New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding) terms of the force field and among the solvent−solvent, solvent−solute, and solute−solute interactions. Optimization of the internal parameters used experimental gas-phase geometries, vibrational spectra, and torsional energy surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized with respect to data for N-methylacetamide and the alanine dipeptide. The interaction parameters, particularly the atomic charges, were determined by fitting ab initio interaction energies and geometries of complexes between water and model compounds that represented the backbone and the various side chains. In addition, dipole moments, experimental heats and free energies of vaporization, solvation and sublimation, molecular volume...

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All-atom empirical potential for molecular modeling and dynamics studies of proteins.

Inference of macromolecular assemblies from crystalline state.

http://experimentationlab.berkeley.edu/sites/default/files/AFMImages/butt_AFM.pdf

Force measurements with the atomic force microscope: Technique, interpretation and applications

Chemical shifts of backbone atoms in proteins are exquisitely sensitive to local conformation, and homologous proteins show quite similar patterns of secondary chemical shifts. The inverse of this relation is used to search a database for triplets of adjacent residues with secondary chemical shifts and sequence similarity which provide the best match to the query triplet of interest. The database contains 13Cα, 13Cβ, 13C′, 1Hα and 15N chemical shifts for 20 proteins for which a high resolution X-ray structure is available. The computer program TALOS was developed to search this database for strings of residues with chemical shift and residue type homology. The relative importance of the weighting factors attached to the secondary chemical shifts of the five types of resonances relative to that of sequence similarity was optimized empirically. TALOS yields the 10 triplets which have the closest similarity in secondary chemical shift and amino acid sequence to those of the query sequence. If the central residues in these 10 triplets exhibit similar φ and Ψ backbone angles, their averages can reliably be used as angular restraints for the protein whose structure is being studied. Tests carried out for proteins of known structure indicate that the root-mean-square difference (rmsd) between the output of TALOS and the X-ray derived backbone angles is about 15°. Approximately 3% of the predictions made by TALOS are found to be in error.

/pdf/protein-backbone-angle-restraints-from-searching-a-database-3gnb1o75zf.pdf

Protein backbone angle restraints from searching a database for chemical shift and sequence homology

All eukaryotic cells have an extensive membranous labyrinth network of branching tubules and flattened sacs called the endoplasmic reticulum (ER). Approximately one-third of all cellular proteins are translocated into the lumen of the ER where post-translational modification, folding, and oligomerization occurs. The ER provides a unique oxidizing compartment for the folding of membrane and secretory proteins that are destined to the cell surface, as well as for proteins destined to other intracellular organelles, such as lysosomes and the Golgi compartment. Numerous cellular proteins reside within the ER through a mechanism that requires their continuous vesicle-mediated retrieval from post-ER compartments within the early secretory pathway. These ERresident proteins are chaperones and catalysts of protein folding that form a matrix on which newly synthesized proteins attain their final conformation. The ER is also the site of synthesis of cellular lipids and sterols. In addition, the ER is the major signal-transducing organelle within the cell that continuously responds to environmental cues to release calcium. The ER is exquisitely sensitive to alterations in homeostasis, where, upon a variety of different stimuli, signals are transduced from the ER to the cytoplasm and the nucleus to eventually result in adaptation for survival or induction of apoptosis. The immediate response occurs at the translational apparatus, whereas changes in gene expression promote long-term adaptation or apoptotic cell death. Recent evidence supports findings that these signaling pathways influence pathogenesis associated with viral infection and genetic disease. The purpose of this review is to summarize what is presently known about the diversity of molecular signaling mechanisms that coordinate the complex ER stress response at the translational and transcriptional level in yeast and in higher eukaryotic cells.

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Stress signaling from the lumen of the endoplasmic reticulum: coordination of gene transcriptional and translational controls

Calcium binding to calmodulin and its globular domains

We have determined the solution structures of the apo and (Ca2+)2 forms of the carboxy-terminal domain of calmodulin using multidimensional heteronuclear nuclear magnetic resonance spectroscopy. The results show that both forms adopt well-defined structures with essentially equal secondary structure. A comparison of the structures of the two forms shows that Ca2+ binding causes major rearrangements of the secondary structure elements with changes in inter-residue distances of up to 15 A and exposure of the hydrophobic interior of the four-helix bundle. Comparisons with previously determined high-resolution X-ray structures and models of calmodulin indicate that this domain is structurally autonomous.

