Sandbox Reserved 1110

Total Structure Weight: 26554.02 Da

Atom Count: 1860

Residue Count: 236

5LSD is the recombinant mouse Nerve Growth Factor (NGF), that does not bind to any ligand. Therefore it allows conclusions on the features of its binding loops. Through 5LSD, 3 questions can be targeted: (i) how is the NGF N-terminus structured in the absence of ligands? (ii) how flexible/rigid are the loops and how does their dynamics may reflect on the overall structural plasticity of mature NGF? (iii) how much do the loops contribute to antibody recognition?^[1]

Structure

Since the X-ray crystal structure of NGF has been known since the ‘90s, the general structure of 5LSD can be described by relatable structures such as a β-sandwich fold, with four loop regions (I,II,III and V) which are the center of interactions with ligands but which are inactive in the case of 5LSD.

In this PDB representation, there are two 118 amino acids chains, and chain B, which are similar to the residues NGF ones, except for these fragments, proper to 5LSD. [1]

In the absence of partners, the NGF N-terminus has a strong tendency to fold into a helix. This challenges the current view that this region is unstructured. Experiments have shown that this N-terminus plays an important role in many processes, and its absence triggers a loss of affinity with the receptor TrkA. The loops, especially II and V, and the C-terminus are relatively more flexible than the more rigid β-sheet regions (showing hetNOE values lower than the average of 0.7). However, the loop variations are relatively small compared to the flexibility of the N- and C-termini, which indicates that the loops are plastic but not flexible. ^[2]

The neurotrophin family

The neurotrophins gather the proteins involved in many mechanisms essential for the growth, maintenance and survival of neuronal populations, As NGF is the prototype of this family, each recombinant form of it targets a special population of neurons in the central as well as in the peripheral nervous system. Each member of this family plays a role on the activation of one of the three tropomyosin-related kinase (Trk) [2] receptor (TrkA, TrkB, and TrkC) and activates the p75 neurotrophin receptor, a member of the tumor necrosis factor receptor superfamily. The members of the neurotrophin family are then as useful in prenatal organisms for the development of cortexes and in adulthood, where they control synaptic function and plasticity and sustain neuronal cell survival.

Disease and use in Biotechnologies/ Relevance

As NGF is the prototype of the neurotrophin family, a better understanding of NGF could lead to a better understanding of the whole family. A better knowledge of NGF, i.e. through 5LSD, is supportive.

It has been shown that Alzheimer’s Disease and the ratio of ProNGF/NGF (ProNGF being the pre-mutine form of NGF) are linked ^[3] , and that this ratio plays a role in neurodegeneration. The matter would be to understand how the different forms of NGF interact, then being able to understand the interactions between the ligands and the loops by modifying the 5LSD structure could help in the medical way. Moreover, it has been experimentally and clinically shown that NGF plays a role in the pain states. Understanding and developing anti-NGF could advance the research of safe and efficient analgesics. ^[4]

In fact, NGF fragments would also lead scientist to their anti-NGF as 5LSD permitted to detect the anti-NGF antagonist antibody αD11.

The NMR structure of 5LSD lead to the conclusion that NGF has long plastic but relatively rigid loops, which is of crucial importance for future drug design.^[5]