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1.
Sci Adv ; 10(25): eadm9228, 2024 Jun 21.
Artículo en Inglés | MEDLINE | ID: mdl-38905339

RESUMEN

Transient receptor potential melastatin 8 (TRPM8) is a temperature- and menthol-sensitive ion channel that contributes to diverse physiological roles, including cold sensing and pain perception. Clinical trials targeting TRPM8 have faced repeated setbacks predominantly due to the knowledge gap in unraveling the molecular underpinnings governing polymodal activation. A better understanding of the molecular foundations between the TRPM8 activation modes may aid the development of mode-specific, thermal-neutral therapies. Ancestral sequence reconstruction was used to explore the origins of TRPM8 activation modes. By resurrecting key TRPM8 nodes along the human evolutionary trajectory, we gained valuable insights into the trafficking, stability, and function of these ancestral forms. Notably, this approach unveiled the differential emergence of cold and menthol sensitivity over evolutionary time, providing a fresh perspective on complex polymodal behavior. These studies provide a paradigm for understanding polymodal behavior in TRPM8 and other proteins with the potential to enhance our understanding of sensory receptor biology and pave the way for innovative therapeutic interventions.


Asunto(s)
Frío , Mentol , Canales Catiónicos TRPM , Canales Catiónicos TRPM/metabolismo , Canales Catiónicos TRPM/genética , Humanos , Mentol/farmacología , Evolución Molecular , Filogenia , Sensación Térmica
2.
Br Poult Sci ; 65(2): 165-178, 2024 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-38372652

RESUMEN

1. It was hypothesised that perch material and design may affect utility and maintenance energy demand in laying hens, affecting their feed form preferences and daily feed consumption. Accordingly, perch design and feed form on hen performance, gastrointestinal tract functions and some behavioural and welfare-related traits were studied in laying hens (ATAK-S) reared in enriched colony cages from 24 to 40 weeks of age.2. The experiment was a 2 × 2 factorial investigating two perch materials and design (circular steel or mushroom-shaped plastic) and feed form (mash or crumble). A total of 396 hens were randomly assigned to one of the four treatment groups with nine replicates each (11 birds per replicate).3. Except for feeding behaviour and prevalence of foot pad dermatitis at 40 weeks of age, the modification of the perch design did not have a significant effect on the traits examined. Mushroom-shaped plastic perches reduced feeding behaviour (p < 0.01) and the incidence of foot pad dermatitis at 40 weeks of age (p < 0.001).4. Performance traits were not affected by feed form. Intake, final body weight and FCR for crumble-fed laying hens were greater than those fed mash (p < 0.01).5. Hens fed mash had higher (p < 0.01) relative gizzard weights along with lower (p < 0.05) pH values, pancreatic chymotrypsin, amylase and lipase activities (p < 0.05), and duodenal absorption surface areas (p < 0.01). Ultimately, this gave higher protein digestibility (p < 0.05) compared to those receiving crumble.6. In conclusion, in enriched cage rearing systems, mashed feed was preferred over crumble to efficiently maintain productive performance. Compared to circular steel, plastic mushroom-shaped perches were associated with better footpad health and welfare.


Asunto(s)
Dermatitis , Animales , Femenino , Alimentación Animal/análisis , Bienestar del Animal , Pollos , Dermatitis/etiología , Dermatitis/veterinaria , Tracto Gastrointestinal , Vivienda para Animales , Acero
3.
bioRxiv ; 2024 Jan 30.
Artículo en Inglés | MEDLINE | ID: mdl-37745560

