Molecular dynamics study of the internalization of cell-penetrating peptides containing unnatural amino acids across membranes

Peptide-based delivery systems that deliver target molecules into cells have been gaining traction. These systems need cell-penetrating peptides (CPPs), which have the remarkable ability to penetrate into biological membranes and help internalize different cargoes into cells through the cell membranes. The molecular internalization mechanism and structure–function relationships of CPPs are not clear, although the incorporation of nonproteinogenic amino acids such as α-aminoisobutyric acid (Aib) has been reported to increase their helicity, biostability and penetration efficiencies. Here, we used molecular dynamics to study two Aib-containing CPPs, poly(LysAibAla)3 (KAibA) and poly(LysAibGly)₃ (KAibG), that previously showed high cell internalization efficiency. KAibA and KAibG displayed the lowest internalization energies among the studied CPPs, showing distinct internalization mechanisms depending on the lipid composition of the model membranes. The presence of Aib residues allows these CPPs to adopt amphipathic folding to efficiently penetrate through the membranes. Elucidating how Aib incorporation affects CPP–membrane binding and interactions is beneficial for the design of CPPs for efficient intracellular delivery

Molecular dynamics simulation of complexation between plasmid DNA and cationic peptides

The elucidation of the process by which cationic peptides condense plasmid DNA (pDNA) is important for unraveling the mechanism of peptide/pDNA complex formation, which plays a vital role in gene delivery for the genetic transformation of living cells. We performed atomic MD simulations of the complexation of pDNA in the presence of two cationic peptides, KH9 (with an alternating sequence of lysine and histidine) and Cytcox (functioning as a mitochondria-targeting signal), to investigate the mechanism of pDNA condensation. The simulations revealed that the cationic peptides bound to the pDNA and that defects in pDNA formed in response to the densely packed cationic peptides, presumably initiating the folding of the double-stranded pDNA into a globule morphology. The decrease in the radius of gyration and the number of hydrogen bonds and the increase in the writhe structure, with a slightly higher tendency for the Cytcox/pDNA system, strongly support the formation of pDNA defects leading to the bending of the double helix. The results provided insight into the mechanism of pDNA complexation with cationic peptides, which should contribute to the future design of highly efficient gene delivery systems using peptide-mediated nanocarriers.This work was financially supported by Japan Science and Technology Agency Exploratory Research for Advanced Technology (JST ERATO; Grant No. JPMJER1602). We acknowledge the RIKEN Advanced Center for Computing and Communication (ACCC) for providing access to HOKUSAI BigWaterfall Supercomputer resources.Peer ReviewedPostprint (published version

Computational study of the interaction between natural rubber α-terminal groups and l-quebrachitol, one of the major components of natural rubber

Natural rubber is a biomaterial with unique physical and chemical features that are indispensable for many industrial applications. It is widely accepted that the α-terminal groups of its biopolymer molecules play a critical role in its exceptional characteristics. Herein, we used molecular dynamics to model recently structurally defined α-terminal groups and their interaction with L-quebrachitol, which is the second most common compound found in natural rubber particles

Papain-Catalyzed, Sequence-Dependent Polymerization Yields Polypeptides Containing Periodic Histidine Residues

His-containing polypeptides, including polyHis, are attractive materials due to the unique characteristics of the imidazole ring of the His residue. In particular, His-containing polypeptides with repetitive sequences have a variety of distinctive features based on their periodic structure. In this study, chemoenzymatic polymerization of ethyl ester monomers with sequences His, GlyHis, HisGly, and GlyHisGly with hydrophobic side chains on the imidazole ring was performed using papain as a catalyst. Sequence dependence in chemoenzymatic polymerization was observed for GlyHis- and HisGly-based monomers: GlyHis-based monomers did not undergo polymerization, whereas polymerization of HisGly-based monomers afforded polypeptides with a degree of polymerization from 6 to 38 and from 5 to 31 and a number-average degree of polymerization of 16.4 and 12.4 for poly(HisGly) and poly[His(Bu)Gly], respectively. The difference in polymerizability of these dipeptide monomers was supported by a docking simulation between these monomers and papain, where the ester group of the HisGly-based monomer was closer to the catalytic center of papain than that of the GlyHis-based monomer. Infrared spectroscopy and synchrotron wide-angle X-ray diffraction measurements indicated that poly(HisGly) formed a β-sheet structure whose crystallinity was 41.6%, whereas the other tripeptide-based polypeptides were more amorphous showing 19.6–30.7% of crystallinity. Poly(HisGly) exhibited the highest thermal stability among all of the polypeptides in the thermogravimetric analysis, reflecting the difference in the secondary structures

Conceptos básicos de mecánica en biomecánica

Peer Reviewe

Synthetic Mitochondria-Targeting Peptides Incorporating α-Aminoisobutyric Acid with a Stable Amphiphilic Helix Conformation in Plant Cells

