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SAXSMoW (SAXS Molecular Weight) is an online platform widely used over the past few years for determination of molecular weights of proteins in dilute solutions. The scattering intensity retrieved from small‐angle X‐ray scattering (SAXS) raw data is the sole input to SAXSMoW for determination of molecular weights of proteins in liquid. The current updated SAXSMoW version 3.0 determines the linear dependence of the true protein volume on their apparent protein volume, based on SAXS curves calculated for 67,000 protein structures selected from the Protein Data Bank. SAXSMoW 3.0 was tested against 43 experimental SAXS scattering curves from proteins with known molecular weights. Our results demonstrate that most of the molecular weights determined for the nonglycosylated and also for the glycosylated proteins are in good agreement with their expected molecular weights. Additionally, the average discrepancies between the calculated molecular weights and their nominal values for glycosylated proteins are similar to those for nonglycosylated ones. [ABSTRACT FROM AUTHOR]

Background: Caries constitute an infectious disease that result from the interaction of bacteria with the host and the oral environment. Streptococcus mutans (S. mutans) represents the main bacterium that causes caries. The ability of S. mutans to form biofilms in the oral cavity is influenced by daily nutrient intake. This study of bacterial biofilm proteins can be used in the manufacture of kits for the detection of infectious diseases such as caries in the oral cavity. A biomarker is required for the manufacture of the detection kit. Consequently, research must first be conducted to determine the molecular weight and density of S. mutans biofilm proteins induced by several different daily nutrients, namely; 5% glucose, 5% lactose, soy protein and 5% iron. Purpose: This study aimed to analyse the density of S. mutans biofilm protein induced by 5% glucose, 5% lactose, soy protein, and 5% iron. Methods: The density of the S. mutans biofilm protein bands induced were measured using EZ Imager Gel DocTM software. Results: A band of biofilm protein (61.7 kDa) was obtained from S. mutans induced by 5% glucose, four bands of biofilm protein (180 kDa; 153,9 kDa; 43,9 kDa; 37,5 kDa) from 5% lactose induction and seven bands of biofilm protein (157,9 kDa; 86,6 kDa; 66,5 kDa; 50,1 kDa; 37,9 kDa; 32,3 kDa; 29,4 kDa) from soy protein induction. In contrast, S. mutans induced by 5% iron did not show any protein bands. The proteins that result from each inducer are of differing densities. Conclusion: The protein bands from each inducer are of different densities which can be used in the further test to make a biomarker for dental caries detection kits.

Hideaki Okawada, Yuta Saito, Shigehiro Iwabuchi, Shotaro Kosuge, Haruo Takahashi, Hidetoshi Onda, Masahiro Kito Department of Ophthalmology, Showa University, Tokyo, Japan Purpose: Vascular endothelial growth factor (VEGF) plays an important role in branch retinal vein occlusion (BRVO) with cystoid macular edema (CME). Monitoring changes in VEGF is crucial for evaluating treatment but requires vitreous or aqueous humor sampling, which hampers its clinical application. We investigated the correlation between VEGF and protein concentration in the aqueous humor (flare) and whether this could be used to monitor treatment-related VEGF changes. Design: This retrospective observational study involved 19 previously untreated patients with BRVO. Aqueous humor was obtained, and intravitreal ranibizumab (IVR) injection was administered to these patients. The correlation between VEGF and flare, central retinal thickness (CRT), and best-corrected visual acuity (BCVA) was investigated. Differences in these values were considered between pre-IVR and 1 week and 1–3 months post-IVR. Moreover, in patients with recurrence who received additional IVR, further changes in VEGF were examined. Main outcome measures: The end point of this study was BCVA, flare, and CRT at the fovea. Results: Significant improvement was seen in BCVA and CRT at all time points and in Flare at 1 vs 3 months post-IVR; nevertheless, additional IVR was necessary in 94% of cases. In a patient with recurrence, CRT did not improve, even though VEGF decreased. Conclusion: Flare may be effective for estimating VEGF levels in aqueous humor pre-IVR. Inflammation-related molecules other than VEGF may be related to recurrence. Keywords: aqueous humor, branch retinal vein occlusion, flare, protein density, ranibizumab, vascular endothelial growth factor