RESUMEN

We integrate evolutionary predictions based on the neutral theory of molecular evolution with protein dynamics to generate mechanistic insight into the molecular adaptations of the SARS-COV-2 Spike (S) protein. With this approach, we first identified Candidate Adaptive Polymorphisms (CAPs) of the SARS-CoV-2 Spike protein and assessed the impact of these CAPs through dynamics analysis. Not only have we found that CAPs frequently overlap with well-known functional sites, but also, using several different dynamics-based metrics, we reveal the critical allosteric interplay between SARS-CoV-2 CAPs and the S protein binding sites with the human ACE2 (hACE2) protein. CAPs interact far differently with the hACE2 binding site residues in the open conformation of the S protein compared to the closed form. In particular, the CAP sites control the dynamics of binding residues in the open state, suggesting an allosteric control of hACE2 binding. We also explored the characteristic mutations of different SARS-CoV-2 strains to find dynamic hallmarks and potential effects of future mutations. Our analyses reveal that Delta strain-specific variants have non-additive (i.e., epistatic) interactions with CAP sites, whereas the less pathogenic Omicron strains have mostly additive mutations. Finally, our dynamics-based analysis suggests that the novel mutations observed in the Omicron strain epistatically interact with the CAP sites to help escape antibody binding.

5.
Eur Rev Med Pharmacol Sci ; 27(18): 8531-8539, 2023 09.
Artículo en Inglés | MEDLINE | ID: mdl-37782169

RESUMEN

OBJECTIVE: Massive hemorrhage is a serious event that threatens the lives of patients. Fibrinogen concentrate (FC) can control bleeding without causing viral complications and without volume loading, which can happen in transfusion-associated circulatory overload and transfusion-associated acute lung injury. FC application is easy and does not require dissolution or extra devices. It is a cost-effective agent when considering the blood and products used in large quantities. PATIENTS AND METHODS: A total of 67 postpartum hemorrhage (PPH) and trauma patients' medical records, who had ASA I-III classification (The American Society of Anesthesiologists classification of physical status), were obtained. Patients were divided into two groups (fibrinogen level ≤ 100 mg/dl and ≥ 101 mg/dl). The following information was obtained from patient files: demographic parameters, history of operations, and laboratory findings (i.e., complete blood counts, coagulation tests, and fibrinogen levels). Also, the duration of intensive care unit stays and mechanical ventilation application days, the administration of fresh frozen plasma (FFP), erythrocytes, platelets, and FC numbers, and tranexamic acid infusion were recorded. RESULTS: There was no mortality in PPH patients in either group (fibrinogen level ≤ 100 mg/dl and ≥ 101 mg/dl). The mortality rate in trauma patients was significantly higher in the group with fibrinogen levels ≤ 100. A total of 170 g of FC were given to PPH patients and 92 g to trauma patients. There were statistically significant differences between the preoperative PT (prothrombin time), postoperative APTT (activated partial thromboplastin time), postoperative PT, and postoperative INR (international normalized ratio) levels of the patients in the group with fibrinogen levels ≤ 100. Mortality rates were also significantly higher, and hospital stays significantly longer in trauma patients in the group with fibrinogen levels ≤ 100. CONCLUSIONS: Therapy may be considered during massive bleeding and transfusion, as it can help to increase fibrinogen levels quickly and efficiently. Compared with FFP, fibrinogen concentrate may have some advantages in reducing the risk of fluid overload. FFP contains a range of clotting factors, including fibrinogen. It also contains other proteins and fluids that can lead to fluid overload, especially when given in large volumes during massive transfusions.


Asunto(s)
Fibrinógeno , Hemorragia Posparto , Femenino , Embarazo , Humanos , Fibrinógeno/uso terapéutico , Hemorragia Posparto/tratamiento farmacológico , Pruebas de Coagulación Sanguínea , Tiempo de Tromboplastina Parcial , Tiempo de Protrombina
6.
Protein Sci ; 32(9): e4759, 2023 09.
Artículo en Inglés | MEDLINE | ID: mdl-37574787

