Functional Mutations in and Characterization of VHH Against Helicobacter pylori Urease

Hoseinpoor, Reyhaneh; Gargari, Seyed Latif Mousavi; Rasooli, Iraj; Rajabibazl, Masoumeh; Shahi, Bahareh

doi:10.1007/s12010-014-0750-4

Cited by 14 publications

(7 citation statements)

References 29 publications

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“…The fold prediction software Phyre2 was used to model V H H against Urease (Hoseinpoor et al, 2014). The popular i-TASSER web server was used for V H H designed against PrA (ProteinA) (Fridy et al, 2015) and HCV Non-structural protein NS3/4A (Jittavisutthikul et al, 2015).…”

Section: (B) Other Generic 3d Prediction Approachesmentioning

confidence: 99%

Discrete analysis of camelid variable domains: sequences, structures, and in-silico structure prediction

Vattekatte

Shinada

Narwani

et al. 2020

PeerJ

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Antigen binding by antibodies requires precise orientation of the complementarity- determining region (CDR) loops in the variable domain to establish the correct contact surface. Members of the family Camelidae have a modified form of immunoglobulin gamma (IgG) with only heavy chains, called Heavy Chain only Antibodies (HCAb). Antigen binding in HCAbs is mediated by only three CDR loops from the single variable domain (VHH) at the N-terminus of each heavy chain. This feature of the VHH, along with their other important features, e.g., easy expression, small size, thermo-stability and hydrophilicity, made them promising candidates for therapeutics and diagnostics. Thus, to design better VHH domains, it is important to thoroughly understand their sequence and structure characteristics and relationship. In this study, sequence characteristics of VHH domains have been analysed in depth, along with their structural features using innovative approaches, namely a structural alphabet. An elaborate summary of various studies proposing structural models of VHH domains showed diversity in the algorithms used. Finally, a case study to elucidate the differences in structural models from single and multiple templates is presented. In this case study, along with the above-mentioned aspects of VHH, an exciting view of various factors in structure prediction of VHH, like template framework selection, is also discussed.

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Section: (B) Other Generic 3d Prediction Approachesmentioning

confidence: 99%

Discrete analysis of camelid variable domains: sequences, structures, and in-silico structure prediction

Vattekatte

Shinada

Narwani

et al. 2020

PeerJ

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“…Most scFv antibodies that are isolated from phage display libraries show affinity of 10 −6 or 10 −7 M (Nissim et al, 1994;Vitaliti et al, 2000). The affinity of isolated scFv can be increased by error-prone PCR on scFv gene or construction of diabodies which results in higher avidity and half-life (Hudson and Kortt, 1999;Vitaliti et al, 2000;Hoseinpoor et al, 2014).…”

Section: Resultsmentioning

confidence: 99%

Inhibiting angiogenesis with human single-chain variable fragment antibody targeting VEGF

Hosseini

Rajabibazl

Ebrahimizadeh

et al. 2015

Microvascular Research

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“…To understand the difference of binding properties between parent anti-UreC V H H and HMR23, structural models were generated using Phyre2. The modelling of parent and mutant V H Hs was essential to understand the structural conservation in terms of fold in the latter [ 171 ].…”

Section: V H H Modellingmentioning

confidence: 99%

VHH Structural Modelling Approaches: A Critical Review

Vishwakarma

Vattekatte

Shinada³

et al. 2022

IJMS

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VHH, i.e., VH domains of camelid single-chain antibodies, are very promising therapeutic agents due to their significant physicochemical advantages compared to classical mammalian antibodies. The number of experimentally solved VHH structures has significantly improved recently, which is of great help, because it offers the ability to directly work on 3D structures to humanise or improve them. Unfortunately, most VHHs do not have 3D structures. Thus, it is essential to find alternative ways to get structural information. The methods of structure prediction from the primary amino acid sequence appear essential to bypass this limitation. This review presents the most extensive overview of structure prediction methods applied for the 3D modelling of a given VHH sequence (a total of 21). Besides the historical overview, it aims at showing how model software programs have been shaping the structural predictions of VHHs. A brief explanation of each methodology is supplied, and pertinent examples of their usage are provided. Finally, we present a structure prediction case study of a recently solved VHH structure. According to some recent studies and the present analysis, AlphaFold 2 and NanoNet appear to be the best tools to predict a structural model of VHH from its sequence.

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Functional Mutations in and Characterization of VHH Against Helicobacter pylori Urease

Cited by 14 publications

References 29 publications

Discrete analysis of camelid variable domains: sequences, structures, and in-silico structure prediction

Discrete analysis of camelid variable domains: sequences, structures, and in-silico structure prediction

Inhibiting angiogenesis with human single-chain variable fragment antibody targeting VEGF

VHH Structural Modelling Approaches: A Critical Review

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