Strain energy in enzyme–substrate binding: An energetic insight into the flexibility versus rigidity of enzyme active site

2012 ◽  
Vol 995 ◽  
pp. 17-23 ◽  
Author(s):  
Xinchun Guo ◽  
Deyong He ◽  
Ling Huang ◽  
Limin Liu ◽  
Lijun Liu ◽  
...  
Keyword(s):  
Active Site ◽  
Strain Energy ◽  
Substrate Binding ◽  
Enzyme Active Site ◽  
Enzyme Substrate ◽  
Insight Into

Structural and mechanistic insight into how antibodies inhibit serine proteases

2010 ◽  
Vol 430 (2) ◽  
pp. 179-189 ◽  
Author(s):  
Rajkumar Ganesan ◽  
Charles Eigenbrot ◽  
Daniel Kirchhofer
Keyword(s):  
Active Site ◽  
Serine Proteases ◽  
Structural Changes ◽  
Competitive Inhibition ◽  
Substrate Binding ◽  
Structural Features ◽  
Inhibition Mechanism ◽  
Interaction Sites ◽  
Binding Cleft ◽  
Insight Into

Antibodies display great versatility in protein interactions and have become important therapeutic agents for a variety of human diseases. Their ability to discriminate between highly conserved sequences could be of great use for therapeutic approaches that target proteases, for which structural features are conserved among family members. Recent crystal structures of antibody–protease complexes provide exciting insight into the variety of ways antibodies can interfere with the catalytic machinery of serine proteases. The studies revealed the molecular details of two fundamental mechanisms by which antibodies inhibit catalysis of trypsin-like serine proteases, exemplified by hepatocyte growth factor activator and MT-SP1 (matriptase). Enzyme kinetics defines both mechanisms as competitive inhibition systems, yet, on the molecular level, they involve distinct structural elements of the active-site region. In the steric hindrance mechanism, the antibody binds to protruding surface loops and inserts one or two CDR (complementarity-determining region) loops into the enzyme's substrate-binding cleft, which results in obstruction of substrate access. In the allosteric inhibition mechanism the antibody binds outside the active site at the periphery of the substrate-binding cleft and, mediated through a conformational change of a surface loop, imposes structural changes at important substrate interaction sites resulting in impaired catalysis. At the centre of this allosteric mechanism is the 99-loop, which is sandwiched between the substrate and the antibody-binding sites and serves as a mobile conduit between these sites. These findings provide comprehensive structural and functional insight into the molecular versatility of antibodies for interfering with the catalytic machinery of proteases.

scholarly journals Characteristics and composition of the vitamin K-dependent γ-glutamyl carboxylase-binding domain on osteocalcin

2002 ◽  
Vol 364 (1) ◽  
pp. 323-328 ◽  
Author(s):  
Roger J.T.J. HOUBEN ◽  
Dirk T.S. RIJKERS ◽  
Thomas B. STANLEY ◽  
Francine ACHER ◽  
Robert AZERAD ◽  
...  
Keyword(s):  
Binding Site ◽  
Vitamin K ◽  
Active Site ◽  
Substrate Binding ◽  
Direct Interaction ◽  
Binding Domain ◽  
High Affinity ◽  
Substrate Interaction ◽  
Enzyme Substrate ◽  
Gla Domain

Two different sites on vitamin K-dependent γ-glutamyl carboxylase (VKC) are involved in enzyme—substrate interaction: the propeptide-binding site required for high-affinity substrate binding and the active site for glutamate carboxylation. Synthetic descarboxy osteocalcin (d-OC) is a low-Km substrate for the VKC, but unique since it possesses a high-affinity recognition site for the VKC, distinct from the propeptide which is essential as a binding site for VKC. However, the exact location and composition of this VKC-recognition domain on d-OC has remained unclear until now. Using a stereospecific substrate analogue [t-butyloxycarbonyl-(2S,4S)-4-methylglutamic acid-Glu-Val (S-MeTPT)] we demonstrate in this paper that the high affinity of d-OC for VKC cannot be explained by a direct interaction with either the active site or with the propeptide-binding site on VKC. It is shown using various synthetic peptides derived from d-OC that there are two domains on d-OC necessary for recognition: one located between residues 1 and 12 and a second between residues 26 and 39, i.e. at the C-terminal side of the γ-carboxyglutamate (Gla) domain. Both internal sequences contribute substantially to the efficiency of carboxylation. On the basis of these data we postulate the presence of a second high-affinity substrate-binding site on VKC capable of specifically binding d-OC, which is the first vitamin K-dependent substrate of which the VKC binding domain is interrupted by the Gla domain.

Copper–oxygen Dynamics in Tyrosinase

2019 ◽  
Author(s):  
Nobutaka Fujieda ◽  
Sachiko Yanagisawa ◽  
Minoru Kubo ◽  
Genji Kurisu ◽  
Shinobu Itoh
Keyword(s):  
Catalytic Mechanism ◽  
Substrate Binding ◽  
Active Form ◽  
Copper Ion ◽  
Atomic Resolution ◽  
Oxygen Species ◽  
X Ray ◽  
Oxygen Dynamics ◽  
Insight Into ◽  
Copper Centre

To unveil the activation of dioxygen on the copper centre (Cu<sub>2</sub>O<sub>2</sub>core) of tyrosinase, we performed X-ray crystallograpy with active-form tyrosinase at near atomic resolution. This study provided a novel insight into the catalytic mechanism of the tyrosinase, including the rearrangement of copper-oxygen species as well as the intramolecular migration of copper ion induced by substrate-binding.<br>

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