RESUMEN

Proteins gain optimal fitness such as foldability and function through evolutionary selection. However, classical studies have found that evolutionarily designed protein sequences alone cannot guarantee foldability, or at least not without considering local contacts associated with the initial folding steps. We previously showed that foldability and function can be restored by removing frustration in the folding energy landscape of a model WW domain protein, CC16, which was designed based on Statistical Coupling Analysis (SCA). Substitutions ensuring the formation of five local contacts identified as "on-path" were selected using the closest homolog native folded sequence, N21. Surprisingly, the resulting sequence, CC16-N21, bound to Group I peptides, while N21 did not. Here, we identified single-point mutations that enable N21 to bind a Group I peptide ligand through structure and dynamic-based computational design. Comparison of the docked position of the CC16-N21/ligand complex with the N21 structure showed that residues at positions 9 and 19 are important for peptide binding, whereas the dynamic profiles identified position 10 as allosterically coupled to the binding site and exhibiting different dynamics between N21 and CC16-N21. We found that swapping these positions in N21 with matched residues from CC16-N21 recovers nature-like binding affinity to N21. This study validates the use of dynamic profiles as guiding principles for affecting the binding affinity of small proteins.


Asunto(s)
Mutación con Ganancia de Función , Proteínas , Ligandos , Dominios WW , Secuencia de Aminoácidos , Proteínas/química , Péptidos/química , Pliegue de Proteína
7.
Protein Sci ; 32(8): e4700, 2023 08.
Artículo en Inglés | MEDLINE | ID: mdl-37313628

RESUMEN

We investigated the relationship between mutations and dynamics in Escherichia coli dihydrofolate reductase (DHFR) using computational methods. Our study focused on the M20 and FG loops, which are known to be functionally important and affected by mutations distal to the loops. We used molecular dynamics simulations and developed position-specific metrics, including the dynamic flexibility index (DFI) and dynamic coupling index (DCI), to analyze the dynamics of wild-type DHFR and compared our results with existing deep mutational scanning data. Our analysis showed a statistically significant association between DFI and mutational tolerance of the DHFR positions, indicating that DFI can predict functionally beneficial or detrimental substitutions. We also applied an asymmetric version of our DCI metric (DCIasym ) to DHFR and found that certain distal residues control the dynamics of the M20 and FG loops, whereas others are controlled by them. Residues that are suggested to control the M20 and FG loops by our DCIasym metric are evolutionarily nonconserved; mutations at these sites can enhance enzyme activity. On the other hand, residues controlled by the loops are mostly deleterious to function when mutated and are also evolutionary conserved. Our results suggest that dynamics-based metrics can identify residues that explain the relationship between mutation and protein function or can be targeted to rationally engineer enzymes with enhanced activity.


Asunto(s)
Proteínas de Escherichia coli , Tetrahidrofolato Deshidrogenasa , Tetrahidrofolato Deshidrogenasa/química , Escherichia coli/metabolismo , Proteínas de Escherichia coli/química , Simulación de Dinámica Molecular , Mutación
8.
Biophys J ; 122(14): 2938-2947, 2023 07 25.
Artículo en Inglés | MEDLINE | ID: mdl-36726312

RESUMEN

Sequencing of the protein coding genome has revealed many different missense mutations of human proteins and different population frequencies of corresponding haplotypes, which consist of different sets of those mutations. Here, we present evidence for pairwise intramolecular epistasis (i.e., nonadditive interactions) between many such mutations through an analysis of protein dynamics. We suggest that functional compensation for conserving protein dynamics is a likely evolutionary mechanism that maintains high-frequency mutations that are individually nonneutral but epistatically compensating within proteins. This analysis is the first of its type to look at human proteins with specific high population frequency mutations and examine the relationship between mutations that make up that observed high-frequency protein haplotype. Importantly, protein dynamics revealed a separation between high and low frequency haplotypes within a target protein cytochrome P450 2A7, with the high-frequency haplotypes showing behavior closer to the wild-type protein. Common protein haplotypes containing two mutations display dynamic compensation in which one mutation can correct for the dynamic effects of the other. We also utilize a dynamics-based metric, EpiScore, that evaluates the epistatic interactions and allows us to see dynamic compensation within many other proteins.


