Single amino acid mutations in the capsid switch the neutralization phenotype of porcine circovirus 2

Porcine circovirus 2 (PCV2) is the causative agent of porcine circovirus-associated diseases in pigs. Previously, it was demonstrated that mAbs 16G12, 38C1, 63H3 and 94H8 directed against the PCV2 capsid protein recognize PCV2 strains Stoon-1010 (PCV2a), 48285 (PCV2b), 1121 (PCV2a), 1147 (PCV2b) and II9F (PCV2b), but only neutralize Stoon-1010 and 48285. This points to the existence of two distinct PCV2 neutralization phenotypes: phenotype α (mAb recognition with neutralization; Stoon-1010 and 48285) and phenotype β (mAb recognition without neutralization; 1121, 1147 and II9F). In the present study, amino acids that are important in determining the neutralization phenotype were identified in the capsid. Mutation of T at position 190 to A in strain 48285 (phenotype α) resulted in a capsid resembling that of strain 1147 (phenotype β) and caused a loss of neutralization (switch from α to β). Mutations of P at position 151 to T and A at position 190 to T in strain II9F (phenotype β) resulted in a capsid resembling that of strain 48285 (phenotype α) and gave a gain of neutralization (switch from β to α). Mutations of T at position 131 to P and of E at position 191 to R in Stoon-1010 (phenotype α) changed the capsid into that of 1121 (phenotype β) and reduced neutralization (switch from α to β). This study demonstrated that single amino acid changes in the capsid result in a phenotypic switch from α to β or β to α.

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Mapping mutational effects along the evolutionary landscape of HIV envelope

eLife ◽

10.7554/elife.34420 ◽

2018 ◽

Vol 7 ◽

Cited By ~ 39

Author(s):

Hugh K Haddox ◽

Adam S Dingens ◽

Sarah K Hilton ◽

Julie Overbaugh ◽

Jesse D Bloom

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Long Range ◽

The Other ◽

Single Amino Acid ◽

Specific Amino Acid ◽

Viral Growth ◽

Amino Acid Mutations ◽

Hiv Envelope ◽

Hiv Evolution

The immediate evolutionary space accessible to HIV is largely determined by how single amino acid mutations affect fitness. These mutational effects can shift as the virus evolves. However, the prevalence of such shifts in mutational effects remains unclear. Here, we quantify the effects on viral growth of all amino acid mutations to two HIV envelope (Env) proteins that differ at>100 residues. Most mutations similarly affect both Envs, but the amino acid preferences of a minority of sites have clearly shifted. These shifted sites usually prefer a specific amino acid in one Env, but tolerate many amino acids in the other. Surprisingly, shifts are only slightly enriched at sites that have substituted between the Envs—and many occur at residues that do not even contact substitutions. Therefore, long-range epistasis can unpredictably shift Env’s mutational tolerance during HIV evolution, although the amino acid preferences of most sites are conserved between moderately diverged viral strains.

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Single Amino Acids G196 and R198 in hr1 of Subgroup K Avian Leukosis Virus Glycoprotein Are Critical for Tva Receptor Binding

Frontiers in Microbiology ◽

10.3389/fmicb.2020.596586 ◽

2020 ◽

Vol 11 ◽

Author(s):

Jian Chen ◽

Jinqun Li ◽

Lizhen Li ◽

Peng Liu ◽

Yong Xiang ◽

...

