1
|
Gavade A, Nagraj AK, Patel R, Pais R, Dhanure P, Scheele J, Seiz W, Patil J. Understanding the Specific Implications of Amino Acids in the Antibody Development. Protein J 2024; 43:405-424. [PMID: 38724751 DOI: 10.1007/s10930-024-10201-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2024] [Indexed: 06/01/2024]
Abstract
As the demand for immunotherapy to treat and manage cancers, infectious diseases and other disorders grows, a comprehensive understanding of amino acids and their intricate role in antibody engineering has become a prime requirement. Naturally produced antibodies may not have the most suitable amino acids at the complementarity determining regions (CDR) and framework regions, for therapeutic purposes. Therefore, to enhance the binding affinity and therapeutic properties of an antibody, the specific impact of certain amino acids on the antibody's architecture must be thoroughly studied. In antibody engineering, it is crucial to identify the key amino acid residues that significantly contribute to improving antibody properties. Therapeutic antibodies with higher binding affinity and improved functionality can be achieved through modifications or substitutions with highly suitable amino acid residues. Here, we have indicated the frequency of amino acids and their association with the binding free energy in CDRs. The review also analyzes the experimental outcome of two studies that reveal the frequency of amino acids in CDRs and provides their significant correlation between the outcomes. Additionally, it discusses the various bond interactions within the antibody structure and antigen binding. A detailed understanding of these amino acid properties should assist in the analysis of antibody sequences and structures needed for designing and enhancing the overall performance of therapeutic antibodies.
Collapse
Affiliation(s)
- Akshata Gavade
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Anil Kumar Nagraj
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Riya Patel
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Roylan Pais
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Pratiksha Dhanure
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | | | | | - Jaspal Patil
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India.
| |
Collapse
|
2
|
Zhang H, Miao H, Li C, Wei L, Duan Y, Ma Q, Kong J, Xu F, Chang S. Ultra-dense SNP genetic map construction and identification of SiDt gene controlling the determinate growth habit in Sesamum indicum L. Sci Rep 2016; 6:31556. [PMID: 27527492 PMCID: PMC4985745 DOI: 10.1038/srep31556] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 07/19/2016] [Indexed: 11/13/2022] Open
Abstract
Sesame (Sesamum indicum L.) is an important oilseed crop and has an indeterminate growth habit. Here we resequenced the genomes of the parents and 120 progeny of an F2 population derived from crossing Yuzhi 11 (indeterminate, Dt) and Yuzhi DS899 (determinate, dt1), and constructed an ultra-dense SNP map for sesame comprised of 3,041 bins including 30,193 SNPs in 13 linkage groups (LGs) with an average marker density of 0.10 cM. Results indicated that the same recessive gene controls the determinacy trait in dt1 and a second determinate line, dt2 (08TP092). The QDt1 locus for the determinacy trait was located in the 18.0 cM-19.2 cM interval of LG8. The target SNP, SiDt27-1, and the determinacy gene, DS899s00170.023 (named here as SiDt), were identified in Scaffold 00170 of the Yuzhi 11 reference genome, based on genetic mapping and genomic association analysis. Unlike the G397A SNP change in the dt1 genotype, the SiDt allele in dt2 line was lost from the genome. This example of map-based gene cloning in sesame provides proof-of-concept of the utility of ultra-dense SNP maps for accurate genome research in sesame.