Asunto(s)
Evolución Biológica , Epistasis Genética , Humanos , Mutación
9.
J Phys Chem B ; 127(3): 616-622, 2023 01 26.
Artículo en Inglés | MEDLINE | ID: mdl-36633931

RESUMEN

Previous studies of the flexibility of ancestral proteins suggest that proteins evolve their function by altering their native state ensemble. Here, we propose a more direct method to analyze such changes during protein evolution by comparing thermally activated vibrations at frequencies below 6 THz, which report on the dynamics of collective protein modes. We analyzed the backbone vibrational density of states of ancestral and extant ß-lactamases and thioredoxins and observed marked changes in the vibrational spectrum in response to evolution. Coupled with previously observed changes in protein flexibility, the observed shifts of vibrational mode densities suggest that protein dynamics and dynamical allostery are critical factors for the evolution of enzymes with specialized catalytic and biophysical properties.


Asunto(s)
Proteínas , Vibración , beta-Lactamasas
10.
Elife ; 112022 12 06.
Artículo en Inglés | MEDLINE | ID: mdl-36472898

RESUMEN

We develop integrated co-evolution and dynamic coupling (ICDC) approach to identify, mutate, and assess distal sites to modulate function. We validate the approach first by analyzing the existing mutational fitness data of TEM-1 ß-lactamase and show that allosteric positions co-evolved and dynamically coupled with the active site significantly modulate function. We further apply ICDC approach to identify positions and their mutations that can modulate binding affinity in a lectin, cyanovirin-N (CV-N), that selectively binds to dimannose, and predict binding energies of its variants through Adaptive BP-Dock. Computational and experimental analyses reveal that binding enhancing mutants identified by ICDC impact the dynamics of the binding pocket, and show that rigidification of the binding residues compensates for the entropic cost of binding. This work suggests a mechanism by which distal mutations modulate function through dynamic allostery and provides a blueprint to identify candidates for mutagenesis in order to optimize protein function.


Asunto(s)
Ejercicio Físico
11.
PLoS Comput Biol ; 18(4): e1010006, 2022 04.
Artículo en Inglés | MEDLINE | ID: mdl-35389981

RESUMEN

Many pathogenic missense mutations are found in protein positions that are neither well-conserved nor fall in any known functional domains. Consequently, we lack any mechanistic underpinning of dysfunction caused by such mutations. We explored the disruption of allosteric dynamic coupling between these positions and the known functional sites as a possible mechanism for pathogenesis. In this study, we present an analysis of 591 pathogenic missense variants in 144 human enzymes that suggests that allosteric dynamic coupling of mutated positions with known active sites is a plausible biophysical mechanism and evidence of their functional importance. We illustrate this mechanism in a case study of ß-Glucocerebrosidase (GCase) in which a vast majority of 94 sites harboring Gaucher disease-associated missense variants are located some distance away from the active site. An analysis of the conformational dynamics of GCase suggests that mutations on these distal sites cause changes in the flexibility of active site residues despite their distance, indicating a dynamic communication network throughout the protein. The disruption of the long-distance dynamic coupling caused by missense mutations may provide a plausible general mechanistic explanation for biological dysfunction and disease.


Asunto(s)
Mutación Missense , Proteínas , Dominio Catalítico/genética , Humanos , Mutación , Mutación Missense/genética , Proteínas/química
12.
Biophys J ; 121(8): 1483-1492, 2022 04 19.
Artículo en Inglés | MEDLINE | ID: mdl-35300968