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Molecular Mechanisms ◽

Virus Titer ◽

Surface Glycoprotein ◽

Single Amino Acid ◽

Cellular Receptor ◽

Recombinant Viruses ◽

Amino Acid Mutations ◽

Segment Substitution

Avian leukosis viruses (ALVs), a type of retrovirus responsible for various tumor diseases in chickens, are divided into 11 subgroups: ALV-A to ALV-K. After the envelope glycoproteins of ALV interact with the cellular receptor to initiate viral invasion, alterations in a few amino acids of the viral glycoproteins or cell receptors may trigger changes in their conformation and binding affinity. To identify the functional determinants of the ALV-K envelope protein that binds to Tva (a recently identified cellular receptor of ALV-K), using the strategy of continuous, segment-by-segment substitution of the gp85-encoded surface glycoprotein (SU) of ALV-K GDFX0602 with ALV-E ev-1 (using Tvb as the receptor), a series of chimeric soluble gp85 proteins were expressed for co-immunoprecipitation (co-IP) analysis and a series of recombinant viruses with replication-competent avian retrovirus vectors containing Bryan polymerase (RCASBP) as their skeleton were created for transfecting to DF-1 cells and titer determination. The co-IP analysis, fluorescence-activated cell sorting, and virus titer measurements revealed that the substitution of residues 194–198, 206–216 of hr1, residues 251–256 between hr1 and hr2, and residues 269–280 of hr2 were identified to reduce the binding of gp85 to Tva. The substitution of residues 194–221 in hr1 nullified the infectiveness of these viruses, similar to the effect of single amino acid mutations in K251E and L252I located between hr1 and hr2; continuous amino acid mutations in hr2 could not produce the same effect despite reducing their infectiveness. Finally, single amino acid mutations G196A and R198H nearly abolished the binding of gp85 to Tva and nullified the infectiveness of these viruses to DF-1. This study paves the way for exploring the molecular mechanisms of the binding of Tva to ALV-K SU.

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Amino acid mutations in the capsid protein produce novel porcine circovirus type 2 neutralizing epitopes

Veterinary Microbiology ◽

10.1016/j.vetmic.2013.03.013 ◽

2013 ◽

Vol 165 (3-4) ◽

pp. 260-267 ◽

Cited By ~ 16

Author(s):

Jianbo Liu ◽

Liping Huang ◽

Yanwu Wei ◽

Qinghai Tang ◽

Dan Liu ◽

...

Keyword(s):

Amino Acid ◽

Capsid Protein ◽

Porcine Circovirus Type ◽

Porcine Circovirus Type 2 ◽

Porcine Circovirus ◽

Amino Acid Mutations ◽

Neutralizing Epitopes

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Mapping mutational effects along the evolutionary landscape of HIV envelope

10.1101/235630 ◽

2017 ◽

Author(s):

Hugh K. Haddox ◽

Adam S. Dingens ◽

Sarah K. Hilton ◽

Julie Overbaugh ◽

Jesse D. Bloom

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Long Range ◽

The Other ◽

Single Amino Acid ◽

Specific Amino Acid ◽

Viral Growth ◽

Amino Acid Mutations ◽

Hiv Envelope ◽

Hiv Evolution

AbstractThe immediate evolutionary space accessible to HIV is largely determined by how single amino-acid mutations affect fitness. These mutational effects can shift as the virus evolves. However, the prevalence of such shifts in mutational effects remains unclear. Here we quantify the effects on viral growth of all amino-acid mutations to two HIV envelope (Env) proteins that differ at >100 residues. Most mutations similarly affect both Envs, but the amino-acid preferences of a minority of sites have clearly shifted. These shifted sites usually prefer a specific amino acid in one Env, but tolerate many amino acids in the other. Surprisingly, shifts are only slightly enriched at sites that have substituted between the Envs -- and many occur at residues that do not even contact substitutions. Therefore, long-range epistasis can unpredictably shift Env's mutational tolerance during HIV evolution, although the amino-acid preferences of most sites are conserved between moderately diverged viral strains.

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Site-saturation mutagenesis of the PALTAVETG motif in coxsackievirus A9 capsid protein VP1 reveals evidence of conservation of a periodic hydrophobicity profile

Journal of General Virology ◽

10.1099/0022-1317-80-8-1919 ◽

1999 ◽

Vol 80 (8) ◽

pp. 1919-1927 ◽

Cited By ~ 3

Author(s):

