Revealing Interaction Of Organic Adsorbates With Semiconductor Surfaces Using Chemically Enhanced Raman

Surface enhanced Raman spectroscopy (SERS) is frequently associated with chemical enhancement (CE), which is an effect of the chemical coupling between reporting molecules and surfaces. While SERS technique is mainly attributed to the studies of metallic surfaces, chemical coupling must be present on semiconductor surfaces as well. Here, we examine binding of trans-1,2-two(4-pyridyl) ethylene (BPE) to various crystallographic facets of PbSe semiconductor. The calculated off-resonant Raman spectra vary significantly on different crystallographic facets of PbSe, correlating with the electronic structure of each type of semiconductor surface. We distinguish situations when the charge transfer is present and when it is not, which raises the question about what exactly should be called the chemical enhancement . We attempt to clarify this situation by introducing the concept of the charge-transfer and charge-transfer-less chemical enhancement. We also demonstrate a transition between these two regimes, which exhibits a nonlinear behavior of the vibrational coupling and a significantly stronger contribution to the Raman intensity

Herbal mixtures in traditional medicine in Northern Peru

The investigation of plant mixtures used in traditional medicine in Northern Peru yielded a total of 974 herbal preparations used to treat 164 different afflictions. Psychosomatic disorders were, with almost 30% of all recipes applied, the most important afflictions treated. In most cases, healers used only one or two mixtures to treat an illness. However, up to 49 different preparations were used to treat the same disease. This indicates a high degree of experimentation. Altogether 330 plant species, representing almost 65% of the medicinal flora used in the region were applied in mixtures. The overwhelming number of plant mixtures contained 2-7 different plant species, although in the most extreme case 27 distinct species were included. The cluster analysis confirmed that mixtures used for applications like inflammations, infections and blood purification, as well as cough, cold, bronchitis or other respiratory disorders, or urinary infection and kidney problems had similar floristic compositions. Mixtures used for nervous system disorders, anxiety and heart problems often had a similar compositio

Computational protein design with explicit consideration of surface hydrophobic patches

De novo protein design requires the identification of amino-acid sequences that favor the target folded conformation and are soluble in water. One strategy for promoting solubility is to disallow hydrophobic residues on the protein surface during design. However, naturally occurring proteins often have hydrophobic amino acids on their surface that contribute to protein stability via the partial burial of hydrophobic surface area or play a key role in the formation of protein-protein interactions. A less restrictive approach for surface design that is used by the modeling program Rosetta is to parameterize the energy function so that the number of hydrophobic amino acids designed on the protein surface is similar to what is observed in naturally occurring monomeric proteins. Previous studies with Rosetta have shown that this limits surface hydrophobics to the naturally occurring frequency (~28%) but that it does not prevent the formation of hydrophobic patches that are considerably larger than those observed in naturally occurring proteins. Here, we describe a new score term that explicitly detects and penalizes the formation of hydrophobic patches during computational protein design. With the new term we are able to design protein surfaces that include hydrophobic amino acids at naturally occurring frequencies, but do not have large hydrophobic patches. By adjusting the strength of the new score term the emphasis of surface redesigns can be switched between maintaining solubility and maximizing folding free energy

Fat-Free Mass Index in a Large Sample of Collegiate American Football Athletes

International Journal of Exercise Science 17(4): 129-139, 2024. High levels of fat-free mass (FFM) are favorable for athletes and are related to sport performance. However, fat-free mass index (FFMI), which includes adjustments for height, may offer a better way to characterize FFM beyond raw values. As FFMI is understudied relative to sport, the purpose of the current study was to assess position and age group differences in FFMI among collegiate American football players. National Collegiate Athletic Association DIII (n=111) football players underwent body composition assessment via bioelectrical impedance analysis. FFMI was calculated by dividing FFM by height squared. One-way analyses of variance with Bonferroni post-hoc tests were conducted to evaluate differences in FFMI by position and age groups (α\u3c0.05). The overall mean FFMI was 23.50 ± 2.04 kg· m−2, with values ranging from 18.1–27.7 kg· m−2. FFMI was highest in linemen (24.8 ± 1.5 kg· m−2) and lowest in specialty players (20.6 ± 1.4 kg· m−2) (p\u3c0.05). No differences in FFMI were apparent across age groups (p\u3e0.05). Current findings demonstrate that an athlete’s upper limit for FFMI may exceed 25 kg· m−2, and differences exist across positions, likely due to position-specific demands. These measurements serve as a foundation for tailoring nutritional and exercise plans, forecasting athletic performance, and supplying coaches with standardized data about the potential for additional FFM accretion in collegiate American football players

Alternative Computational Protocols for Supercharging Protein Surfaces for Reversible Unfolding and Retention of Stability

