Engineering trypsin for inhibitor resistance

Prebound State Discovered in the Unbinding Pathway of Fluorinated Variants of the Trypsin-BPTI Complex Using Random Acceleration Molecular Dynamics Simulations

The serine protease trypsin forms a tightly bound inhibitor complex with the bovine pancreatic trypsin inhibitor (BPTI). The complex is stabilized by the P1 residue Lys15, which interacts with negatively charged amino acids at the bottom of the S1 pocket. Truncating the P1 residue of wildtype BPTI to α-aminobutyric acid (Abu) leaves a complex with moderate inhibitor strength, which is held in place by additional hydrogen bonds at the protein-protein interface. Fluorination of the Abu residue partially restores the inhibitor strength. The mechanism with which fluorination can restore the inhibitor strength is unknown, and accurate computational investigation requires knowledge of the binding and unbinding pathways. The preferred unbinding pathway is likely to be complex, as encounter states have been described before, and unrestrained umbrella sampling simulations of these complexes suggest additional energetic minima. Here, we use random acceleration molecular dynamics to find a new metastable state in the unbinding pathway of Abu-BPTI variants and wildtype BPTI from trypsin, which we call the prebound state. The prebound state and the fully bound state differ by a substantial shift in the position, a slight shift in the orientation of the BPTI variants, and changes in the interaction pattern. Particularly important is the breaking of three hydrogen bonds around Arg17. Fluorination of the P1 residue lowers the energy barrier of the transition between the fully bound state and prebound state and also lowers the energy minimum of the prebound state. While the effect of fluorination is in general difficult to quantify, here, it is in part caused by favorable stabilization of a hydrogen bond between Gln194 and Cys14. The interaction pattern of the prebound state offers insights into the inhibitory mechanism of BPTI and might add valuable information for the design of serine protease inhibitors.

Effects of graded inclusion levels of raw garbanzo beans on apparent total tract digestibility, fecal quality, and fecal fermentative end-products and microbiota in extruded feline diets

Garbanzo beans (GB; Cicer arietinum) are a readily available pulse crop that have gained popularity as a plant-based protein source in the pet food industry. However, raw GB contain anti-nutritional factors that can reduce digestibility and cause digestive upsets in pets that are undesirable to owners. The objective of this study was to determine the effects of the inclusion of raw or cooked GB in extruded feline diets on macronutrient digestibility, gastrointestinal tolerance, and fermentative end-products in cats. Five diets were formulated to contain raw GB at 0%, 7.5%, 15%, or 30% or cooked GB at 30%. Ten adult, male cats (mean age: 1.0 ± 0.0 yr, mean BW: 4.7 ± 0.4 kg) were used in a replicated 5 × 5 Latin square design. Each period consisted of 14 d, with 10 d of diet adaptation followed by 4 d of total fecal and urine collection. At the end of each period, 4 mL of blood were collected and analyzed for a serum chemistry and complete blood count to ensure all animals remained healthy throughout the study. Cats were fed twice daily and food intake was calculated to maintain body weight. Food intake was highest (P < 0.05) for cats fed 0% raw GB (72.2 g/d, dry matter basis [DMB]) compared with GB inclusions of 7.5% or greater (average 70.3 g/d, DMB). Dry matter and organic matter apparent total tract digestibility (ATTD) were lowest (P < 0.05) for cats consuming the 30% cooked GB diet (77.3% and 81.7%, respectively). Cats fed 7.5% raw GB had greater (P < 0.05) crude protein ATTD (86.2%) than cats fed 15% raw GB (82.3%) or 30% cooked GB (81.6%). Total short-chain fatty acid concentrations were highest (P < 0.05) for 30% cooked GB at 682 μmol/g but not different (P > 0.05) than 15% GB (528 μmol/g) or 30% raw GB (591 μmol/g) diets. In terms of fecal microbial abundance, the predominant phyla were Firmicutes, Bacteroidota, and Actinobacteria. Cats fed the 0% GB diet had a greater relative abundance of Firmicutes (62.1%) and Fusobacteria (4.0%) than the remaining diets (average 54% and 1.6%, respectively). In conclusion, all inclusion levels of raw GB resulted in high digestibility (average > 80%) and ideal fecal scores (average 2.9), demonstrating their adequacy as a protein source in feline diets up to a 30% inclusion level.

Mechanical couplings of protein backbone and side chains exhibit scale-free network properties and specific hotspots for function

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Statistical learning from protein dynamics unravels rigidities in interaction network.

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Backbone and side-chain mechanical couplings exhibit scale-free network properties.

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Graphical depiction of network rigidities captures sequence co-evolution patterns.

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Functional sites at secondary structure peripheries are mechanical hotspots.

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Our rigidity scores are compelling metrics for residue biological significance.

A backbone-side-chain elastic network model (bsENM) is devised in this contribution to decipher the network of molecular interactions during protein dynamics. The chemical details in 5 μs all-atom molecular dynamics (MD) simulation are mapped onto the bsENM spring constants by self-consistent iterations. The elastic parameters obtained by this structure-mechanics statistical learning are then used to construct inter-residue rigidity graphs for the chemical components in protein amino acids. A key discovery is that the mechanical coupling strengths of both backbone and side chains exhibit heavy-tailed distributions and scale-free network properties. In both rat trypsin and PDZ3 proteins, the statistically prominent modes of rigidity graphs uncover the sequence-specific coupling patterns and mechanical hotspots. Based on the contributions to graphical modes, our residue rigidity scores in backbone and side chains are found to be very useful metrics for the biological significance. Most functional sites have high residue rigidity scores in side chains while the biologically important glycines are generally next to mechanical hotspots. Furthermore, prominent modes in the rigidity graphs involving side chains oftentimes coincide with the co-evolution patterns due to evolutionary restraints. The bsENM specifically devised to resolve the protein chemical character thus provides useful means for extracting functional information from all-atom MD.