RESUMEN

The SARS-CoV-2 coronavirus has become one of the most immediate and widely studied systems since its identification and subsequent global outbreak from 2019 to 2022. In an effort to understand the biophysical changes as a result of mutations, the mechanistic details of multiple different proteins within the SARS-CoV-2 virus have been studied and compared with SARS-CoV-1. Focusing on the main protease (mPro), we explored the long-range dynamics using the Dynamic Coupling Index (DCI) to investigate the dynamic coupling between the catalytic site residues and the rest of the protein, both inter- and intrachain, for the CoV-1 and CoV-2 mPro. We found that there is significant cross-chain coupling between these active sites and specific distal residues in the CoV-2 mPro not present in CoV-1. The enhanced long-distance interactions, particularly between the two chains, suggest subsequently enhanced cooperativity for CoV-2. A further comparative analysis of the dynamic flexibility using the dynamic flexibility index (DFI) between the CoV-1 and CoV-2 mPros shows that the inhibitor binding near active sites induces change in flexibility to a distal region of the protein, opposite in behavior between the two systems; this region becomes more flexible upon inhibitor binding in CoV-1, while it becomes less flexible in the CoV-2 mPro. Upon inspection, we show that, on average, the dynamic flexibility of the sites substituted from CoV-1 to CoV-2 changes significantly less than the average calculated across all residues within the structure, indicating that the differences in behaviors between the two systems is likely the result of allosteric influence, in which the new substitutions in CoV-2 induce flexibility and dynamic changes elsewhere in the structure.


Asunto(s)
COVID-19 , Inhibidores de Proteasas , Endopeptidasas , Humanos , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Péptido Hidrolasas , Inhibidores de Proteasas/farmacología , SARS-CoV-2
13.
Br Poult Sci ; 63(1): 21-30, 2022 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-34309443

RESUMEN

1. This study evaluated the effect of a higher incubation temperature on body weight, plasma profile, histology and expression of myogenin (MYOG), insulin-like growth factor-I (IGF-I) and vascular endothelial growth factor A (VEGFA) genes in breast muscle of embryos and broilers from two commercial strains.2. A total of 784 eggs from Ross 308 and Cobb 500 broiler breeder flocks were used. Half of the eggs per strain were incubated at control temperature (37.8°C), whereas the other half were exposed to heat treatment (HT) of 38.8°C between embryonic day (ED) 10 and 14, for 6 h/day. Embryos and chicks were sampled on ED 19 and at hatch. A total of 480, one-day-old chicks per strain and incubation temperature were reared up to 42 d post-hatch.3. The HT increased hatch weight of Ross chicks and 42-d body weight of broilers from both strains. Lower plasma triacylglycerol levels were measured for HT embryos and broilers on ED 19 and 42 d post-hatch, respectively. HT reduced plasma T3 levels in Ross embryos and broilers for the same periods. Hepatic TBARS concentrations were elevated by HT compared to the control incubation.4. The HT reduced breast muscle VEGFA gene expression of Cobb embryos on ED 19, whereas expression was stimulated in day-old chicks. At 42 d post-hatch, fibre area was increased by HT regardless of strain. Compared to the control incubation, HT increased the breast yield of Ross broilers and leg yield of Cobb. Ross-HT broilers had a higher pH at 24 h after slaughter and better water holding capacity than Cobb-HT broilers.5. These results suggested that HT increased body weight, fibre area, IGF-I gene expression and lowered plasma triacylglycerol levels of broiler chickens from both strains at 42 d. However, HT influenced the expression of VEGF-A and MYOG genes and meat quality differently between the broiler strains.


Asunto(s)
Pollos , Factor A de Crecimiento Endotelial Vascular , Animales , Peso Corporal , Pollos/genética , Óvulo , Músculos Pectorales , Temperatura , Factor A de Crecimiento Endotelial Vascular/genética
15.
Int J Mol Sci ; 22(6)2021 Mar 12.
Artículo en Inglés | MEDLINE | ID: mdl-33809335

