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Title: An assessment of the conformational profile of bombesin and its mammalian analogues using computational chemistry methods
Authors: Sharma, Parul 
Issue Date: 2011
Understanding the dynamics and mechanism of protein folding continues to be one of
the central problems in molecular biology. Peptide folding experiments characterize the
dynamics and molecular mechanisms of the early events of protein folding. However,
generally the highly flexible nature of peptides makes their bioactive conformation
assessment reasonably difficult as peptides fold at very fast rates experimentally,
requiring probing on the nanosecond time resolution. On the other hand, determining
the bioactive conformation of biological peptides is a requirement for the design of
peptidomimetics in computer-aided drug design.
Peptides offer a unique opportunity to bridge the gap between theoretical and
experimental understanding of protein folding. Therefore, the present work focuses on
the exploration of the conformational space of biologically active neuropeptides with the
aim of characterizing their conformational profile. Specifically, bombesin, neuromedin B
(NMB) and neuromedin C (NMC), have been chosen for the current investigations.
These peptides are widely distributed in the gastrointestinal tract, spinal cord and brain,
and are known to elicit various physiological effects, including inhibition of feeding,
smooth muscle contraction, exocrine and endocrine secretions, thermoregulation, blood
pressure and sucrose regulations and cell growth. These peptides act as a growth
factor in a wide range of tumours including carcinomas of the pancreas, stomach,
breast, prostate, and colon. This work is intended to get some insight into the
performance of different procedures used to explore the configurational space to
provide an adequate atomic description of these systems.
Different methodological studies involving utilization of molecular dynamics (MD),
multicanonical replica exchange molecular dynamics (REMD) and simulate annealing
(SA) are undertaken to explore the folding characteristics and thermodynamics of these
neuropeptides. MD and REMD calculations on bombesin peptide have revealed its dual
conformational behaviour never discovered before and is described in chapter 3. These
results explain the known structure-activity studies and open the door to the
understanding of the affinity of this peptide to two different receptors: BB1 and BB2. In
the case of NMC, REMD calculations are carried out in explicit and implicit solvents,
using the Generalized Born (GB) surface area, and are then complemented with two
additional MD simulations performed using Langevin and Berendsen thermostats. The
results obtained clearly reveal that REMD, performed under explicit solvent conditions,
is more efficient and samples preferentially folded conformations with a higher content
of  and γ turns. Moreover, these results show good agreement with the experimental
results supporting the role of two -turns for its biological action, as reported in the
literature. Finally, the results obtained from MD, REMD and SA calculations on NMB
reveal that the peptide has a tendency to adopt both turns and helices suggesting its
two different receptor recognizing and binding conformations during its biological action.
Hence, the present work provides comprehensive information about the conformational
preferences of neuropeptides which could lead to a better understanding of their native
conformations for future investigations and point the way towards developing their new
Submitted in fulfilment of the requirements of the Degree of Doctor of Technology: Chemistry, Durban University of Technology, Durban, South Africa, 2011.
Appears in Collections:Theses and dissertations (Applied Sciences)

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