Calcium-induced structural changes and domain autonomy in calmodulin.

Despite the marked differences in their chemical structure, members of a heterogeneous group of pharmacological agents are thought specifically to block Ca2+ influx through calcium channels1 and thus mediate negative inotropic cardiac effects and vasodilatation. Electrophysiological studies of the myocardium have shown that the slow inward Ca2+ current is blocked1, but the cellular mechanism of these agents in vascular smooth muscle is largely unknown. Felodipine [4-(2,3-dichlorophenyl)-1,4-dihydropyridine-2,6-dimethyl 3,5-dicarboxylic 3-ethylester and 5-methylester)] is a new antihypertensive agent which seems specifically to dilate precapillary resistance vessels in vivo. It is a structural analogue of nifedipine1 and SKF 242602, both of which have been classified as ‘calcium antagonists’, implying that their vascular as well as myocardial actions are due to a blockade of Ca2+ influx. However, the findings reported here point rather to an interaction between felodipine and calcium-binding proteins such as calmodulin.

Interaction of the antihypertensive drug felodipine with calmodulin

A combination of low-angle X-ray diffraction and NMR diffusion techniques may be used for the elucidation of the internal structure of cubic lyotropic liquid crystalline lipid systems. The advantage of the NMR method for this kind of struc- ture determinations lies in the facts that restricted diffusion can be observed and that the lateral diffusion in lamellar systems can be measured directly. The value of the apparent diffusion coefficient depends strongly on the overall structural geometry. Previous X-ray diffraction findings for the cubic phase occurring in aqueous monoglyceride systems have been reevaluated and supplemented and arguments are presented for an internal structure built up of small lamellar bilayer units. The lamellar units are ideally hexagon-shaped disks connected in such a manner that they form a close-packed system of tetrakaidecahedra in which the quadrilateral faces are missing. Thus is obtained an open structure which is optically isotropic and is continuous in three axial directions both with respect to the nonpolar lipid and the polar aqueous regions. This structure concept of two con- tinuous regions where the lipid regions consist of a system of lamellar units obtains support from values for the translational diffusion coefficients of the lipid (and water) measured with the NMR pulsed magnetic field gradient method. This type of cubic phases, which occurs in many monoglyceride systems and which can be mixed with other lipids such as lecithin or choles- terol and also with proteins, may be used as model membrane systems.

The Cubic Phase of Monoglyceride-Water Systems. Arguments for a Structure Based upon Lamellar Bilayer Units

Water oxygen-17 magnetic relaxation is shown to be a powerful technique for studying protein hydration. Longitudinal and transverse 170 relaxation rates were measured at variable frequency (4-35 MHz), temperature, pH, and protein concentration in aqueous solutions of seven proteins. The data were analyzed in terms of a fast exchange two-state model with local anisotropy. A water 170 quadrupole coupling constant of 6.67 MHz and an order parameter of 0.06 (from I7O splittings in lyotropic liquid crystals) results in approximately two layers of hydration water having a reorientational rate less than 1 order of magnitude slower than that of bulk water. This rapid local motion has a small anisotropic component, which is averaged out by protein reorientation with a correlation time of the order of 10 ns. Due to electrostatic protein-protein interaction the protein reorientation is considerably slower than predicted by the Debye-Stokes-Einstein equation. Charged residues, particularly carboxylate, are more extensively hydrated than other residues, accounting for the variation in the extent of hydration between different proteins.

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Sture Forsén

Papers

Calcium binding to calmodulin and its globular domains

Calcium-induced structural changes and domain autonomy in calmodulin.

Interaction of the antihypertensive drug felodipine with calmodulin

The Cubic Phase of Monoglyceride-Water Systems. Arguments for a Structure Based upon Lamellar Bilayer Units

Protein hydration from water oxygen-17 magnetic relaxation