledge the financing of the MINECO project (PID2021-127907NB-I00) founded by the Spanish Ministry of Science and Innovation, and the financing from the Basque Government (IT1584-22). The authors also thank the IZO-SGI SGIker (UPV/EHU/ERDF,EU) and DIPC for technical and human support and for the allocation of computational resources. D. D. S. receives support from a Ramón y Cajal contract (RYC-2016-19590) from the Spanish Ministry of Science and Innovation. J. A. thankfully acknowledges the University of the Basque Country for the scholarship for the completion of a masters degree in the academic years 2020/2021–2021/2022 and the Donostia International Physics Center for a summer internship