Starting with the Rayleigh charge limiting model, a slightly different approach is used to account for the well-known discrepancy that exists between the said model and experimental ESI MS data for globular proteins. It is shown using published datasets that for globular proteins, the mass density ρ exhibits a weak second-order dependence on its mass M, according to ρ(M)∝M-α, α ~ 0.14. A direct equivalence established between ESI MS and x-ray techniques suggests a minimum but critical surface tension of 15.6 ± 5.2 mN/m for the droplet at the liquid-to-gas phase transition point. The packing density factor η for globular proteins is believed to lie between 1 (very tightly packed) and 4.6 (less tight, natively packed). While the Rayleigh charge limiting model has been linked historically to the CRM (J. Chem. Phys. 49:2240-2249, 1968; Anal. Chim. Acta 406:93-104, 2000), this paper does not expressly seek to justify the CRM, but rather uses empirical data and existing knowledge across subfields to help build a consistent picture of ESI MS phenomena that might be difficult to explain otherwise. These results would be useful in molecular dynamics (MD) simulations, understanding liquid-to-gas phase transitions and in opening up new routes for cross-calibration between ESI MS, IM MS, NMR and x-ray crystallography studies.ᅟ [ABSTRACT FROM AUTHOR]

Summary Protein is the only dietary macronutrient required for life. As such, it is reasonable to consider dietary protein as the centerpiece of a healthy eating pattern. To do so requires consideration of what type of protein should be eaten. Account should be taken of the quality of the protein, the density of the protein in the protein food source, and the non-protein components of protein food source. The quality of protein can be quantified based on the amount and profile of essential amino acids (EAAs), as well as the true ileal digestibility of the EAAs in the protein. The density of protein in a food source can be quantified on the basis of the amount of total calories ingested to achieve intake of the daily requirement of all EAAs. Non-protein components of protein food sources can be considered in terms of the amount and nature of fat, carbohydrate and fiber, as well as the content of micronutrients. Potential beneficial effects of high-quality protein food sources should be balanced against any possible adverse effects. When all of these factors are considered we conclude that animal-based protein foods (e.g., eggs, dairy, meat, fish, poultry) occupy an important place in a healthy eating pattern. [ABSTRACT FROM AUTHOR]

The development of prophylactic vaccines remains largely empirical in nature and rarely have general rules been applied in the strategic decision and the formulation of a viral vaccine. Currently, there are a total of 15 virus agents from 12 unique virus families with vaccines licensed by the U.S. Food and Drug Administration. Extensive structural information on these viral particles and potential mechanisms of protection are available for the majority of these virus pathogens and their respective vaccines. Here I review the quantitative features of these viral surface antigens in relation to the molecular mechanisms of B-cell activation and point out a potential correlation between the density of immunogenic proteins displayed on the surface of the vaccine antigen carrier and the success of a vaccine. These features help us understand the humoral immunity induced by viral vaccines on a quantitative ground and re-emphasize the importance of antigen density on the activation of the immune system. Although the detailed mechanisms behind this phenomenon remain to be explored, it implies that both the size of antigen carriers and the density of immunogenic proteins displayed on these carriers are important parameters that may need to be optimized for the formulation of a vaccine. [ABSTRACT FROM AUTHOR]

Abstract: Biological membranes undergo constant shape remodeling involving the formation of highly curved structures. The lipid bilayer represents the fundamental architecture of the cellular membrane with its shapes determined by the Helfrich curvature bending energy. However, the dynamics of bilayer shape transitions, especially their modulation by membrane proteins, and the resulting shape instabilities, are still not well understood. Here, we review in a unifying manner several theories that describe the fluctuations (i.e. undulations) of bilayer shapes as well as their local coupling with lipid or protein density variation. The coupling between local membrane curvature and lipid density gives rise to a ‘slipping mode’ in addition to the conventional ‘bending mode’ for damping the membrane fluctuation. This leads to a number of interesting experimental phenomena regarding bilayer shape dynamics. More importantly, curvature-inducing proteins can couple with membrane shape and eventually render the membrane unstable. A criterion for membrane shape instability is derived from a linear stability analysis. The instability criterion reemphasizes the importance of membrane tension in regulating the stability and dynamics of membrane geometry. Recent progresses in understanding the role of membrane tension in regulating dynamical cellular processes are also reviewed. Protein density is emphasized as a key factor in regulating membrane shape transitions: a threshold density of curvature coupling proteins is required for inducing membrane morphology transitions. [Copyright &y& Elsevier]