Antero Airaksinen ◽

Merja Roivainen ◽

Glyn Stanway ◽

Tapani Hovi

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Capsid Protein ◽

Amino Acid Substitution ◽

Saturation Mutagenesis ◽

Single Amino Acid ◽

Site Saturation ◽

Coxsackievirus A9 ◽

Capsid Protein Vp1 ◽

Hydrophobicity Profile

Enteroviruses possess a highly conserved 9 amino acid stretch of mainly hydrophobic character in the capsid protein VP1. A novel strategy, combining site-saturation mutagenesis and a single-tube cloning and transfection procedure, has been developed for the analysis of this motif in coxsackievirus A9 (CAV-9). Four individual amino acids were separately mutated. Mutagenesis of three of the four positions in CAV-9 resulted in a number of viable but impaired mutant strains, each containing a single amino acid substitution. In contrast, no mutants with amino acid substitutions at leucine 31 were isolated, although three different leucine codons were found among the viruses recovered. Small plaque size was regularly associated with reduced yields of infectious virus and an amino acid substitution at the target site in the viruses isolated from the site-saturated virus pools. From the range of amino acids observed in viable mutants, it was possible to estimate the characteristics that are required at individual amino acid positions. It seems that in the motif studied here, a periodic hydrophobicity profile needs to be conserved. The constraints observed on the ranges of acceptable amino acids presumably reflect the structural–functional requirements that have resulted in the conservation of the motif.

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Single Amino Acid Based Self-Assemblies of Cysteine and Methionine

10.26434/chemrxiv.5972173.v1 ◽

2018 ◽

Author(s):

Nidhi Gour ◽

Bharti Koshti ◽

Chandra Kanth P. ◽

Dhruvi Shah ◽

Vivek Shinh Kshatriya ◽

...

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Self Assembly ◽

Aromatic Amino Acids ◽

Neutral Condition ◽

Single Amino Acid ◽

Binding Assays ◽

Human Neuroblastoma ◽

Cytotoxicity Assays ◽

First Time

We report for the very first time self-assembly of Cysteine and Methionine to discrenible strucutres under neutral condition. To get insights into the structure formation, thioflavin T and Congo red binding assays were done which revealed that aggregates may not have amyloid like characteristics. The nature of interactions which lead to such self-assemblies was purported by coincubating assemblies in urea and mercaptoethanol. Further interaction of aggregates with short amyloidogenic dipeptide diphenylalanine (FF) was assessed. While cysteine aggregates completely disrupted FF fibres, methionine albeit triggered fibrillation. The cytotoxicity assays of cysteine and methionine structures were performed on Human Neuroblastoma IMR-32 cells which suggested that aggregates are not cytotoxic in nature and thus, may not have amyloid like etiology. The results presented in the manuscript are striking, since to the best of our knowledge,this is the first report which demonstrates that even non-aromatic amino acids (cysteine and methionine) can undergo spontaneous self-assembly to form ordered aggregates.

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Genetic Variation and Evolution of the 2019 Novel Coronavirus

Public Health Genomics ◽

10.1159/000513530 ◽

2021 ◽

pp. 1-13

Author(s):

Salvatore Dimonte ◽

Muhammed Babakir-Mina ◽

Taib Hama-Soor ◽

Salar Ali

Keyword(s):

Amino Acid ◽

Receptor Binding ◽

Rapid Evolution ◽

Single Amino Acid ◽

Angiotensin Converting Enzyme 2 ◽

New Type ◽

Amino Acid Mutations ◽

Host Infection ◽

Human Coronaviruses ◽

Novel Coronavirus

Introduction: SARS-CoV-2 is a new type of coronavirus causing a pandemic severe acute respiratory syndrome (SARS-2). Coronaviruses are very diverting genetically and mutate so often periodically. The natural selection of viral mutations may cause host infection selectivity and infectivity. Methods: This study was aimed to indicate the diversity between human and animal coronaviruses through finding the rate of mutation in each of the spike, nucleocapsid, envelope, and membrane proteins. Results: The mutation rate is abundant in all 4 structural proteins. The most number of statistically significant amino acid mutations were found in spike receptor-binding domain (RBD) which may be because it is responsible for a corresponding receptor binding in a broad range of hosts and host selectivity to infect. Among 17 previously known amino acids which are important for binding of spike to angiotensin-converting enzyme 2 (ACE2) receptor, all of them are conservative among human coronaviruses, but only 3 of them significantly are mutated in animal coronaviruses. A single amino acid aspartate-454, that causes dissociation of the RBD of the spike and ACE2, and F486 which gives the strength of binding with ACE2 remain intact in all coronaviruses. Discussion/Conclusion: Observations of this study provided evidence of the genetic diversity and rapid evolution of SARS-CoV-2 as well as other human and animal coronaviruses.

