Simulated annealing with restrained molecular dynamics using a flexible restraint potential: Theory and evaluation with simulated NMR constraints

Abstract

A new functional representation of NMR-derived distance constraints, the flexible restraint potential, has been implemented in the program CONGEN (Bruccoleri RE, Karplus M, 1987, Biopolymers 26:137-168) for molecular structure generation. In addition, flat-bottomed restraint potentials for representing dihedral angle and vicinal scalar coupling constraints have been introduced into CONGEN. An effective simulated annealing (SA) protocol that combines both weight annealing and temperature annealing is described. Calculations have been performed using ideal simulated NMR constraints, in order to evaluate the use of restrained molecular dynamics (MD) with these target functions as implemented in CONGEN. In this benchmark study, internuclear distance, dihedral angle, and vicinal coupling constant constraints were calculated from the energy-minimized X-ray crystal structure of the 46-amino acid polypeptide crambin (ICRN). Three-dimensional structures of crambin that satisfy these simulated NMR constraints were generated using restrained MD and SA. Polypeptide structures with extended backbone and side-chain conformations were used as starting conformations. Dynamical annealing calculations using extended starting conformations and assignments of initial velocities taken randomly from a Maxwellian distribution were found to adequately sample the conformational space consistent with the constraints. These calculations also show that loosened internuclear constraints can allow molecules to overcome local minima in the search for a global minimum with respect to both the NMR-derived constraints and conformational energy. This protocol and the modified version of the CONGEN program described here are shown to be reliable and robust, and are applicable generally for protein structure determination by dynamical simulated annealing using NMR data.Keywords: coupling constants; energy minimization; solution NMR structure determination It is now well established that three-dimensional structures of small proteins and oligonucleotides can be determined using a combined approach of multidimensional NMR spectroscopy and computational techniques (Wiithrich, 1986; Clore &Gronen-born, 1991. Recent advances in NMR methodology make it possible to extract a large amount of structural information, Reprint requests to: Gaetano T.

Simulated annealing with restrained molecular dynamics using CONGEN: Energy refinement of the NMR solution structures of epidermal and type‐α transforming growth factors

“…Using both simulated (Bassolino-Klimas et al, 1996) and real (in this work) distance constraints, we see improved energies in structures computed with relaxed constraints. Comparing the total conformational energy and van der Waals component of the total conformational energy in Table 3, it is clear that a major part of energetic improvement is due to improved electrostatics in the "relaxed" structures.…”

“…We first studied the effects of "relaxing" experimental upper-bound NMR distance constraints. in CONGEN calculations carried out with simulated constraints described in the companion paper, we observed improved convergence and lower energy structures when each of the exact distance constraints generated from the X-ray crystal structure of crambin was loosened by 5-10% (Bassolino-Klimas et al, 1996). In addition, our calibration of the relationship between NOE intensities and internuclear distances (see the Materials and methods) assumes uniform isotropic tumbling with an identical autocorrelation function for every proton-proton pair and error-free intensity measurements, resulting in both over-and underestimates of some internuclear distances.…”

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AbstractThe new functionality of the program CONGEN (Bruccoleri RE, Karplus M, 1987, Biopolymers 26:137-168;Bassolino-Klimas D et al, 1996, Protein Sci5:593-603) has been applied for energy refinement of two previously determined solution NMR structures, murine epidermal growth factor (mEGF) and human type-a transforming growth factor (hTGFa). A summary of considerations used in converting experimental NMR data into distance constraints for CONGEN is presented.

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Homology modeling of an RNP domain from a human RNA-binding protein: Homology-constrained energy optimization provides a criterion for distinguishing potential sequence alignments

“…We employed our recently published 21 automated method of homology modeling using simulated annealing and restrained molecular dynamics calculations with the molecular mechanics program CONGEN 22,23 and the CHARMM force field. 28 This procedure generates a family of three-dimensional protein structures for a homologous protein based on the atomic coordinates of a known protein structure.…”

“…20,21 We have recently described an automated and objective approach for homology modeling 21 using simulated annealing with restrained molecular dynamics methods available in the molecular mechanics program CONGEN. 22,23 In these ''homology constrained'' CONGEN calculations, the relative positions of atoms of the unknown protein structure that are ''homologous'' to atoms of the known template structure are constrained by ''homology distance constraints,'' whereas the conformations of the ''non-homologous regions'' of the unknown protein are defined by the potential energy function. A full energy function (without explicit solvent) is employed to ensure that the calculated structures have good conformational energies and are physically reasonable.…”