RESUMEN

The relationship between protein motions (i.e., dynamics) and enzymatic function has begun to be explored in ß-lactamases as a way to advance our understanding of these proteins. In a recent study, we analyzed the dynamic profiles of TEM-1 (a ubiquitous class A ß-lactamase) and several ancestrally reconstructed homologues. A chief finding of this work was that rigid residues that were allosterically coupled to the active site appeared to have profound effects on enzyme function, even when separated from the active site by many angstroms. In the present work, our aim was to further explore the implications of protein dynamics on ß-lactamase function by altering the dynamic profile of TEM-1 using computational protein design methods. The Rosetta software suite was used to mutate amino acids surrounding either rigid residues that are highly coupled to the active site or to flexible residues with no apparent communication with the active site. Experimental characterization of ten designed proteins indicated that alteration of residues surrounding rigid, highly coupled residues, substantially affected both enzymatic activity and stability; in contrast, native-like activities and stabilities were maintained when flexible, uncoupled residues, were targeted. Our results provide additional insight into the structure-function relationship present in the TEM family of ß-lactamases. Furthermore, the integration of computational protein design methods with analyses of protein dynamics represents a general approach that could be used to extend our understanding of the relationship between dynamics and function in other enzyme classes.


Asunto(s)
Proteínas Mutantes/genética , Conformación Proteica , Ingeniería de Proteínas , beta-Lactamasas/genética , Aminoácidos/genética , Bacterias/enzimología , Sitios de Unión/genética , Dominio Catalítico/genética , Biología Computacional , Estabilidad de Enzimas/genética , Escherichia coli/enzimología , Modelos Moleculares , Simulación de Dinámica Molecular , Proteínas Mutantes/ultraestructura , Homología de Secuencia de Aminoácido , Relación Estructura-Actividad , beta-Lactamasas/ultraestructura
16.
Nat Commun ; 12(1): 1852, 2021 03 25.
Artículo en Inglés | MEDLINE | ID: mdl-33767175

RESUMEN

TEM-1 ß-lactamase degrades ß-lactam antibiotics with a strong preference for penicillins. Sequence reconstruction studies indicate that it evolved from ancestral enzymes that degraded a variety of ß-lactam antibiotics with moderate efficiency. This generalist to specialist conversion involved more than 100 mutational changes, but conserved fold and catalytic residues, suggesting a role for dynamics in enzyme evolution. Here, we develop a conformational dynamics computational approach to rationally mold a protein flexibility profile on the basis of a hinge-shift mechanism. By deliberately weighting and altering the conformational dynamics of a putative Precambrian ß-lactamase, we engineer enzyme specificity that mimics the modern TEM-1 ß-lactamase with only 21 amino acid replacements. Our conformational dynamics design thus re-enacts the evolutionary process and provides a rational allosteric approach for manipulating function while conserving the enzyme active site.


Asunto(s)
beta-Lactamasas/genética , beta-Lactamasas/metabolismo , Secuencia de Aminoácidos/genética , Dominio Catalítico/genética , Biología Computacional , Escherichia coli/efectos de los fármacos , Escherichia coli/enzimología , Evolución Molecular , Simulación de Dinámica Molecular , Penicilinas/metabolismo , Conformación Proteica , Especificidad por Sustrato
17.
Animal ; 15(1): 100023, 2021 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-33515989

RESUMEN

Improved animal health can reduce greenhouse gas (GHG) emissions intensity in livestock systems while increasing productivity. Integrated modelling of disease impacts on farm-scale emissions is important in identifying effective health strategies to reduce emissions. However, it requires that modellers understand the pathways linking animal health to emissions and how these might be incorporated into models. A key barrier to meeting this need has been the lack of a framework to facilitate effective exchange of knowledge and data between animal health experts and emissions modellers. Here, these two communities engaged in workshops, online exchanges and a survey to i) identify a comprehensive list of disease-related model parameters and ii) test its application to evaluating models. Fifty-six parameters were identified and proved effective in assessing the potential of farm-scale models to characterise livestock disease impacts on GHG emissions. Easy wins for the emissions models surveyed include characterising disease impacts related to feeding.


