PMID- 19132876
OWN - NLM
STAT- MEDLINE
DCOM- 20090406
LR  - 20090205
IS  - 1520-6106 (Print)
IS  - 1520-5207 (Linking)
VI  - 113
IP  - 6
DP  - 2009 Feb 12
TI  - Simulated mutagenesis of the hypervariable loops of a llama VHH domain for the 
      recovery of canonical conformations.
PG  - 1785-95
LID - 10.1021/jp805866j [doi]
AB  - In this work, wildtype and mutated hypervariable regions of an anti-hCG llama VHH 
      antibody were simulated via a molecular dynamics replica exchange method (REM). 
      Seven mutants were simulated with the goal of identifying structural determinants 
      that return the noncanonical H1 loop of the wildtype antibody to the type 1 
      canonical structure predicted by database methods formulated for conventional 
      antibodies. Two cases with three point mutations yielded a stable type 1 H1 
      structure. In addition, other mutants with fewer mutations showed evidence of 
      such conformations. Overall, the mutagenesis results suggest a marked influence 
      of interloop interactions on the attainment of canonical conformations for this 
      antibody. On the methodological front, a novel REM scheme was developed to 
      quickly screen diverse mutants based on their relative propensities for attaining 
      favorable structures. This multimutant REM (MMREM) was used to successfully 
      identify mutations that stabilize a canonical H1 loop grafted on the llama 
      antibody scaffold. The use of MMREM and REM for screening mutants and assessing 
      structural stability may be useful in the rational design of antibody 
      hypervariable loops.
FAU - Velez-Vega, Camilo
AU  - Velez-Vega C
AD  - School of Chemical and Biomolecular Engineering, Department of Molecular 
      Medicine, Cornell University, Ithaca, New York 14853, USA.
FAU - Fenwick, Michael K
AU  - Fenwick MK
FAU - Escobedo, Fernando A
AU  - Escobedo FA
LA  - eng
PT  - Journal Article
PT  - Research Support, U.S. Gov't, Non-P.H.S.
PL  - United States
TA  - J Phys Chem B
JT  - The journal of physical chemistry. B
JID - 101157530
RN  - 0 (Antibodies)
RN  - 0 (Complementarity Determining Regions)
RN  - 0 (Immunoglobulin Heavy Chains)
SB  - IM
MH  - Animals
MH  - Antibodies/chemistry/genetics
MH  - *Camelids, New World
MH  - Complementarity Determining Regions/*chemistry/*genetics
MH  - *Computer Simulation
MH  - Crystallography, X-Ray
MH  - Immunoglobulin Heavy Chains/*chemistry/*genetics
MH  - Magnetic Resonance Spectroscopy
MH  - Models, Molecular
MH  - *Mutagenesis
MH  - Protein Conformation
MH  - Time Factors
EDAT- 2009/01/10 09:00
MHDA- 2009/04/07 09:00
CRDT- 2009/01/10 09:00
PHST- 2009/01/10 09:00 [entrez]
PHST- 2009/01/10 09:00 [pubmed]
PHST- 2009/04/07 09:00 [medline]
AID - 10.1021/jp805866j [pii]
AID - 10.1021/jp805866j [doi]
PST - ppublish
SO  - J Phys Chem B. 2009 Feb 12;113(6):1785-95. doi: 10.1021/jp805866j.