Loop dynamics and the evolution of enzyme activity
In the early 2000s, Tawfik presented his 'New View'on enzyme evolution, highlighting the
role of conformational plasticity in expanding the functional diversity of limited repertoires of …
role of conformational plasticity in expanding the functional diversity of limited repertoires of …
Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis
RA Friesner, V Guallar - Annu. Rev. Phys. Chem., 2005 - annualreviews.org
▪ Abstract We describe large scale ab initio quantum chemical and mixed quantum
mechanics/molecular mechanics (QM/MM) methods for studying enzymatic reactions. First …
mechanics/molecular mechanics (QM/MM) methods for studying enzymatic reactions. First …
[HTML][HTML] Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ
Biological processes are regulated by intermolecular interactions and chemical
modifications that do not affect protein levels, thus escaping detection in classical proteomic …
modifications that do not affect protein levels, thus escaping detection in classical proteomic …
[HTML][HTML] De novo enzyme design using Rosetta3
The Rosetta de novo enzyme design protocol has been used to design enzyme catalysts for
a variety of chemical reactions, and in principle can be applied to any arbitrary chemical …
a variety of chemical reactions, and in principle can be applied to any arbitrary chemical …
Mechanisms and free energies of enzymatic reactions
Most enzymatic reactions have very large and remarkably similar apparent second-order
rate constants, kcat/KM, at mean values of about 107 M-1 s-1 with kcat in the range of 10 …
rate constants, kcat/KM, at mean values of about 107 M-1 s-1 with kcat in the range of 10 …
Triosephosphate isomerase: a highly evolved biocatalyst
RK Wierenga, EG Kapetaniou… - Cellular and molecular life …, 2010 - Springer
Triosephosphate isomerase (TIM) is a perfectly evolved enzyme which very fast
interconverts dihydroxyacetone phosphate and d-glyceraldehyde-3-phosphate. Its catalytic …
interconverts dihydroxyacetone phosphate and d-glyceraldehyde-3-phosphate. Its catalytic …
[HTML][HTML] The self-inhibitory nature of metabolic networks and its alleviation through compartmentalization
Metabolites can inhibit the enzymes that generate them. To explore the general nature of
metabolic self-inhibition, we surveyed enzymological data accrued from a century of …
metabolic self-inhibition, we surveyed enzymological data accrued from a century of …
Computational design of a biologically active enzyme
MA Dwyer, LL Looger, HW Hellinga - Science, 2004 - science.org
Rational design of enzymes is a stringent test of our understanding of protein chemistry and
has numerous potential applications. Here, we present and experimentally validate the …
has numerous potential applications. Here, we present and experimentally validate the …
A role for flexible loops in enzyme catalysis
MM Malabanan, TL Amyes, JP Richard - Current opinion in structural …, 2010 - Elsevier
Triosephosphate isomerase (TIM), glycerol 3-phosphate dehydrogenase, and orotidine 5′-
monophosphate decarboxylase each use the binding energy from the interaction of …
monophosphate decarboxylase each use the binding energy from the interaction of …
Loop motion in triosephosphate isomerase is not a simple open and shut case
Conformational changes are crucial for the catalytic action of many enzymes. A prototypical
and well-studied example is loop opening and closure in triosephosphate isomerase (TIM) …
and well-studied example is loop opening and closure in triosephosphate isomerase (TIM) …