Collapse
Affiliation(s)
- Haiyang Zhang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, People’s Republic of China
| | - Hongmei Miao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, People’s Republic of China
| | - Chun Li
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, People’s Republic of China
| | - Libin Wei
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, People’s Republic of China
| | - Yinghui Duan
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, People’s Republic of China
| | - Qin Ma
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, People’s Republic of China
| | - Jingjing Kong
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, People’s Republic of China
| | - Fangfang Xu
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, People’s Republic of China
| | - Shuxian Chang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, People’s Republic of China
| |
Collapse
|
3
|
Fukuda N, Suwa Y, Uchida M, Kobashigawa Y, Yokoyama H, Morioka H. Role of the mobility of antigen binding site in high affinity antibody elucidated by surface plasmon resonance. J Biochem 2016; 161:37-43. [PMID: 27507818 DOI: 10.1093/jb/mvw050] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 07/20/2016] [Indexed: 11/12/2022] Open
Abstract
Antibody is known to exhibit conformational change in the antigen recognition site after forming the initial complex. This structural change, which is widely known as "induced fit", is believed to be critical for high affinity (Kd of nM range) of antigen-antibody interaction. Elucidation of this 'induced fit' process is essential for rational design of high affinity antibody, while it is prevented by limitation of the available biophysical and biochemical data of the initial complex. Here, we performed kinetic and thermodynamic analysis of the interaction between single-chain variable fragment (denoted as scFv) of 64M5 antibody and a (6-4) photoproduct by using surface plasmon resonance (denoted as SPR). It revealed that the 64M5scFv associates the (6-4) photoproduct at initial step by hydrophobic interactions, and enthalpy-driving interactions, hydrogen bonds and van der Waals interactions, were formed by second step structural rearrangement. Furthermore, mutational analysis revealed that the mobility of the antigen-binding site is critical for the second step. It could be assumed that optimization of the mobility of the antigen recognition site is a clue for rational design of high affinity antibody.
Collapse
Affiliation(s)
- Natsuki Fukuda
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Yoshiaki Suwa
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Makiyo Uchida
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Yoshihiro Kobashigawa
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Hideshi Yokoyama
- Labratory of Physical Biochemistry, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Hiroshi Morioka
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| |
Collapse
|
4
|
Structural biology of DNA (6-4) photoproducts formed by ultraviolet radiation and interactions with their binding proteins. Int J Mol Sci 2014; 15:20321-38. [PMID: 25383676 PMCID: PMC4264169 DOI: 10.3390/ijms151120321] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 10/24/2014] [Accepted: 10/29/2014] [Indexed: 01/09/2023] Open
Abstract
Exposure to the ultraviolet component of sunlight causes DNA damage, which subsequently leads to mutations, cellular transformation, and cell death. DNA photoproducts with (6-4) pyrimidine-pyrimidone adducts are more mutagenic than cyclobutane pyrimidine dimers. These lesions must be repaired because of the high mutagenic potential of (6-4) photoproducts. We here reviewed the structures of (6-4) photoproducts, particularly the detailed structures of the (6-4) lesion and (6-4) lesion-containing double-stranded DNA. We also focused on interactions with their binding proteins such as antibody Fabs, (6-4) photolyase, and nucleotide excision repair protein. The (6-4) photoproducts that bound to these proteins had common structural features: The 5'-side thymine and 3'-side pyrimidone bases of the T(6-4)T segment were in half-chair and planar conformations, respectively, and both bases were positioned nearly perpendicularly to each other. Interactions with binding proteins showed that the DNA helices flanking the T(6-4)T segment were largely kinked, and the flipped-out T(6-4)T segment was recognized by these proteins. These proteins had distinctive binding-site structures that were appropriate for their functions.
Collapse
|
5
|
Mitchell D, Brooks B. Antibodies and DNA Photoproducts: Applications, Milestones and Reference Guide. Photochem Photobiol 2010; 86:2-17. [DOI: 10.1111/j.1751-1097.2009.00673.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
6
|
Burmann BM, Uc-Mass A, Schweimer K, Gottesman ME, Rösch P. The Y39A mutation of HK022 Nun disrupts a boxB interaction but preserves termination activity. Biochemistry 2008; 47:7335-41. [PMID: 18563916 DOI: 10.1021/bi8004347] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Coliphage HK022 Nun protein targets phage lambda nut boxB RNA and acts as a transcriptional terminator, counteracting the phage lambda N protein, a suppressor of transcription termination. Both Nun and N protein interact directly with RNA polymerase, and Nun competes with N protein for boxB binding and prevents superinfection of Escherichia coli HK022 lysogens by lambda. Interaction of Trp18 of lambda N and A7 of boxB RNA in the N- boxB complex is essential for efficient antitermination. We found that the corresponding Nun mutation, Nun Y39A, disrupts the interaction between the aromatic ring of Y39 and A7, but the mutant retains in vivo termination activity. Stabilization of the complex by interaction of A7 with an aromatic amino acid is thus less important for Nun activity than it is for N activity. Structural investigations show similar binding of mutant and wild-type (wt) Nun protein to boxB RNA. The dissociation constants of the wt Nun(20-44)- boxB and mutant Nun(20-44)- boxB complex as well as the structures of the boxB RNA in both complexes are identical.