The mass density of proteins is a relevant basic biophysical quantity. It is also a useful input parameter, for example, for three-dimensional structure determination by protein crystallography and studies of protein oligomers in solution by analytic ultracentrifugation. We have performed a critical analysis of published, theoretical, and experimental investigations about this issue and concluded that the average density of proteins is not a constant as often assumed. For proteins with a molecular weight below 20 kDa, the average density exhibits a positive deviation that increases for decreasing molecular weight. A simple molecular-weight-depending function is proposed that provides a more accurate estimate of the average protein density. [ABSTRACT FROM AUTHOR]

A high-protein diet can reduce body weight and increase insulin sensitivity, but whether the type of dietary protein affects these outcomes is unknown. We hypothesized that feeding insulin-resistant rats a high-protein diet (32%) containing whey protein concentrate (WPC) would reduce body weight and tissue lipid levels and increase insulin sensitivity more than a diet containing red meat (RM). Rats were fed a high-fat diet (300 g fat/kg diet) for 9 wk, then switched to a diet containing either 80 or 320 g protein/kg diet, provided by either WPC or RM, for 6 wk (n = 8). The rats were then killed after overnight food deprivation. High dietary protein reduced energy intake (P < 0.001) and visceral (P < 0.001), subcutaneous (P < 0.001), and carcass fat (P < 0.05). Increasing the dietary density of WPC, but not of RM, reduced body weight gain by 4% (P < 0.001). Dietary WPC also reduced plasma insulin concentration by 40% (P < 0.05) and increased insulin sensitivity, compared to RM (P < 0.05). These findings support the conclusions that a high-protein diet reduces energy intake and adiposity and that whey protein is more effective than red meat in reducing body weight gain and increasing insulin sensitivity. [ABSTRACT FROM AUTHOR]

Protein type and density have been shown to influence colon cancer risk using a carcinogen-induced rat model. It is suggested that red meat may promote colon cancer risk more than whey proteins. The aim of this study was to evaluate the influence of red meat, whey protein and their density in the diet on the number of aberrant crypt foci (ACF), preneoplastic markers in Wistar rats.The sources of protein, red meat as barbecued kangaroo muscle meat, and whey protein concentrate were fed to rats to provide 8, 16 and 32% protein by weight in a modified AIN-93 diet with low fiber, low calcium and high polyunsaturated fat. Adult Wistar rats (13 weeks of age) were fed these diets for 4 weeks and then two s.c. injections of azoxymethane, 15 mg/kg BW, were administered 1 week apart. Diets were fed for a further 8 weeks, rats were then killed, their colons fixed in formalin saline and stained with methylene blue to quantify ACF number. Fecal samples were collected and the fecal water was isolated for quantification of heme and thiobarbituric acid reactive substances.Increasing red meat density correlated positively, while increasing dairy protein density correlated negatively with rate of weight gain (p<0.05). Dietary intake was not significantly affected by protein type or density. The 32% whey protein group had significantly less ACF in the proximal colon in comparison to the 16 and 32% red meat groups (p<0.05). This reduction in ACF number in the whey protein group may be caused by hormones associated with the reduction in weight gain, and/or by components of whey protein concentrate such as cysteine, lactose and conjugated linoleic acid which have been shown to have anti-cancer effects. Using ACF number as an index, whey protein appeared to be more protective than red meat. [Copyright &y& Elsevier]

SAXSMoW (SAXS Molecular Weight) is an online platform widely used over the past few years for determination of molecular weights of proteins in dilute solutions. The scattering intensity retrieved from small-angle X-ray scattering (SAXS) raw data is the sole input to SAXSMoW for determination of molecular weights of proteins in liquid. The current updated SAXSMoW version 3.0 determines the linear dependence of the true protein volume on their apparent protein volume, based on SAXS curves calculated for 67,000 protein structures selected from the Protein Data Bank. SAXSMoW 3.0 was tested against 43 experimental SAXS scattering curves from proteins with known molecular weights. Our results demonstrate that most of the molecular weights determined for the nonglycosylated and also for the glycosylated proteins are in good agreement with their expected molecular weights. Additionally, the average discrepancies between the calculated molecular weights and their nominal values for glycosylated proteins are similar to those for nonglycosylated ones., (© 2021 The Protein Society.)