Asunto(s)
Gases de Efecto Invernadero , Animales , Granjas , Efecto Invernadero , Gases de Efecto Invernadero/análisis , Ganado
18.
Mol Biol Evol ; 38(1): 201-214, 2021 01 04.
Artículo en Inglés | MEDLINE | ID: mdl-32780837

RESUMEN

Amino acid substitutions at nonconserved protein positions can have noncanonical and "long-distance" outcomes on protein function. Such outcomes might arise from changes in the internal protein communication network, which is often accompanied by changes in structural flexibility. To test this, we calculated flexibilities and dynamic coupling for positions in the linker region of the lactose repressor protein. This region contains nonconserved positions for which substitutions alter DNA-binding affinity. We first chose to study 11 substitutions at position 52. In computations, substitutions showed long-range effects on flexibilities of DNA-binding positions, and the degree of flexibility change correlated with experimentally measured changes in DNA binding. Substitutions also altered dynamic coupling to DNA-binding positions in a manner that captured other experimentally determined functional changes. Next, we broadened calculations to consider the dynamic coupling between 17 linker positions and the DNA-binding domain. Experimentally, these linker positions exhibited a wide range of substitution outcomes: Four conserved positions tolerated hardly any substitutions ("toggle"), ten nonconserved positions showed progressive changes from a range of substitutions ("rheostat"), and three nonconserved positions tolerated almost all substitutions ("neutral"). In computations with wild-type lactose repressor protein, the dynamic couplings between the DNA-binding domain and these linker positions showed varied degrees of asymmetry that correlated with the observed toggle/rheostat/neutral substitution outcomes. Thus, we propose that long-range and noncanonical substitutions outcomes at nonconserved positions arise from rewiring long-range communication among functionally important positions. Such calculations might enable predictions for substitution outcomes at a range of nonconserved positions.


Asunto(s)
Sustitución de Aminoácidos , Evolución Molecular , Represoras Lac/genética
19.
Entropy (Basel) ; 22(6)2020 Jun 16.
Artículo en Inglés | MEDLINE | ID: mdl-33286439

RESUMEN

Understanding the underlying mechanisms behind protein allostery and non-additivity of substitution outcomes (i.e., epistasis) is critical when attempting to predict the functional impact of mutations, particularly at non-conserved sites. In an effort to model these two biological properties, we extend the framework of our metric to calculate dynamic coupling between residues, the Dynamic Coupling Index (DCI) to two new metrics: (i) EpiScore, which quantifies the difference between the residue fluctuation response of a functional site when two other positions are perturbed with random Brownian kicks simultaneously versus individually to capture the degree of cooperativity of these two other positions in modulating the dynamics of the functional site and (ii) DCIasym, which measures the degree of asymmetry between the residue fluctuation response of two sites when one or the other is perturbed with a random force. Applied to four independent systems, we successfully show that EpiScore and DCIasym can capture important biophysical properties in dual mutant substitution outcomes. We propose that allosteric regulation and the mechanisms underlying non-additive amino acid substitution outcomes (i.e., epistasis) can be understood as emergent properties of an anisotropic network of interactions where the inclusion of the full network of interactions is critical for accurate modeling. Consequently, mutations which drive towards a new function may require a fine balance between functional site asymmetry and strength of dynamic coupling with the functional sites. These two tools will provide mechanistic insight into both understanding and predicting the outcome of dual mutations.