Collapse
Affiliation(s)
- Björn M Burmann
- Department of Biopolymers and Research Center for Bio-Macromolecules, Universität Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
| | | | | | | | | |
Collapse
|
7
|
Morioka H, Kurihara M, Kobayashi H, Satou K, Komatsu Y, Uchida M, Ohtsuka E, Torizawa T, Kato K, Shimada I, Matsunaga T, Nikaido O. DNA-binding properties of the antibody specific for the Dewar photoproduct of thymidylyl-(3-5')-thymidine. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2006; 25:667-79. [PMID: 16838854 DOI: 10.1080/15257770600686469] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
A monoclonal antibody (DEM-1) specific for the Dewar photoproduct is used for detection and quantification of photolesions in DNA. To help understand the molecular recognition of damaged DNA by the antibody protein, we have cloned and sequenced the variable region genes of DEM-1. We have also prepared Fab fragments of DEM-1 (DEM1Fab), and synthesized two kinds of 3'-biotinylated oligonucleotides of different lengths containing a central Dewar photoproduct of TpT to analyze the effects of the antigen size on the binding rates by means of surface plasmon resonance (SPR). Results obtained from SPR analyses suggest that DEM1Fab may recognize tetranucleotide unit as the epitope.
Collapse
Affiliation(s)
- Hiroshi Morioka
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-ku, Sapporo, Japan.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Kobayashi H, Komatsu Y, Morioka H, Ohtsuka E. DNA Binding Mode of Antibody Fragments Specific for TT Photo-Dimers. PHOSPHORUS SULFUR 2002. [DOI: 10.1080/10426500212301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Hiroyuki Kobayashi
- a Graduate School of Pharmaceutical Sciences , Hokkaido University , Sapporo , 060-0812 , Japan
| | - Yasuo Komatsu
- a Graduate School of Pharmaceutical Sciences , Hokkaido University , Sapporo , 060-0812 , Japan
| | - Hiroshi Morioka
- a Graduate School of Pharmaceutical Sciences , Hokkaido University , Sapporo , 060-0812 , Japan
| | - Eiko Ohtsuka
- a Graduate School of Pharmaceutical Sciences , Hokkaido University , Sapporo , 060-0812 , Japan
| |
Collapse
|
9
|
Jirholt P, Strandberg L, Jansson B, Krambovitis E, Söderlind E, Borrebaeck CA, Carlsson R, Danielsson L, Ohlin M. A central core structure in an antibody variable domain determines antigen specificity. PROTEIN ENGINEERING 2001; 14:67-74. [PMID: 11287680 DOI: 10.1093/protein/14.1.67] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Antibody binding sites provide an adaptable surface capable of interacting with essentially any molecular target. Using CDR shuffling, residues important for the assembly of mucin-1 specific paratopes were defined by random recombination of the complementarity determining regions derived from a set of mucin-1 specific clones, previously selected from an antibody fragment library. It was found that positions 33 and 50 in the heavy chain and 32, 34, 90, 91 and 96 in the light chain were conserved in many of the clones. These particular residues seem to be located centrally in the binding site as indicated by a structure model analysis. The importance of several of these conserved residues was supported by their presence in a mouse monoclonal antibody with a known structure and the same epitope specificity. Several of these corresponding residues in the mouse monoclonal antibody are known to interact with the antigen. In conclusion, critical residues important for maintaining a human antigen-specific binding site during the process of in vitro antibody evolution were defined. Furthermore, an explanation for the observed restricted germline gene usage in certain antibody responses against protein epitopes is provided.
Collapse
Affiliation(s)
- P Jirholt
- Department of Immunotechnology, Lund University, S-220 07 Lund, Sweden
| | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Abstract
The application of surface plasmon resonance biosensors in life sciences and pharmaceutical research continues to increase. This review provides a comprehensive list of the commercial 1999 SPR biosensor literature and highlights emerging applications that are of general interest to users of the technology. Given the variability in the quality of published biosensor data, we present some general guidelines to help increase confidence in the results reported from biosensor analyses.
Collapse
Affiliation(s)
- R L Rich
- Center for Biomolecular Interaction Analysis, University of Utah School of Medicine, Salt Lake City 84132, USA
| | | |
Collapse
|