Phaser is a program for phasing macromolecular crystal structures by both molecular replacement and experimental phasing methods. The novel phasing algorithms implemented in Phaser have been developed using maximum likelihood and multivariate statistics. For molecular replacement, the new algorithms have proved to be significantly better than traditional methods in discriminating correct solutions from noise, and for single-wavelength anomalous dispersion experimental phasing, the new algorithms, which account for correlations between F+ and F−, give better phases (lower mean phase error with respect to the phases given by the refined structure) than those that use mean F and anomalous differences ΔF. One of the design concepts of Phaser was that it be capable of a high degree of automation. To this end, Phaser (written in C++) can be called directly from Python, although it can also be called using traditional CCP4 keyword-style input. Phaser is a platform for future development of improved phasing methods and their release, including source code, to the crystallographic community.

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Phaser crystallographic software

Reviewing the thermodynamic parameters characterizing self-association and ligand binding of proteins at 25 OC, we find AGO, AHo, AS\", and ACpo are often all of negative sign. It is thus not possible to account for the stability of association complexes of proteins on the basis of hydrophobic interactions alone. We present a conceptual model of protein association consisting of two steps: the mutual penetration of hydration layers causing disordering of the solvent followed by further short-range interactions. The net AGO for the complete association process is primarily determined by the positive entropy change accompanying the first step and the negative enthalpy change of the second step. On the basis of the thermochemical behavior of small molecule interactions, we conclude that the strengthening of hydrogen bonds in the I n the past decade, a complete thermodynamic description of the self-association of many proteins and their interactions From the Laboratory of Molecular Biology (P.D.R.) and Laboratory of Nutrition and Endocrinology (S.S.), National Institute of Arthritis, Metabolism and Digestive Diseases, National Institutes of Health, Bethesda, Maryland 20205. Received September 23, 1980. low dielectric macromolecular interior and van der Waals' interactions introduced as a consequence of the hydrophobic effect are the most important factors contributing to the observed negative values of AHo and ASo and hence to the stability of protein association complexes. The X-ray crystallographic structures of these complexes are consonant with this analysis. The tendency for protein association reactions to become entropy dominated and/or entropy-enthalpy assisted at low temperatures and enthalpy dominated at high temperatures (a consequence of the typically negative values of AC,\") arises from the diminution of the hydrophobic effect with increasing temperature which is a general property of the solvent, water. with small molecular substrates has become available. Concomitantly, X-ray crystallography has provided a detailed picture of some of these associations, and this has stimulated a number of theoretical studies (Levitt & Warshel, 1975; Gelin & Karplus, 1975; Chothia & Janin, 1975), based upon energetic considerations, to account for these structures. The This article not subject to U S . Copyright. Published 1981 by the American Chemical Society T H E R M O D Y N A M I C S O F P R O T E I N A S S O C I A T I O N V O L . 2 0 , N O . 1 1 , 1 9 8 1 3097 Table I: Thermodynamics of Protein Association' association process A G \" ~ AiY A s o , A c p o (kcal mol-') (kcal mol-l) (cal K-I mol-') (cal K-I mol-I) refb trypsin (bovine) + inhibitor (soybean) -14.6 8.6 78 -440 c, d deoxyhemoglobin S gelation -3.4 2.0 18 -200 e, f lysozyme self-association (indefinite) -3.9 -6 .4 -8.3 g glucagon trimerization -12.1 -3 1 -64 -430 h, i hemoglobin t haptoglobin -11.5 -3 3 -7 3 -940 i a-chymotrypsin dimerization -7.1 -35 -9 5 k, I S-peptide + S-protein (ribonuclease) -13 -40 -90 -1100 m, n All thermodynamic parameters expressed per mole of complex formed except the indefinite association cases of hemoglobin S and lysozyme for which the mole refers to the monomeric protein reacted. Unitary entropy and free energy are given for processes of defined stoichiometry. Standard states are hypothetical 1 M protein, pH at which the reaction was measured. All pHs were close to 7 except for trypsin, pH 5, haptoglobin, pH 5.5, and glucagon, pH 10.5. All data for 25 \"C except glucagon, T = 30 \"C. ence is to calorimetric work and the second is to X-ray crystallographic structure determination. al. (1974). e Rosset al. (1977). Wishner e t al. (1975). g Banerjee et al. (1975). Johnson et al. (1979). * Sasaki et al. (1975). For each entry, the first referSweet et Baugh & Trowbridge (1972). Lavialle et al. (1974). Shiao & Sturtevant (1969). lVandlen &Tulinsky (1973). Hearn et al. (1971). Wyckoff e t al. (1970). methodology and problems involved in such calculations have been critically reviewed by NBmethy & Scheraga (1977). In this paper we review the thermodynamics of protein association processes for the examples best characterized in terms of their chemistry and structure. From this survey we find that the thermodynamic parameters AGO, Ai?, AS\", and ACpo are predominantly of negative sign. This result poses severe difficulties for interpretations of protein association based upon the entropically driven hydrophobic effect. The aim of this paper is to attempt to account for the signs and magnitudes of these thermodynamic parameters for protein association reactions in terms of known molecular forces and the thermochemistry of small molecule interactions.

