Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids

Némethy, George; Pottle, Marcia S.; Scheraga, Harold A.

doi:10.1021/j100234a011

Cited by 954 publications

(427 citation statements)

References 2 publications

Supporting

Mentioning

425

Contrasting

Order By: Relevance

“…Table 3 also provides a comparison of conformational energies and residual constraint violations for sets of mEGF and hTGFa structures calculated by our laboratory over the last few years. For mEGF, these are designated as coordinate sets: DISMAN-1, five structures calculated with the DISMAN program using 333 NMR constraints (Montelione et al, 1987); DISMAN-2, 16 structures calculated with DISMAN using 730 NMR constraints (Montelione et al, 1992; PDB ascension number IEGF); ECEPP, 16 structures calculated with DISMAN using 730 NMR constraints and energy minimized with the ECEPP (Nemethy et al, 1983(Nemethy et al, , 1992 potential energy function (Montelione et al, 1992; PDB ascension number 3EGF); and five ensembles of CONGEN structures from this work, each consisting of 16 structures calculated with CONGEN using 730 NMR constraints and protocols i-v. All of these statistics were computed using the same set of mEGF NMR constraints (i.e., the complete set of 730 constraints with 15% relaxation of the distance constraints) and the CHARMM potential function of CONGEN. Whereas there is a clear correlation between improved convergence with respect to residual constraint violations, VDW energies, and Conf.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 1996

View full text Add to dashboard Cite

The 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. A general protocol for simulated annealing with restrained molecular dynamics is applied to generate NMR solution structures using CONGEN together with real experimental NMR data. A total of 730 NMR-derived constraints for mEGF and 424 NMR-derived constraints for hTGFa were used in these energy-refinement calculations. Different weighting schemes and starting conformations were studied to check and/or improve the sampling of the low-energy conformational space that is consistent with all constraints. The results demonstrate that loosened (i.e., "relaxed") sets of the EGF and hTGFa internuclear distance constraints allow molecules to overcome local minima in the search for a global minimum with respect to both distance restraints and conformational energy. The resulting energy-refined structures of mEGF and hTGFa are compared with structures determined previously and with structures of homologous proteins determined by NMR and X-ray crystallography.

show abstract

Section: Discussionmentioning

confidence: 99%

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

et al. 1996

View full text Add to dashboard Cite

show abstract

“…The construction of the C2 spatial structure includes the following steps: (a) analysis of the local structure and evaluation of the effective rotational correlation time with the program CONFORNMR ; (b) structure calculation with the distance geometry program DIANA (Guntert et al, 1991); (c) systematic search for allowed sidechain rotamers consistent with NOESY cross-peak volumes and normalized cross-peak intensities in NOESY-HMQC spectra by the program CONFORNMR; (d) DIANA calculations with additional constraints on the torsion angles of side chains obtained at stage c; (e) unrestrained energy minimization with the program CONFORNMR using the ECEPPI2 force field (Nemethy et al, 1983). An electrostatic term was excluded in all energy-minimization calculations.…”

Section: Computation Of C2 Spatial Structuresmentioning

confidence: 99%

“…We choose the DIANA-derived conformation with the lowest penalty function as a starting point, but the results were not dependent on this. The starting C2 conformation was refined by energy minimization using CONFORNMR with ECEPP/ 2 parameters (Nemethy et al, 1983). Then for each residue i, all side-chain rotamers were considered with evaluation of the energy minimization and penalty functions for the region i 2 5 of the a helix.…”

Section: Computation Of C2 Spatial Structuresmentioning

confidence: 99%

Three‐dimensional structure of (1–71)bacterioopsin solubilized in methanol/chloroform and SDS micelles determined by ¹⁵N‐¹H heteronuclear NMR spectroscopy

