TY - JOUR
T1 - Steered molecular dynamics investigations of protein function
AU - Isralewitz, Barry
AU - Baudry, Jerome
AU - Gullingsrud, Justin
AU - Kosztin, Dorina
AU - Schulten, Klaus
N1 - Funding Information:
All figures in this article were created using VMD. 51 This work was supported by the National Institutes of Health (NIH PHS 5 P41 RR05969, NIH 1 R01 GM60946-01).
PY - 2001
Y1 - 2001
N2 - Molecular recognition and mechanical properties of proteins govern molecular processes in the cell that can cause disease and can be targeted for drug design. Single molecule measurement techniques have greatly advanced knowledge but cannot resolve enough detail to be interpreted in terms of protein structure. We seek to complement the observations through so-called Steered Molecular Dynamics (SMD) simulations that link directly to experiments and provide atomic-level descriptions of the underlying events. Such a research program has been initiated in our group and has involved, for example, studies of elastic properties of immunoglobulin and fibronectin domains as well as the binding of biotin and avidin. In this article we explain the SMD method and suggest how it can be applied to the function of three systems that are the focus of modern molecular biology research: Force transduction by the muscle protein titin and extracellular matrix protein fibronectin, recognition of antibody-antigene pairs, and ion selective conductivity of the K+ channel.
AB - Molecular recognition and mechanical properties of proteins govern molecular processes in the cell that can cause disease and can be targeted for drug design. Single molecule measurement techniques have greatly advanced knowledge but cannot resolve enough detail to be interpreted in terms of protein structure. We seek to complement the observations through so-called Steered Molecular Dynamics (SMD) simulations that link directly to experiments and provide atomic-level descriptions of the underlying events. Such a research program has been initiated in our group and has involved, for example, studies of elastic properties of immunoglobulin and fibronectin domains as well as the binding of biotin and avidin. In this article we explain the SMD method and suggest how it can be applied to the function of three systems that are the focus of modern molecular biology research: Force transduction by the muscle protein titin and extracellular matrix protein fibronectin, recognition of antibody-antigene pairs, and ion selective conductivity of the K+ channel.
UR - http://www.scopus.com/inward/record.url?scp=0035003803&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=0035003803&partnerID=8YFLogxK
U2 - 10.1016/S1093-3263(00)00133-9
DO - 10.1016/S1093-3263(00)00133-9
M3 - Article
C2 - 11381523
AN - SCOPUS:0035003803
VL - 19
SP - 13
EP - 25
JO - Journal of Molecular Graphics and Modelling
JF - Journal of Molecular Graphics and Modelling
SN - 1093-3263
IS - 1
ER -