Thermodynamics of protein association reactions: forces contributing to stability

The three-dimensional structure of human serum albumin has been determined crystallographically to a resolution of 2.8 A. It comprises three homologous domains that assemble to form a heart-shaped molecule. Each domain is a product of two subdomains that possess common structural motifs. The principal regions of ligand binding to human serum albumin are located in hydrophobic cavities in subdomains IIA and IIIA, which exhibit similar chemistry. The structure explains numerous physical phenomena and should provide insight into future pharmacokinetic and genetically engineered therapeutic applications of serum albumin.

Atomic structure and chemistry of human serum albumin.

Prediction of the secondary structure of proteins from their amino acid sequence.

Publisher Summary The chapter discusses the stability of proteins and presents the results obtained on small compact globular proteins, which represent one single cooperative system. Protein is a cooperative system and behaves in an all-or-none fashion. Sharp changes in the properties of a protein do not mean anything in themselves because sequential multistep transitions exhibit the same sharp sigmoidal changes in the observed parameters. The problem of stability of native proteins is closely connected with the problem of protein denaturation, as stability can be judged only by breaking the native structure—that is, denaturing protein by various treatments. The pH of the solution is one of the most important factors determining the state of a protein. Potentiometric titration of protein revealed that smooth changes are connected with the titration of groups with a pK not very different from that of free amino acids, while the gross conformational changes associated with pH denaturation are accompanied by the unmasking of buried groups. The chapter also discusses the temperature-induced changes in protein, denaturational and predenaturational changes in protein, thermodynamics of protein unfolding, and thermodynamic properties of protein.

Stability of Proteins Small Globular Proteins

Publisher Summary The structural similarity of myoglobin to both α and β chains of hemoglobin suggests the hypothesis that proteins of similar function have similar tertiary structures. Anticipation of structural similarities among dehydrogenases has been implicit in comparisons of amino acid sequences aligned on the basis of essential cysteine residues and on other physical properties. One of the motivations for the study of the lactate dehydrogenase (LDH) structure was the possibility that a structure-function correlation might be revealed in a comparison with soluble malate dehydrogenase (s-MDH) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). This first recognition of the similarity between LADH and LDH was remarkable in the sense that cognizance was taken of the greater similarity in one-half of the subunit and in the differing subunit associations. It is improbable that this would have been found without some expectation of a structure-function relationship among dehydrogenases. This chapter discusses the comparison and contrasts the structural results. Sophisticated enzymes such as dehydrogenases are mostly constructed out of a variety of structural domains, which may represent gene fusion of proteins of simpler functions. The chapter first compares the subunit structures of known dehydrogenases and then reviews the alignments arrived at by using only amino acid sequence information. This is followed by a comparison of amino acid sequences in light of tertiary structure, which in case of homology gives pointers to measure evolutionary distance as well as to residues important in the conservation of structure and function. The chapter explores functional properties in the development of the oligomeric structures of dehydrogenases and a larger group of enzymes, which are functionally or structurally related possibly because of common nucleotide binding properties.

2 Evolutionary and Structural Relationships among Dehydrogenases

The term molecular replacement encompasses a variety of techniques designed to utilize the occurrence of a molecule, molecular subunit, or molecular fragment in more than one crystallographic environment for the purpose of phase refinement. The limited size of nature’s building blocks and the necessity of their aggregation into molecules with closed point symmetries (Crick and Watson, 1956; Monod et al., 1965) provide the basis of the subject and its application to macromolecules. For example, a particular compound may be induced to crystallize in different forms, or a given molecule might be composed of several identical subunits.

Molecular Replacement Method

Letter: Recognition of structural domains in globular proteins.

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2 Evolutionary and Structural Relationships among Dehydrogenases

Molecular Replacement Method

Letter: Recognition of structural domains in globular proteins.