Use of Legumes and Yeast as Novel Dietary Protein Sources in Extruded Canine Diets

The popularity of plant-based protein sources has increased as consumer demand for grain-free and novel protein sources increase. Minimal research has been conducted as regards to use of legumes and yeast and their effects on acceptability and digestibility in canine diets. The objective of this study was to evaluate macronutrient apparent total tract digestibility (ATTD), gastrointestinal tolerance, and fermentative end-products in extruded, canine diets. Five diets were formulated to be isocaloric and isonitrogenous with either garbanzo beans (GBD), green lentils (GLD), peanut flour (PFD), dried yeast (DYD), or poultry by-product meal (CON) as the primary protein sources. Ten adult, intact, female beagles (mean age: 4.2 ± 1.1 yr, mean weight: 11.9 ± 1.3 kg) were used in a replicated, 5 × 5 Latin square design with 14 d periods. Each experimental period consisted of 10 d of diet adaptation, followed by 4 d of total fecal and urine collection. A fasted, 5 ml blood sample was collected at the end of each period and analyzed for serum metabolites and complete blood count. Serum metabolites were within normal ranges and all dogs remained healthy throughout the study. Fecal quality, evaluated on a 5-point scale, was considered ideal. Macronutrient ATTD was similar among dietary treatments, with diets highly digestible (>80%). Total fecal branched-chain fatty acid concentrations were highest (P < 0.05) for DYD (23.4 μmol/g) than GLD (16.1 μmol/g) and PFD (16.0 μmol/g) but not different (P > 0.05) than other treatments. The plant-based protein treatments had greater (P < 0.05) total fecal short chain fatty acid (SCFA) concentrations (average 627.6 μmol/g) compared with CON (381.1 μmol/g). Fecal butyrate concentration was highest (P < 0.05) for DYD than all other dietary treatments (103.9 μmol/g vs. average 46.2 μmol/g). Fecal microbial communities showed Firmicutes, Bacteroidetes, Fusobacteria, and Proteobacteria as abundant phyla. There was greater β-diversity for dogs fed DYD which differed from all other diets in both weighted and unweighted UNIFRAC analyses. Inclusion of these novel, plant-based, protein sources showed no detrimental effects on nutrient digestibility or fecal characteristics and represent viable protein sources in canine diets that can produce beneficial shifts in fecal metabolites.

Dimerization misalignment in human glutamate-oxaloacetate transaminase variants is the primary factor for PLP release

The active form of vitamin B6, pyridoxal 5’-phosphate (PLP), plays an essential role in the catalytic mechanism of various proteins, including human glutamate-oxaloacetate transaminase (hGOT1), an important enzyme in amino acid metabolism. A recent molecular and genetic study showed that the E266K, R267H, and P300L substitutions in aspartate aminotransferase, the Arabidopsis analog of hGOT1, genetically suppress a developmentally arrested Arabidopsis RUS mutant. Furthermore, CD analyses suggested that the variants exist as apo proteins and implicated a possible role of PLP in the regulation of PLP homeostasis and metabolic pathways. In this work, we assessed the stability of PLP bound to hGOT1 for the three variant and wildtype (WT) proteins using a combined 6 μs of molecular dynamics (MD) simulation. For the variants and WT in the holo form, the MD simulations reproduced the “closed-open” transition needed for substrate binding. This conformational transition was associated with the rearrangement of the P15-R32 small domain loop providing substrate access to the R387/R293 binding motif. We also showed that formation of the dimer interface is essential for PLP affinity to the active site. The position of PLP in the WT binding site was stabilized by a unique hydrogen bond network of the phosphate binding cup, which placed the cofactor for formation of the covalent Schiff base linkage with K259 for catalysis. The amino acid substitutions at positions 266, 267, and 300 reduced the structural correlation between PLP and the protein active site and/or integrity of the dimer interface. Principal component analysis and energy decomposition clearly suggested dimer misalignment and dissociation for the three variants tested in our work. The low affinity of PLP in the hGOT1 variants observed in our computational work provided structural rationale for the possible role of vitamin B6 in regulating metabolic pathways.

A distance geometry-based description and validation of protein main-chain conformation

Understanding the protein main-chain conformational space forms the basis for the modelling of protein structures and for the validation of models derived from structural biology techniques. Presented here is a novel idea for a three-dimensional distance geometry-based metric to account for the fine details of protein backbone conformations. The metrics are computed for dipeptide units, defined as blocks of Cαi-1-O i-1-Cαi -O i -Cαi+1 atoms, by obtaining the eigenvalues of their Euclidean distance matrices. These were computed for ∼1.3 million dipeptide units collected from nonredundant good-quality structures in the Protein Data Bank and subjected to principal component analysis. The resulting new Euclidean orthogonal three-dimensional space (DipSpace) allows a probabilistic description of protein backbone geometry. The three axes of the DipSpace describe the local extension of the dipeptide unit structure, its twist and its bend. By using a higher-dimensional metric, the method is efficient for the identification of Cα atoms in an unlikely or unusual geometrical environment, and its use for both local and overall validation of protein models is demonstrated. It is also shown, for the example of trypsin proteases, that the detection of unusual conformations that are conserved among the structures of this protein family may indicate geometrically strained residues of potentially functional importance.