Crystal structure of a complex formed between proteolytically-generated lactoferrin fragment and proteinase K

Hydrolysis improves the inhibition efficacy of bovine lactoferrin against infection by SARS-CoV-2 pseudovirus

The entry of SARS-CoV-2 into host cells may involve the spike protein cleavage by cathepsin L (CTSL). Certain food proteins such as lactoferrin (Lf) inhibit CTSL. The current study investigated the impact of hydrolysis (0-180 min) by proteinase K on electrophoretic pattern, secondary structure, cathepsin inhibitory and SARS-CoV-2 pseudovirus infectivity inhibitory of bovine Lf. Gel electrophoresis indicated that hydrolysis cut Lf molecules to half lobes (∼40 kDa) and produced peptides ≤18 kDa. Approximation of the secondary structural features through analysis of the second-derivative amide I band collected by infra-red spectroscopy suggested a correlative-causative relationship between cathepsin inhibition and the content of helix-unordered structures in Lf hydrolysate. The half maximal inhibitory concentration (IC50) of Lf hydrolysed for 90 min (H90) against CTSL was about 100 times smaller than that of the Lf hydrolysed for 0 min (H0). H90 had also double activity against SARS-CoV-2 pseudo-types infectivity compared with H0.

Improving the catalytic activity of a detergent-compatible serine protease by rational design

Serine proteases are among the most important biological additives in various industries such as detergents, leather, animal feed and food. A serine protease gene, Fgapt4, from Fusarium graminearum 2697 was identified, cloned and expressed in Pichia pastoris. The optimal pH and temperature of FgAPT4 were 8.5 and 40°C, respectively. The relative activity was >30% even at 10°C. It had a wide range of pH stability (4.0-12.0) and detergent compatibility. To improve the catalytic activity, a strategy combining molecular docking and evolutionary analysis was adopted. Twelve amino acid residue sites and three loops (A, B and C) were selected as potential hot spots that might play critical roles in the enzyme's functional properties. Twenty-eight mutants targeting changes in individual sites or loops were designed, and mutations with good performance were combined. The best mutant was FgAPT4-M3 (Q70N/D142S/A143S/loop C). The specific activity and catalytic efficiency of FgAPT4-M3 increased by 1.6 (1008.5 vs. 385.9 U/mg) and 2.2-fold (3565.1 vs. 1106.3/s/mM), respectively. Computational analyses showed that the greater flexibility of the substrate pocket may be responsible for the increased catalytic activity. In addition, its application in detergents indicated that FgAPT4-M3 has great potential in washing.

A Peptide Bond from the Inter-lobe Segment in the Bilobal Lactoferrin Acts as a Preferred Site for Cleavage for Serine Proteases to Generate the Perfect C-lobe: Structure of the Pepsin Hydrolyzed Lactoferrin C-lobe at 2.28 Å Resolution

C-lobe represents the C-terminal half of lactoferrin which is a bilobal 80 kDa iron binding glycoprotein. The two lobes are designated as N-lobe (Ser1-Glu333) and C-lobe (Arg344-Arg689). The N- and C-lobes are connected by a 10-residue long α-helical peptide (Thr334-Thr343). Both lobes adopt similar conformations and have identical iron binding sites. The bilobal lactoferrin was hydrolyzed in a limited proteolysis using pepsin at pH 2.0. It produced a 40 kDa and fully functional C-lobe which was purified and crystallized at pH 8.0. The structure determination revealed that the structure contained residues from Tyr342 to Arg689 representing a fully functional monoferric C-lobe. It showed that pepsin cleaved lactoferrin at the peptide bond Arg341-Tyr342 which is part of the inter-lobe decapeptide. Interestingly, the two previously determined structures of the enzymatically produced C-lobe using trypsin and proteinase K also cleaved lactoferrin at the same peptide bond Arg341-Tyr342. This was a striking result as the three enzymes, pepsin, trypsin and proteinase K have different specificity requirements and yet they cleaved the bilobal lactoferrin at the same peptide bond and generated an identical and fully functional C-lobe. This shows that the observed cleavage site in lactoferrin adopts a highly favourable conformation for proteolysis. It is noteworthy that the three enzymes with different specificities cut the protein at the same peptide bond which may be of physiological significance because the antibacterial action of lactoferrin is extended further through the C-lobe.

Tuning Transport Phenomena in Agarose Gels for the Control of Protein Nucleation Density and Crystal Form

Agarose gels provide the ideal environment for studying the nucleation step of complex biomacromolecules under diffusion-controlled conditions. In the present paper, we characterized the influence of agarose on the nucleation of three model proteins, i.e., lysozyme, insulin, and proteinase K, as a function of the agarose concentration using a batch method set-up inside flat capillaries. By using this set-up, we were able to directly count the number of crystals in a given volume and correlate it with the amount of agarose and with the average crystal size. We also studied the crystallization behavior of proteinase K with free-interface diffusion so that batch conditions were achieved through slow diffusion of the precipitant. Thanks to the control over the protein mass transport imposed by the network, a previously unknown crystal form, P212121, was obtained, and the three-dimensional structure was determined at a 1.6 Å resolution. Overall, the versatility of agarose gels makes them ideal candidates for the preparation of microcrystalline suspensions of biopharmaceuticals with precise and reproducible crystal attributes or for the exploration of the existence of different polymorphs.