Bryan S. Der, Ron Jacak, Brian Kuhlman, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of AmericaChristien Kluwe, Aleksandr E. Miklos, Andrew D. Ellington , Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, United States of AmericaChristien Kluwe, Aleksandr E. Miklos, George Georgiou, Andrew D. Ellington, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of AmericaAleksandr E. Miklos, Andrew D. Ellington , Applied Research Laboratories, University of Texas at Austin, Austin, Texas, United States of AmericaSergey Lyskov, Jeffrey J. Gray, Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of AmericaBrian Kuhlman, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of AmericaReengineering protein surfaces to exhibit high net charge, referred to as “supercharging”, can improve reversibility of unfolding by preventing aggregation of partially unfolded states. Incorporation of charged side chains should be optimized while considering structural and energetic consequences, as numerous mutations and accumulation of like-charges can also destabilize the native state. A previously demonstrated approach deterministically mutates flexible polar residues (amino acids DERKNQ) with the fewest average neighboring atoms per side chain atom (AvNAPSA). Our approach uses Rosetta-based energy calculations to choose the surface mutations. Both protocols are available for use through the ROSIE web server. The automated Rosetta and AvNAPSA approaches for supercharging choose dissimilar mutations, raising an interesting division in surface charging strategy. Rosetta-supercharged variants of GFP (RscG) ranging from −11 to −61 and +7 to +58 were experimentally tested, and for comparison, we re-tested the previously developed AvNAPSA-supercharged variants of GFP (AscG) with +36 and −30 net charge. Mid-charge variants demonstrated ~3-fold improvement in refolding with retention of stability. However, as we pushed to higher net charges, expression and soluble yield decreased, indicating that net charge or mutational load may be limiting factors. Interestingly, the two different approaches resulted in GFP variants with similar refolding properties. Our results show that there are multiple sets of residues that can be mutated to successfully supercharge a protein, and combining alternative supercharge protocols with experimental testing can be an effective approach for charge-based improvement to refolding.This work was supported by the Defense Advanced Research Projects Agency (HR-0011-10-1-0052 to A.E.) and the Welch Foundation (F-1654 to A.E.), the National Institutes of Health grants GM073960 (B.K.) and R01-GM073151 (J.G. and S.L.), the Rosetta Commons (S.L.), the National Science Foundation graduate research fellowship (2009070950 to B.D.), the UNC Royster Society Pogue fellowship (B.D.), and National Institutes of Health grant T32GM008570 for the UNC Program in Molecular and Cellular Biophysics. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Center for Systems and Synthetic BiologyCellular and Molecular BiologyApplied Research LaboratoriesEmail: [email protected]

Light-induced nuclear export reveals rapid dynamics of epigenetic modifications

We engineered a photoactivatable system for rapidly and reversibly exporting proteins from the nucleus by embedding a nuclear export signal in the LOV2 domain from phototropin 1. Fusing the chromatin modifier Bre1 to the photoswitch, we achieved light-dependent control of histone H2B monoubiquitylation in yeast, revealing fast turnover of the ubiquitin mark. Moreover, this inducible system allowed us to dynamically monitor the status of epigenetic modifications dependent on H2B ubiquitylation

SwiftLib: rapid degenerate-codon-library optimization through dynamic programming

Degenerate codon (DC) libraries efficiently address the experimental library-size limitations of directed evolution by focusing diversity toward the positions and toward the amino acids (AAs) that are most likely to generate hits; however, manually constructing DC libraries is challenging, error prone and time consuming. This paper provides a dynamic programming solution to the task of finding the best DCs while keeping the size of the library beneath some given limit, improving on the existing integer-linear programming formulation. It then extends the algorithm to consider multiple DCs at each position, a heretofore unsolved problem, while adhering to a constraint on the number of primers needed to synthesize the library. In the two library-design problems examined here, the use of multiple DCs produces libraries that very nearly cover the set of desired AAs while still staying within the experimental size limits. Surprisingly, the algorithm is able to find near-perfect libraries where the ratio of amino-acid sequences to nucleic-acid sequences approaches 1; it effectively side-steps the degeneracy of the genetic code. Our algorithm is freely available through our web server and solves most design problems in about a second

Computationally Designed Bispecific Antibodies using Negative State Repertoires

A challenge in the structure-based design of specificity is modeling the negative states, i.e., the complexes that you do not want to form. This is a difficult problem because mutations predicted to destabilize the negative state might be accommodated by small conformational rearrangements. To overcome this challenge, we employ an iterative strategy that cycles between sequence design and protein docking in order to build up an ensemble of alternative negative state conformations for use in specificity prediction. We have applied our technique to the design of heterodimeric CH3 interfaces in the Fc region of antibodies. Combining computationally and rationally designed mutations produced unique designs with heterodimer purities greater than 90%. Asymmetric Fc crystallization was able to resolve the interface mutations; the heterodimer structures confirmed that the interfaces formed as designed. With these CH3 mutations, and those made at the heavy-/light-chain interface, we demonstrate one-step synthesis of four fully IgG-bispecific antibodies