• Protein-enriched diet significantly reduced body weight and fat percentage without losing muscle. • Higher protein density improved physical endurance but increased inflammation. • Sufficient protein intake is not inferior to high protein diet if no exercise intervention is performed. Maintaining sufficient dietary protein intake is important for nutritional status, muscle mass, and healthy aging, but the clinical effects of high protein diet remained controversial.. This 12-week randomized controlled trial enrolled community-dwelling middle-aged and older adults to evaluate clinical effects of daily diet with different protein density.. All participants received 10 frozen meals per week for 12 weeks containing either 15% daily calorie of protein (regular-protein group, RPG), or 25% daily calorie of protein (high-protein group, HPG). Bioimpedance analysis was used to assess body composition, and the magnetic resonance imaging on both mid-thighs was performed to measure muscle mass and the intramuscular adiposity. This trial enrolled 70 participants, and data of 52 participants (mean age: 53.7 ± 8.3 years, 53.8% male; 25 in RPG and 27 in HPG) were available for analysis. Baseline demographic characteristics, functional assessment, body composition and muscle parameters, and laboratory data were similar between groups. During the study period, participants of both groups significantly reduced body weight, body mass index, total body fat percentage, and handgrip strength, but not in the relative appendicular muscle mass). Compared to participants of RPG, HPG participants showed significant improvement in 6-minute walking distance, increased high-sensitivity C-reactive protein and marginal reduction in intramuscular adiposity than RPG participants. Higher dietary protein intake significantly improved physical endurance and marginally reduced intramuscular adiposity, but increased the inflammatory biomarker among middle-aged and older adults. Further study is needed to explore long-term effects of high-protein diet among middle-aged and older adults.. [ABSTRACT FROM AUTHOR]

Incorporation of membrane proteins into reconstituted lipid membranes is a common approach for studying their structure and function relationship in a native-like environment. In this work, we investigated fluorescence properties of liposome-reconstituted major light-harvesting complexes of plants (LHCII). By utilizing liposome labelling with the fluorescent dye molecules and single-molecule microscopy techniques, we were able to study truly liposome-reconstituted LHCII and compare them with bulk measurements and liposome-free LHCII aggregates bound to the surface. Our results showed that fluorescence lifetime obtained in bulk and in single liposome measurements were correlated. The fluorescence lifetimes of LHCII were shorter for liposome-free LHCII than for reconstituted LHCII. In the case of liposome-reconstituted LHCII, fluorescence lifetime showed dependence on the protein density reminiscent to concentration quenching. The dependence of fluorescence lifetime of LHCII on the liposome size was not significant. Our results demonstrated that fluorescence quenching can be induced by LHCII – LHCII interactions in reconstituted membranes, most likely occurring via the same mechanism as photoprotective non-photochemical quenching in vivo. • Co-localization analysis allows discriminating between liposome-free and reconstituted LHCIIs. • High heterogeneity in liposome sizes, LHCII fluorescence intensity and lifetimes detected. • FL quenching of LHCII in protein-dense liposomes is aggregation-related. • LHCII FL quenching in liposomes is reminiscent of Chl FL concentration quenching in solution. [ABSTRACT FROM AUTHOR]

Despite an intense interest and a remarkable number of studies on the subject, the relationships between thermostability and (primary, secondary and tertiary) structure of proteins are still not fully understood. Here, comparing the protein density - defined by the ratio between the residue number and protein excluded volume - for a set of thermophilic/mesophilic pairs, we provide evidence that this property is connected to the optimal growth temperature. In particular, our results indicate that thermophilic proteins have - in general - a lower density with respect to the mesophilic counterparts, being such a correlation more pronounced for optimal growth temperature differences greater than 40°C. The effect of the protein thermostability changes on the molecular shape is also presented.

Dietary guidelines suggest consuming a mixed-protein diet, consisting of high-quality animal, dairy, and plant-based foods. However, current data on the distribution and the food sources of protein intake in a free-living, representative sample of US adults are not available. Data from the National Health and Nutrition Examination Survey (NHANES), 2007-2010, were used in these analyses (n = 10,977, age ≥ 19 years). Several US Department of Agriculture (USDA) databases were used to partition the composition of foods consumed into animal, dairy, or plant components. Mean ± SE animal, dairy, and plant protein intakes were determined and deciles of usual intakes were estimated. The percentages of total protein intake derived from animal, dairy, and plant protein were 46%, 16%, and 30%, respectively; 8% of intake could not be classified. Chicken and beef were the primary food sources of animal protein intake. Cheese, reduced-fat milk, and ice cream/dairy desserts were primary sources of dairy protein intake. Yeast breads, rolls/buns, and nuts/seeds were primary sources of plant protein intake. This study provides baseline data for assessing the effectiveness of public health interventions designed to alter the composition of protein foods consumed by the American public.