Digestive diversity and kinetic intrigue among heated and unheated β-lactoglobulin species

Food processing often alters the structure of proteins, and proteins are deliberately denatured and aggregated to improve technological functionality in many cases. However, the digestive consequences of processing-induced alterations to protein structure have only recently been studied. Here we explored the process-structure-digestibility relationship in the context of heat-processing effects on the structure and gastric digestibility of the bovine whey protein β-lactoglobulin (β-lg). Heating β-lg produces an array of non-native monomers, dimers and aggregates, and we have characterised these with reverse-phase high performance liquid chromatography (RP-HPLC) as a complement to our earlier work using polyacrylamide gel electrophoresis (PAGE) techniques. Using a combination of SDS-PAGE and RP-HPLC we have identified pepsin-resistant dimers and peptides that appear early in digestion. In an unexpected finding, native β-lg underwent complete hydrolysis during prolonged incubation (48 h) with pepsin. Two phases of hydrolysis were identified, and the transition between phases appears to result from alterations to the secondary structure of β-lg at 3-4 h, as measured with circular dichroism spectroscopy, and/or the binding and release of a pepsin inhibitor peptide. This work has unpacked some of the complexities of the processing-structure-digestibility relationship in a highly simplified system; further work is needed to explore the implications of these findings for food processors, regulatory authorities and consumers.

Predicting Ca2+ -binding sites using refined carbon clusters

Identifying Ca(2+) -binding sites in proteins is the first step toward understanding the molecular basis of diseases related to Ca(2+) -binding proteins. Currently, these sites are identified in structures either through X-ray crystallography or NMR analysis. However, Ca(2+) -binding sites are not always visible in X-ray structures due to flexibility in the binding region or low occupancy in a Ca(2+) -binding site. Similarly, both Ca(2+) and its ligand oxygens are not directly observed in NMR structures. To improve our ability to predict Ca(2+) -binding sites in both X-ray and NMR structures, we report a new graph theory algorithm (MUG(C) ) to predict Ca(2+) -binding sites. Using carbon atoms covalently bonded to the chelating oxygen atoms, and without explicit reference to side-chain oxygen ligand co-ordinates, MUG(C) is able to achieve 94% sensitivity with 76% selectivity on a dataset of X-ray structures composed of 43 Ca(2+) -binding proteins. Additionally, prediction of Ca(2+) -binding sites in NMR structures was obtained by MUG(C) using a different set of parameters, which were determined by the analysis of both Ca(2+) -constrained and unconstrained Ca(2+) -loaded structures derived from NMR data. MUG(C) identified 20 of 21 Ca(2+) -binding sites in NMR structures inferred without the use of Ca(2+) constraints. MUG(C) predictions are also highly selective for Ca(2+) -binding sites as analyses of binding sites for Mg(2+) , Zn(2+) , and Pb(2+) were not identified as Ca(2+) -binding sites. These results indicate that the geometric arrangement of the second-shell carbon cluster is sufficient not only for accurate identification of Ca(2+) -binding sites in NMR and X-ray structures but also for selective differentiation between Ca(2+) and other relevant divalent cations.

Predicting calcium-binding sites in proteins - a graph theory and geometry approach

Identifying calcium-binding sites in proteins is one of the first steps towards predicting and understanding the role of calcium in biological systems for protein structure and function studies. Due to the complexity and irregularity of calcium-binding sites, a fast and accurate method for predicting and identifying calcium-binding protein is needed. Here we report our development of a new fast algorithm (GG) to detect calcium-binding sites. The GG algorithm uses a graph theory algorithm to find oxygen clusters of the protein and a geometric algorithm to identify the center of these clusters. A cluster of four or more oxygen atoms has a high potential for calcium binding. High performance with about 90% site sensitivity and 80% site selectivity has been obtained for three datasets containing a total of 123 proteins. The results suggest that a sphere of a certain size with four or more oxygen atoms on the surface and without other atoms inside is necessary and sufficient for quickly identifying the majority of the calcium-binding sites with high accuracy. Our finding opens a new avenue to visualize and analyze calcium-binding sites in proteins facilitating the prediction of functions from structural genomic information.