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Phylogenetic analysis and predicted functional effect of protein mutations of E6 and E7 HPV16 strains isolated in Indonesia

Medical Journal of Indonesia ◽

10.13181/mji.v24i4.1197 ◽

2015 ◽

Vol 24 (4) ◽

pp. 197-205

Author(s):

Dwi Wulandari ◽

Lisnawati Rachmadi ◽

Tjahjani M. Sudiro

Keyword(s):

Amino Acids ◽

Phylogenetic Analysis ◽

Amino Acid ◽

Asian American ◽

Protein Function ◽

Single Amino Acid ◽

Hpv16 E6 ◽

E6 And E7 ◽

Neutral Mutations

Background: E6 and E7 are oncoproteins of HPV16. Natural amino acid variation in HPV16 E6 can alter its carcinogenic potential. The aim of this study was to analyze phylogenetically E6 and E7 genes and proteins of HPV16 from Indonesia and predict the effects of single amino acid substitution on protein function. This analysis could be used to reduce time, effort, and research cost as initial screening in selection of protein or isolates to be tested in vitro or in vivo.Methods: In this study, E6 and E7 gene sequences were obtained from 12 samples of Indonesian isolates, which were compared with HPV16R (prototype) and 6 standard isolates in the category of European (E), Asian (As), Asian-American (AA), African-1 (Af-1), African-2 (Af-2), and North American (NA) branch from Genbank. Bioedit v.7.0.0 was used to analyze the composition and substitution of single amino acids. Phylogenetic analysis of E6 and E7 genes and proteins was performed using Clustal X (1.81) and NJPLOT softwares. Effects of single amino acid substitutions on protein function of E6 and E7 were analysed by SNAP.Results: Java variants and isolate ui66* belonged to European branch, while the others belonged to Asian and African branches. Twelve changes of amino acids were found in E6 and one in E7 proteins. SNAP analysis showed two non neutral mutations, i.e. R10I and C63G in E6 proteins. R10I mutations were found in Af-2 genotype (AF472509) and Indonesian isolates (Af2*), while C63G mutation was found only in Af2*.Conclusion: E6 proteins of HPV16 variants were more variable than E7. SNAP analysis showed that only E6 protein of African-2 branch had functional differences compared to HPV16R.

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Transforming growth factor alpha: mutation of aspartic acid 47 and leucine 48 results in different biological activities.

Molecular and Cellular Biology ◽

10.1128/mcb.8.3.1247 ◽

1988 ◽

Vol 8 (3) ◽

pp. 1247-1252 ◽

Cited By ~ 35

Author(s):

E Lazar ◽

S Watanabe ◽

S Dalton ◽

M B Sporn

Keyword(s):

Amino Acids ◽

Biological Activity ◽

Amino Acid ◽

Growth Factor ◽

Aspartic Acid ◽

Transforming Growth Factor ◽

Biologically Active ◽

Single Amino Acid ◽

Transforming Growth Factor Alpha ◽

Factor Alpha

To study the relationship between the primary structure of transforming growth factor alpha (TGF-alpha) and some of its functional properties (competition with epidermal growth factor (EGF) for binding to the EGF receptor and induction of anchorage-independent growth), we introduced single amino acid mutations into the sequence for the fully processed, 50-amino-acid human TGF-alpha. The wild-type and mutant proteins were expressed in a vector by using a yeast alpha mating pheromone promoter. Mutations of two amino acids that are conserved in the family of the EGF-like peptides and are located in the carboxy-terminal part of TGF-alpha resulted in different biological effects. When aspartic acid 47 was mutated to alanine or asparagine, biological activity was retained; in contrast, substitutions of this residue with serine or glutamic acid generated mutants with reduced binding and colony-forming capacities. When leucine 48 was mutated to alanine, a complete loss of binding and colony-forming abilities resulted; mutation of leucine 48 to isoleucine or methionine resulted in very low activities. Our data suggest that these two adjacent conserved amino acids in positions 47 and 48 play different roles in defining the structure and/or biological activity of TGF-alpha and that the carboxy terminus of TGF-alpha is involved in interactions with cellular TGF-alpha receptors. The side chain of leucine 48 appears to be crucial either indirectly in determining the biologically active conformation of TGF-alpha or directly in the molecular recognition of TGF-alpha by its receptor.

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