Antigens
Constantin A. Bona, Francisco A. Bonilla in Textbook of Immunology, 2019
Since T cells recognize antigen fragments, T cell epitopes are of the sequential type. Immunodominant T cell epitopes appear to be regions of a protein which are amphipathic (have both hydrophilic and hydrophobic residues) and which are capable of forming helical secondary structure. In particular, a pattern of periodic hydrophobicity appears to be important. That is, within an amphipathic helix, the non-polar residues are all aligned along one edge of the helix (Figure 3–7). Presumably, this would orient the helix such that the lipophilic side would lie in the peptide-binding groove of the MHC molecule (see Figure 8–9) while the polar residues protruded from the surface. Algorithms which detect such recurrent hydrophobicity patterns in primary protein sequences are often (but not always) very successful at predicting which segments will be T cell epitopes. As an example, consider two regions of the Plasmodium falciparum circumsporozoite protein. The two immunodominant helper T cell (Th) epitopes of this molecule are amino acids 326–345 and 361–380 (Table 3–II). The amphipathic nature of these segments is readily apparent, as is some periodicity of hydrophobic residues.
Debaryomyces
Dongyou Liu in Handbook of Foodborne Diseases, 2018
Pseudohyphal formation can be observed in some D. hansenii strains, while invasive growth was not observed. The hydrophobicity is also variable within the species.13 In this species, pseudomycelium can be absent, primitive, or occasionally well developed.6 Hyphae formation by D. hansenii is observed in the continuous fermentation of xylose for the production of xylitol, of which this yeast is one of the best producers, in media made from acid hydrolysates of barley bran. The yeast-to-mycelia transition occurs earlier at a lower dilution rate, and at some dilution rates the yeast morphology is reversibly affected by the dissolved O2: low aeration causes the transition from oval cells to hyphae, while the increase of dissolved O2 concentration results in recuperation of the oval shape. Xylitol is the major fermentation product when the yeast is in both morphological forms, whereas when the yeast grows under hyphal morphology and oxygen limitation, the production of ethanol increases. The lower xylose consumption corresponds to the yeast-to-mycelia transition. In media made with commercial xylose or glucose, the yeast-to-mycelia transition is induced by adding selected amounts of acid-soluble lignin.14
Exon globin mutation of β-thalassemia in Indonesian ethnic groups: A bioinformatics approach
Robert Hofstra, Noriyuki Koibuchi, Suthat Fucharoen in Advances in Biomolecular Medicine, 2017
The mutant residue is smaller than the wild-type residue. The wild-type residue was positively charged, and the mutant residue is neutral. The mutant residue is more hydrophobic than the wild-type residue. The wild-type residue forms a hydrogen bond with glutamic acid at position 122. The difference in hydrophobicity will affect hydrogen bond formation. The wild-type residue forms a salt bridge with glutamic acid at position 122. The difference in charge will disturb the ionic interaction made by the original, wild-type residue. The mutated residue is located on the surface of a domain with unknown function. The residue was not found to be in contact with other domains, the function of which is known within the used structure. However, contact with other molecules or domains is still possible and might be affected by this mutation.
Challenges in antibody structure prediction
Published in mAbs, 2023
Monica L. Fernández-Quintero, Janik Kokot, Franz Waibl, Anna-Lena M. Fischer, Patrick K. Quoika, Charlotte M. Deane, Klaus R. Liedl
To show the effect of starting structures with cis-amide bonds and D-amino acids in the CDR loops, we compared the surface hydrophobicity of structure models for the CIS43 antibody variant with the X-ray structure (Figure 2). The surface hydrophobicity was assigned using the hydrophobicity scale by Wimley and White.42 We found differences in the surface hydrophobicity, which is expected as hydrophobicity is potentially a strongly conformation-dependent property, since small sidechain rearrangements may expose otherwise buried hydrophobic groups. While small inaccuracies in the atomic positions can be fixed by MD simulations, the correct sidechain packing is often impossible when D-amino acids or cis-amide bonds are present, leading to almost irreparable errors in the biophysical property estimation. The same is true for antibody-antigen docking, where an accurate representation of the surface is required to find the correct interactions with the antigen.
A computational method for predicting the aggregation propensity of IgG1 and IgG4(P) mAbs in common storage buffers
Published in mAbs, 2022
James T. Heads, Sebastian Kelm, Kerry Tyson, Alastair D. G. Lawson
A high surface hydrophobicity is an undesirable characteristic and is often cited as a principal component of aggregation. To determine hydrophobicity values that might impede the development of therapeutic mAbs due to increased aggregation propensity, we analyzed 97 clinical stage Fv domain sequences (76 IgG1 mAbs and 21 IgG4(P) mAbs SITable 1). The therapeutic Fv domains exhibited a wide range of hydrophobicity scores, with a mean absolute solvent-accessible surface areas (ABSASA) hydrophobicity score of 545.6 Å2 (Figure 1). We elected to use the 90th percentile as a reasonable cutoff point for molecules displaying a favorable surface hydrophobicity score. Therefore, based on this sample set, Fv domains with ABSASA hydrophobicity scores > 638.5 Å2 would be expected to show a high probability of poor developability due to high aggregation propensity (depending on charge characteristics and environmental conditions such as buffer pH).
Biofouling control of membrane distillation for seawater desalination: Effect of air-backwash and chemical cleaning on biofouling formation
Published in Biofouling, 2022
Ardiyan Harimawan, Vita Wonoputri, Jonathan Ariel, Helen Julian
At this step, the increased membrane’s wettability properties seem to originate from the presence of EPS and/or soluble microbial products (SMP) commonly produced by the microbes, and SMP production is increased at high salinity such as the feed water used here (Wang & Zhang 2010; Xie et al. 2014). The amphiphilic nature of the proteins in the SMP created a hydrophilic layer that decreased feed surface tension, increased membrane surface energy, and altered membrane hydrophobicity (Nguyen et al. 2012). The reduced hydrophobicity of the membrane led to the gradual intrusion of liquid feed solution into the membrane pores and permeate stream. This was supported by the SEM of the membrane cross-section in test with seawater model solution containing bacterial suspension (Figure 3d), which indicated crystals deposition inside the membrane pores. Based on the test performances and fouling analysis, biofouling impacted the membrane performance more significantly than the inorganic fouling as more rapid flux decline and wetting occurred with biofouling deposition. Biofouling also deposited faster than inorganic fouling and could induce the deposition of inorganic fouling later during the test.
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