20.
Int J Cosmet Sci ; 42(6): 536-547, 2020 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-32441822

RESUMEN

OBJECTIVE: Conventional rheological techniques in the linear viscoelastic region provide insights about the spatial configuration of the microstructural components of personal care formulations in their 'at-rest' state. However, they fail to describe the textural experience associated with large and fast deformations during daily consumer application. In this study we present a non-conventional rheological technique-large amplitude oscillatory shear (LAOS)-for probing the transformation of a material during its application. This technique is proposed a practical tool for formulators in their efforts to design products with desired textural attributes. METHODS: A non-linear rheological technique termed LAOS was utilized to capture the textural expression perceived by consumers. Lissajous plots (stress vs. strain or strain rate) provide a fingerprint of the formula and are utilized to both analyse the thickening mechanism and monitor the influence of various parameters, such as the chemistry, molecular properties, colloidal parameters and processing conditions. RESULTS: In this study, we showcased several approaches for modifying the texture of personal care formulations and show the influence of various parameters on the characteristics of the Lissajous curves and their relation to sensorial perception. This fingerprinting technique shows that increasing the molecular weight or hydrophobic modification boosts the elasticity and thickening efficiency of a given polymer. Differences in the chemistry of rheological ingredients also influence the characteristic Lissajous fingerprint. In high concentration surfactant systems, which tend to form worm-like micelles, their unique Lissajous fingerprints indicate structure rebuild because of fast kinetics at large but slow deformations. Analysis of lamellar gel-based hair conditioner formulations demonstrates the unique high yield stress of these types of materials, accompanied by the fast breakdown transition from a solid to viscous structure because of their crystalline lamellar gel structure. CONCLUSION: The LAOS technique presented in this article is intended to better capture the textural expression perceived by consumers. Lissajous plots-generated from the LAOS experimental data-provide a fingerprint of the tested formula and are utilized to both analyse the thickening mechanism and monitor the influence of various parameters, such as the chemistry and molecular weight of the thickener, pH of the formula medium and influence of other ingredients in the formula (surfactants, emulsifiers, etc.).


OBJECTIF: Les techniques rhéologiques conventionnelles dans la région viscoélastique linéaire fournissent des informations sur la configuration spatiale des composants microstructurels des formulations de produits cosmétiques dans leur état « au repos ¼. Mais elles ne décrivent pas l'expérience de texture associée à des déformations importantes et rapides lors de l'application quotidienne par les consommateurs. Dans cette étude, nous présentons une technique rhéologique non conventionnelle, le cisaillement oscillatoire à grande amplitude (Large Amplitude Oscillatory Shear, LAOS), pour examiner la transformation d'un matériau pendant son application. Cette technique est proposée comme outil pratique pour aider les formulateurs dans leurs efforts pour concevoir des produits qui ont les attributs texturaux désirés. MÉTHODES: Une technique rhéologique non linéaire appelée LAOS a été utilisée pour capturer le style textural perçu par les consommateurs. Les courbes de Lissajous (stress vs contrainte ou taux de déformation) fournissent une empreinte de la formule et sont utilisées pour analyser le comportement épaississant et surveiller l'influence de divers paramètres, tels que les propriétés moléculaires et chimiques, les paramètres colloïdaux et les conditions de traitement. RÉSULTATS: Dans cette étude, nous avons présenté plusieurs approches pour modifier la texture des formulations cosmétiques et montrer l'influence de divers paramètres sur les caractéristiques des courbes de Lissajous et leur relation avec la perception sensorielle. Cette technique d'empreintes montre que l'augmentation du poids moléculaire ou la modification hydrophobe stimule l'élasticité et l'épaississement d'un polymère donné. Les différences dans la chimie des ingrédients rhéologiques influencent également l'empreinte caractéristique de Lissajous. Dans les systèmes de tensioactifs à haute concentration, qui ont tendance à former des micelles semblables à des vers, leurs empreintes Lissajous uniques indiquent une reconstruction de la structure à cause de cinétiques rapides dans leur ensemble mais des déformations lentes. L'analyse des des formulations lamellaires d'après-shampooing à base de gel démontre le stress unique à haut rendement de ces types de matériaux, accompagnés par la transition de répartition rapide d'une structure solide à visqueuse à cause de leur structure lamellaire cristalline. CONCLUSION: La technique LAOS présentée dans cet article vise à mieux appréhender le style de texture perçu par les consommateurs. Les graphiques de Lissajous, générées à partir de données LAOS expérimentales, fournissent une empreinte de la formule testée et sont utilisés pour analyser le mécanisme épaississant et surveiller l'influence de divers paramètres, tels que la chimie et le poids moléculaire de l'épaississant, le Ph moyen et l'influence des autres ingrédients (tensioactifs, émulsifiants, etc.) dans la formule.


Asunto(s)
Cosméticos/química , Reología , Composición de Medicamentos , Humanos , Interacciones Hidrofóbicas e Hidrofílicas , Estructura Molecular , Peso Molecular , Polímeros/química
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