Crystal structure of a proteolytically generated functional monoferric C-lobe of bovine lactoferrin at 1.9A resolution

This is the first crystal structure of a proteolytically generated functional C-lobe of lactoferrin. The purified samples of iron-saturated C-lobe were crystallized in 0.1 M Mes buffer (pH 6.5) containing 25% (v/v) polyethyleneglycol monomethyl ether 550 M and 0.1 M zinc sulphate heptahydrate. The X-ray intensity data were collected with 300 mm imaging plate scanner mounted on a rotating anode generator. The structure was determined by the molecular replacement method using the coordinates of the C-terminal half of bovine lactoferrin as a search model and refined to an R-factor of 0.193 for all data to 1.9A resolution. The final model comprises 2593 protein atoms (residues 342-676 and 681-685), 124 carbohydrate atoms (from ten monosaccharide units, in three glycan chains), one Fe(3+), one CO(3)(2-), two Zn(2+) and 230 water molecules. The overall folding of the C-lobe is essentially the same as that of C-terminal half of bovine lactoferrin but differs slightly in conformations of some of the loops and reveals a number of new interactions. There are 20 Cys residues in the C-lobe forming ten disulphide links. Out of these, one involving Cys481-Cys675 provides an inter-domain link at 2.01A while another Cys405-Cys684 is formed between the main C-lobe 342-676 and the hydrolyzed pentapeptide 681-685 fragment. Six inter-domain hydrogen bonds have been observed in the structure whereas only four were reported in the structure of intact lactoferrin, although domain orientations have been found similar in the two structures. The good quality of electron density has also revealed all the ten oligosaccharide units in the structure. The observation of two metal ions at sites other than the iron-binding cleft is another novel feature of the present structure. These zinc ions stabilize the crystal packing. This structure is also notable for extensive inter-molecular hydrogen bonding in the crystals. Therefore, the present structure appears to be one of the best packed crystal structures among the proteins of the transferrin superfamily.

Enhancement of catalytic efficiency of enzymes through exposure to anhydrous organic solvent at 70 degrees C. Three-dimensional structure of a treated serine proteinase at 2.2 A resolution

The enzyme behavior in anhydrous media has important applications in biotechnology. So far chemical modifications and protein engineering have been used to alter the catalytic power of the enzymes. For the first time, it is demonstrated that an exposure of enzyme to anhydrous organic solvents at optimized high temperature enhances its catalytic power through local changes at the binding region. Six enzymes: proteinase K, wheat germ acid phosphatase, alpha-amylase, beta-glucosidase, chymotrypsin and trypsin have been exposed to acetonitrile at 70 degrees C for three hours. The activities of these enzymes were found to be considerably enhanced. In order to understand the basis of this change in the activity of these enzymes, the structure of one of these treated enzymes, proteinase K has been analyzed in detail using X-ray diffraction method. The overall structure of the enzyme is similar to the native structure in aqueous environment. The hydrogen bonding system of the catalytic triad is intact after the treatment. However, the water structure in the substrate binding site undergoes some rearrangement as some of the water molecules are either displaced or completely absent. The most striking observation concerning the water structure pertains to the complete deletion of the water molecule which occupied the position at the so-called oxyanion hole in the active site of the native enzyme. Three acetonitrile molecules were found in the present structure. All the acetonitrile molecules are located in the recognition site. The sites occupied by acetonitrile molecules are independent of water molecules. The acetonitrile molecules are involved in extensive interactions with the protein atoms. All of them are interlinked through water molecules. The methyl group of one of the acetonitrile molecules (CCN1) interacts simultaneously with the hydrophobic side chains of Leu-96, Ile-107, and Leu-133. The development of such a hydrophobic environment at the recognition site introduces a striking conformation change in Ile-107 by rotating its side chain about C(alpha)--C(beta) bond by 180 degrees to bring about the delta-methyl group within the range of attractive van der Waals interactions with the methyl group of CCN1. A similar change has earlier been observed in proteinase K when it is complexed to a substrate analog lactoferrin fragment.

Three-dimensional structure of mare diferric lactoferrin at 2.6 A resolution

Lactoferrin is a monomeric glycoprotein with a molecular mass of approximately 80 kDa. The three-dimensional structure of mare diferric lactoferrin (mlf) has been determined at 2.6 A resolution. The protein crystallizes in the space group P 212121with a=85.2 A, b=99.5 A, c=103.1 A with a solvent content of 55 % (v/v). The structure was solved by the molecular replacement method using human diferric lactoferrin as the model. The structure has been refined using XPLOR to a final R -factor of 0.194 for all data in the 15-2.6 A resolution range. The amino acid sequence of mlf was determined using a cDNA method. The final refined model comprises 5281 protein atoms, 2 Fe3+, 2 CO32-and 112 water molecules. The overall folding of mlf is similar to that of other proteins of the transferrin family. The protein folds into two globular lobes, N and C. The lobes are further divided into two domains, N1 and N2, and C1 and C2. The iron-binding cleft is situated between the domains in each lobe. The N lobe appears to be well ordered and is more stable than the C lobe in mlf unlike in other lactoferrins, where the C lobe is the more stable. The opening of the binding cleft in the N lobe of mlf is narrower than those in other proteins of the transferrin family. This is very unusual and is found only in mare lactoferrin. Apart from certain hydrophobic interactions at the mouth of the cleft, one salt-bridge (Lys301 . . . . . . . . Glu216) crosses between the two walls of the cleft. The two lobes are connected covalently by a three-turn alpha-helix involving residues 334-344. The N lobe displays a highly ordered structure with appreciably low temperature factors. The iron coordination is more symmetrical in the N lobe than in the C lobe. There are only 16 intermolecular hydrogen bonds in the structure of mlf.