Pervushin

Orekhov

Popov

et al. 1994

European Journal of Biochemistry

102

View full text Add to dashboard Cite

Spatial structures of a chymotryptic fragment C2 (residues 1-71) of bacterioopsin from HaEobacterium halobium, solubilized in a mixture of methanolkhloroform (1: 1, by vol.) and 0.1 M 'HCO,N&, or in perdeuterated sodium (2H)dodecyl sulfate (SDS) micelles in the presence of perdeuterated (2,2,2-2H)trifluoroethanol, were determined by two-dimensional and three-dimensional heteronuclear "N-lH NMR techniques. The influence of (2,2,2-'H)trifluoroethanol on the conformational dynamics of C2 in micelles and the effect of the salt (organic mixture) were studied. Under the best conditions, 'H and I5N resonances of 15N-uniformly enriched protein were assigned in both milieus by homonuclear two-dimensional NOE (NOESY) and two-dimensional total-correlated (TOCSY) spectra and heteronuclear three-dimensional NOESY-multiple-quantum-correlation (HMQC) and TOCSY-HMQC spectra. 651 (organic mixture) and 520 (micelles) interproton-distance constraints, derived from volumes of cross-peaks in two-dimensional NOESY and three-dimensional NOESY-HMQC spectra, along with deuterium exchange rates of amide groups measured in both milieus and 51 HN-CaH coupling constants obtained in the case of the organic mixture, were used in the construction of C2 spatial structures. Obtained structures are similar in both milieus and have two right-handed a-helical regions stretching from Pro8 to Met32 and Phe42 to Tyr64 (organic mixture), and from Pro8 to Met32 and Ala39 to Leu62 (micelles). In micelles, the second a helix is terminated by C-cap Gly63, adopting a conformation characteristic of a left-handed helix. Residues Gly65 to Thr67 form the turn of a right-handed helix. In the isotropic medium of the organic mixture, the C-terminal region of residues 65-71 lacks an ordered structure. Torsion angles x' were unequivocally determined for 18 a-helical residues in both milieus. In the isotropic organic mixture and anisotropic micellar system, C2 remains a compact structure with a characteristic size of 3.0-3.5 nm. C2 seems to be present in at least two conformational states, packed and unpacked. Using NMR data, along with the electron cryomicroscopy model of bacteriorhodopsin [Henderson, R., Baldwin, J. M., Ceska, T. A., Zemlin, F., Beckman, E. & Downing, K. H. (1990) J. Mol. Biol. 213, 899-9291, we suggested a model for the conformation of C2 in this putative close-packed state. However, no NOE contact between a helices was found in either milieu.Bacteriorhodopsin (BR) is a transmembrane protein acting as a light-dependent proton pump in the purple membrane of Halobacterium halobium (for a review see Ovchinnikov, 1982). Electron cryomicroscopy (ECM) data suggested a seven-a-helix structural motif for BR (Henderson et al., 1990). Arseniev et al. (1987) and Abdulaeva et al. (1991) used methanolkhloroform (1 : 1, by vol.), 0.1 M LiClO, for the I9F-NMR study of BR. The individual signals in the IT-NMR spectra of "F-Trp-labeled and IgF-Phe-labeled BR species were assigned and several long-range contacts between Correspondence to A. S. Arseniev, Shemyakin ...

show abstract

“…A series of attempts by Levitt and Lifson, 12 Hagler and coworkers, 13 and Brant and Flory 14 followed to derive improved potential functions. Our efforts in this regard led to our empirical conformational energy program for peptides, ECEPP, 15 which was subsequently upgraded twice as ECEPP/2 16,17 and ECEPP/3. 18 Several other force fields, for example, AMBER 19 and CHARMM 20 have since been introduced.…”

Section: Introductionmentioning

confidence: 99%

Evolution of physics‐based methodology for exploring the conformational energy landscape of proteins

Scheraga¹,

Pillardy²,

Liwo³

et al. 2001

J Comput Chem

Self Cite

View full text Add to dashboard Cite

Abstract:The evolution of our physics-based computational methods for determining protein conformation without the introduction of secondary-structure predictions, homology modeling, threading, or fragment coupling is described. Initial use of a hard-sphere potential captured much of the structural properties of polypeptide chains, and subsequent more refined force fields, together with efficient methods of global optimization provide indications that progress is being made toward an understanding of the interresidue interactions that underlie protein folding.

show abstract

Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids

Cited by 954 publications

References 2 publications

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

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

Three‐dimensional structure of (1–71)bacterioopsin solubilized in methanol/chloroform and SDS micelles determined by ¹⁵N‐¹H heteronuclear NMR spectroscopy

Evolution of physics‐based methodology for exploring the conformational energy landscape of proteins

Contact Info

Product

Resources

About

Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids

Cited by 954 publications

References 2 publications

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

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

Three‐dimensional structure of (1–71)bacterioopsin solubilized in methanol/chloroform and SDS micelles determined by 15N‐1H heteronuclear NMR spectroscopy

Evolution of physics‐based methodology for exploring the conformational energy landscape of proteins

Contact Info

Product

Resources

About

Three‐dimensional structure of (1–71)bacterioopsin solubilized in methanol/chloroform and SDS micelles determined by ¹⁵N‐¹H heteronuclear NMR spectroscopy