In the genetic modification of plant cells, the mitochondrion is an important target in addition to the nucleus and plastid. However, gene delivery into the mitochondria of plant cells has yet to be established by conventional methods, such as particle bombardment, because of the small size and high mobility of mitochondria. To develop an efficient mitochondria-targeting signal (MTS) that functions in plant cells, we designed the artificial peptide (LURL)₃ and its analogues, which periodically feature hydrophobic α-aminoisobutyric acid (Aib, U) and cationic arginine (R), considering the consensus motif recognized by the mitochondrial import receptor Tom20. Circular dichroism measurements and molecular dynamics simulation studies revealed that (LURL)₃ had a propensity to form a stable α-helix in 0.1 M phosphate buffer solution containing 1.0 wt % sodium dodecyl sulfate. After internalization into plant cells via particle bombardment, (LURL)₃ revealed highly selective accumulation in the mitochondria, whereas its analogue (LARL)₃ was predominantly located in the vacuoles in addition to mitochondria. The high selectivity of (LURL)₃ can be attributed to the incorporation of Aib, which promotes the hydrophobic interaction between the MTS and Tom20 by increasing the hydrophobicity and helicity of (LURL)₃. The present study provided a prospective mitochondrial targeting system using the simple design of artificial peptides

Non-Invasive Blood Glucose Sensor: A Feasibility Study

[EN] Diabetes is a chronic disease characterized by abnormal blood glucose levels which has short and long term complications. Management of diabetes relies on a regular control of blood glucose levels, commonly measured with invasive sensors, which are painful and cause patient discomfort. Scientific community is trying to develop noninvasive monitoring sensors to measure blood glucose continuously. Whereas previous work are focused on single methods and techniques, we present hereby a feasibility study of a non-invasive sensor integrating three different types of techniques: electromagnetic, acoustic speed and near infra-red spectroscopy. Our prototype is subject to different sources of bias, however, the cross-compensation of these three techniques can minimize the low performance of single-technique approaches. The results are promising and show the potential of using combined techniques for non-invasive blood glucose measurement.López Albalat, A.; Sanz Alaman, MB.; Dejoz Diez, MC.; Martinez-Millana, A.; Traver Salcedo, V. (2019). Non-Invasive Blood Glucose Sensor: A Feasibility Study. IEEE. 1179-1182. https://doi.org/10.1109/EMBC.2019.8857261S1179118

Técnica histológica para la inclusión en metilmetacrilato de muestras óseas no descalcificadas

La preparación de muestras óseas descalcificadas incluidas en par-alma ha sido durante mucho tiempo una técnica histológica rutinaria en numerosos hospitales y centros de investigación, pero presenta el inconveniente de modificar la estructura de la fase mineral del tejido óseo. Se describe una técnica histológica que permite la obtención de secciones de tejido óseo no descalcificado partiendo de su infiltración e inclusión de metil-metacrilato (MMA). Esta técnica posibilita la cuantificación histomorfométrica del proceso de remodelación ósea y la localización histoquímica de enzimas y diversas sustancias.Demineralized paraffin embedded bone biopsies have been a routine histological technique in many hospitals and research centres, but this technique does not preserve the mineral phase of the bone tissue. A simple polymethyl-methacrylate embedding method is described for undecalcified bone specimens. This method permits an accurate histomorphometrical evaluation of bone remodelling and enzymes and other substances can be histochemically localized

Nueva plataforma dinamométrica para el análisis y valoración del rendimiento deportivo

Un nuevo modelo de plataforma dinamométrica ha sido desarrollado por el Instituto de Biomecánica de Valencia (IBV) y se han fabricado sus primeros prototipos. Permite la medida de la fuerza de reaccipón tridimensional, en momento torsor y el punto de aplicación de la fuerza, a una velocidad de muestre0 de hasta 1000 Hz (500 Hz para dos plataformas). El nuevo diseño se caracteriza por poseer cuatro captadores bidimensionales octogonales mecánicamente desacoplados, placa superior de rigidez optimizada y sensibilidad cruzada mínima

Criterios biomecánicos de diseño de un nuevo sistema de fijación externa: Stronger®

Se presenta el desarrollo de un nuevo sistema de fijación externa basado en estudios de investigación aplicada, cuyos resultados se han plasmado en criterios de diseño clínicos y biomecánicos. Los aspectos novedosos contemplados se refieren a un aumento de la rigidez del montaje en base a la fijación y el dentado de las rótulas de articulación. Asimismo, se facilita la técnica quirúrgica mediante el taladrado y colocación de las agujas sin la utilización de plantillas y la posibilidad de corregir desplazamientos en el foco fractuario de forma independiente en los tres planos del espacio. Finalmente, se ha diseñado un sistema de monitorización, acoplable al fijador, para caracterizar mecánicamente el callo de fractura durante el período de consolidación.A new external fixation system has been designed based on previous applied research studies. The design criteria generated were focused on both clinical and biomechanical aspects. An increase in frame stiffness was obtained by means of an independent fixation system of the pins, clamp sleeves and striated hinges. Furthermore, surgical technique has been simplified by means of independent adjustment in the three space planes of movement. The use of a previous guide fixator for drilling and pin insertion was eliminated. Finally, a strain gauge monitoring system has been developed to characterize mechanical callus features during fracture healing