Enzymes are complex proteins capable of catalyzing specific biochemical reactions in cells. While it has long been recognized that dynamic fluctuations in protein conformation or structure play a central role in enzyme catalysis, the new findings indicate that the "dynamic energy landscape" of the enzyme funnels it along a preferred pathway that actually minimizes the number and dimension of the energetic barriers to these catalytic changes.
"There is a growing awareness that the inherent motions of proteins are essential to their functions," said Peter Wright, who is chair of the Scripps Research Department of Molecular Biology and a member of the Skaggs Institute for Chemical Biology at Scripps Research. "The importance of this study is that it reveals how dynamic structural fluctuations channel an enzyme through its reaction cycle-the thermal motions of the protein are harnessed to perform its biological function, in this case, catalysis. Knowledge of the excited-state conformations of proteins may offer new opportunities for drug design."
The researchers used nuclear magnetic resonance (NMR) to detect and characterize higher energy structural sub-states (excited states) of E. coli dihydrofolate reductase, which has been used extensively as a model enzyme for investigating the relations between structure, dynamics, and function in proteins. The researchers found that, at each stage in the catalytic cycle, the excited-state conformations resembled the ground-state structures of both the preceding and the following intermediates. This means that the dynamic fluctuations between the ground state and the excited state were "priming" the enzyme to take up the conformation of the adjacent intermediate state, facilitating the progress of catalysis by aiding the movement of ligands (molecules that bind to one chemical entity to form a larger complex) on and off the enzyme.
"These findings contrast with the traditional 'induced fit' hypothesis," Wright said. "One of the tenets of that hypothesis is that the binding of ligands induces a structural change that increases the complementary relationship between the ligand and the enzyme."
As the study points out, most proteins do not have rigid molecular structures but are structurally heterogeneous; the motion and plasticity in their structure allows them to achieve a far greater range of functions than would be possible with static structures.
However, despite considerable evidence that many enzymes are inherently flexible, the fundamental mechanisms by which protein fluctuations couple with catalytic function remain poorly understood.
In the new conformational model, a small number of minor conformational sub-states that resemble the ligand-bound conformations are already present in solution. When the ligand binds to the minor sub-state, it causes an equilibrium shift so that the ligand-bound conformation becomes the new major sub-state.
"Our study can be placed in the broader context of the catalytic cycle," Wright said. "The results imply that for each of the intermediates in the catalytic cycle of DHFR, the lowest energy excited states are the most functionally relevant conformations. The enzyme structure responds to ligands by taking up a preferred ground-state conformation, but also samples other relevant conformations of higher energy, enabling it to rapidly advance to the next steps in catalysis. As ligands change, the energy landscape and the accessible states of the enzyme change in response. Consequently, this dynamic energy landscape efficiently funnels the enzyme along a specific kinetic path, where the number and heights of the barriers between consecutive conformations have been minimized."
Keith McKeown | EurekAlert!
One step closer to reality
20.04.2018 | Max-Planck-Institut für Entwicklungsbiologie
The dark side of cichlid fish: from cannibal to caregiver
20.04.2018 | Veterinärmedizinische Universität Wien
University of Connecticut researchers have created a biodegradable composite made of silk fibers that can be used to repair broken load-bearing bones without the complications sometimes presented by other materials.
Repairing major load-bearing bones such as those in the leg can be a long and uncomfortable process.
Study published in the journal ACS Applied Materials & Interfaces is the outcome of an international effort that included teams from Dresden and Berlin in Germany, and the US.
Scientists at the Helmholtz-Zentrum Dresden-Rossendorf (HZDR) together with colleagues from the Helmholtz-Zentrum Berlin (HZB) and the University of Virginia...
Novel highly efficient and brilliant gamma-ray source: Based on model calculations, physicists of the Max PIanck Institute for Nuclear Physics in Heidelberg propose a novel method for an efficient high-brilliance gamma-ray source. A giant collimated gamma-ray pulse is generated from the interaction of a dense ultra-relativistic electron beam with a thin solid conductor. Energetic gamma-rays are copiously produced as the electron beam splits into filaments while propagating across the conductor. The resulting gamma-ray energy and flux enable novel experiments in nuclear and fundamental physics.
The typical wavelength of light interacting with an object of the microcosm scales with the size of this object. For atoms, this ranges from visible light to...
Stable joint cartilage can be produced from adult stem cells originating from bone marrow. This is made possible by inducing specific molecular processes occurring during embryonic cartilage formation, as researchers from the University and University Hospital of Basel report in the scientific journal PNAS.
Certain mesenchymal stem/stromal cells from the bone marrow of adults are considered extremely promising for skeletal tissue regeneration. These adult stem...
In the fight against cancer, scientists are developing new drugs to hit tumor cells at so far unused weak points. Such a “sore spot” is the protein complex...
13.04.2018 | Event News
12.04.2018 | Event News
09.04.2018 | Event News
20.04.2018 | Physics and Astronomy
20.04.2018 | Interdisciplinary Research
20.04.2018 | Physics and Astronomy