Biophysical properties of human antibody variable domains.


Abstract

There are great demands on the stability, expression yield and resistance to aggregation of antibody fragments. To untangle intrinsic domain effects from domain interactions, we present first a systematic evaluation of the isolated human immunoglobulin variable heavy (V(H)) and light (V(L)) germline family consensus domains and then a systematic series of V(H)-V(L) combinations in the scFv format. The constructs were evaluated in terms of their expression behavior, oligomeric state in solution and denaturant-induced unfolding equilibria under non-reducing conditions. The seven V(H) and seven V(L) domains represent the consensus sequences of the major human germline subclasses, derived from the Human Combinatorial Antibody Library (HuCAL). The isolated V(H) and V(L) domains with the highest thermodynamic stability and yield of soluble protein were V(H)3 and V(kappa)3, respectively. Similar measurements on all domain combinations in scFv fragments allowed the scFv fragments to be classified according to thermodynamic stability and in vivo folding yield. The scFv fragments containing the variable domain combinations H3kappa3, H1bkappa3, H5kappa3 and H3kappa1 show superior properties concerning yield and stability. Domain interactions diminish the intrinsic differences of the domains. ScFv fragments containing V(lambda) domains show high levels of stability, even though V(lambda) domains are surprisingly unstable by themselves. This is due to a strong interaction with the V(H) domain and depends on the amino acid sequence of the CDR-L3. On the basis of these analyses and model structures, we suggest possibilities for further improvement of the biophysical properties of individual frameworks and give recommendations for library design. Study holds ProTherm entries: 15698, 15699, 15700, 15701, 15702, 15703, 15704, 15705, 15706, 15707, 15708, 15709, 15710, 15711 Extra Details: VH-1a family antibody engineering; protein stability; expression; scFv fragment

Submission Details

ID: 8QMTy5k53

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:46 p.m.

Version: 1

Publication Details
Ewert S;Huber T;Honegger A;Pl├╝ckthun A,J. Mol. Biol. (2003) Biophysical properties of human antibody variable domains. PMID:12498801
Additional Information

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P
 

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)


Relevant PDB Entries

Structure ID Release Date Resolution Structure Title
2Q20 2008-04-08 1.3 Structure of the germline Vk1 O18/O8 light chain variable domain homodimer
1EEQ 2001-02-01 1.5 M4L/Y(27D)D/T94H Mutant of LEN
3CDF 2008-09-02 1.53 kI O18/O8 Y87H immunoglobulin light chain variable domain
3CDC 2008-09-02 1.53 kI O18/O8 N34I/Y87H immunoglobulin light chain variable domain
1EEU 2001-02-03 1.6 M4L/Y(27D)D/Q89D/T94H mutant of LEN
1EFQ 2001-02-09 1.6 Q38D mutant of LEN
4L1H 2014-06-04 1.68 Bence-Jones immunoglobulin REI variable portion with seven point mutations
1BWW 1998-10-07 1.7 BENCE-JONES IMMUNOGLOBULIN REI VARIABLE PORTION, T39K MUTANT
1QAC 2000-02-23 1.8 CHANGE IN DIMERIZATION MODE BY REMOVAL OF A SINGLE UNSATISFIED POLAR RESIDUE
1B0W 1998-11-16 1.8 Structural comparison of amyloidogenic light chain dimer in two crystal forms with nonamyloidogenic counterparts
1EK3 2001-03-06 1.9 KAPPA-4 IMMUNOGLOBULIN VL, REC
1WTL 1994-11-01 1.9 COMPARISON OF CRYSTAL STRUCTURES OF TWO HOMOLOGOUS PROTEINS: STRUCTURAL ORIGIN OF ALTERED DOMAIN INTERACTIONS IN IMMUNOGLOBULIN LIGHT CHAIN DIMERS
1LVE 1998-01-21 1.95 STRUCTURE OF THE VARIABLE DOMAIN OF HUMAN IMMUNOGLOBULIN K-4 LIGHT CHAIN LEN
1REI 1976-05-19 2.0 THE MOLECULAR STRUCTURE OF A DIMER COMPOSED OF THE VARIABLE PORTIONS OF THE BENCE-JONES PROTEIN REI REFINED AT 2.0 ANGSTROMS RESOLUTION
3LVE 1999-05-18 2.0 LEN Q38E MUTANT: A DOMAIN FLIP FROM A SINGLE AMINO ACID SUBSTITUTION
5LVE 2000-02-18 2.0 STRUCTURE OF THE VARIABLE DOMAIN OF HUMAN IMMUNOGLOBULIN K-4 LIGHT CHAIN LEN
1QP1 1999-06-17 2.06 KAPPA VARIABLE LIGHT CHAIN
1JV5 2002-01-09 2.2 Anti-blood group A Fv
4LVE 1999-05-18 2.3 LEN K30T MUTANT: A DOMAIN FLIP AS A RESULT OF A SINGLE AMINO ACID SUBSTITUTION
3CDY 2008-09-02 2.43 AL-09 H87Y, immunoglobulin light chain variable domain
2LVE 1999-05-18 2.7 RECOMBINANT LEN
1AR2 1997-11-12 2.8 DISULFIDE-FREE IMMUNOGLOBULIN FRAGMENT
4K07 2013-10-30 2.83 Crystal structure of the amyloid-forming immunoglobulin AL-103 cis-proline 95 mutant
5XP1 2017-08-02 2.88 Structure of monomeric mutant of REI immunoglobulin light chain variable domain crystallized at pH 6

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
100.0 Immunoglobulin kappa variable 1D-33 P01593 KVD33_HUMAN
100.0 Immunoglobulin kappa variable 1D-33 P01594 KV133_HUMAN
99.0 Immunoglobulin kappa variable 4-1 P06312 KV401_HUMAN