Article

The role of entropy and polarity in intermolecular contacts in protein crystals.

Department of Molecular Physiology and Biological Physics and the PSI2 Integrated Center for Structure-Function Innovation, University of Virginia, Charlottesville, VA 22908, USA.
Acta Crystallographica Section D Biological Crystallography (Impact Factor: 7.23). 06/2009; 65(Pt 5):500-9. DOI: 10.1107/S0907444909009500
Source: PubMed

ABSTRACT The integrity and X-ray diffraction quality of protein crystals depend on the three-dimensional order of relatively weak but reproducible intermolecular contacts. Despite their importance, relatively little attention has been paid to the chemical and physical nature of these contacts, which are often regarded as stochastic and thus not different from randomly selected protein surface patches. Here, logistic regression was used to analyze crystal contacts in a database of 821 unambiguously monomeric proteins with structures determined to 2.5 A resolution or better. It is shown that the propensity of a surface residue for incorporation into a crystal contact is not a linear function of its solvent-accessible surface area and that amino acids with low exposed surfaces, which are typically small and hydrophobic, have been underestimated with respect to their contact-forming potential by earlier area-based calculations. For any given solvent-exposed surface, small and hydrophobic residues are more likely to be involved in crystal contacts than large and charged amino acids. Side-chain entropy is the single physicochemical property that is most negatively correlated with the involvement of amino acids in crystal contacts. It is also shown that crystal contacts with larger buried surfaces containing eight or more amino acids have cores that are depleted of polar amino acids.

0 Followers
 · 
100 Views
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Protein crystallization is dependent upon, and sensitive to, the intermolecular contacts that assist in ordering proteins into a three dimensional lattice. Here we used protein engineering and mutagenesis to affect the crystallization of single chain antibody fragments (scFvs) that recognize the EE epitope (EYMPME) with high affinity. These hypercrystallizable scFvs are under development to assist difficult proteins, such as membrane proteins, in forming crystals, by acting as crystallization chaperones. Guided by analyses of intermolecular crystal lattice contacts, two second-generation anti-EE scFvs were produced, which bind to proteins with installed EE tags. Surprisingly, although non-complementarity determining region (CDR) lattice residues from the parent scFv framework remained unchanged through the processes of protein engineering and rational design, crystal lattices of the derivative scFvs differ. Comparison of energy calculations and the experimentally-determined lattice interactions for this basis set provides insight into the complexity of the forces driving crystal lattice choice and demonstrates the availability of multiple well-ordered surface features in our scFvs capable of forming versatile crystal contacts. © Proteins 2014;. © 2014 Wiley Periodicals, Inc.
    Proteins Structure Function and Bioinformatics 09/2014; 82(9). DOI:10.1002/prot.24542 · 2.92 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Proteins are dynamic systems and interact with their environment. The analysis of crystal contacts in the most accurately determined protein structures (d < 1.5 Å) reveals that in contrast to current views, static disorder and high side-chain entropy are common in the crystal contact area. These observations challenge the validity of the theory that presumes that the occurrence of well ordered patches of side chains at the surface is an essential prerequisite for a successful crystallization event. The present paper provides evidence in support of the approach for understanding protein crystallization as a process dependent on multiple factors, each with its relative contribution, rather than a phenomenon driven by a few dominant physicochemical characteristics. The role of the molecular shape as a factor in the crystallization of proteins by surface mutagenesis is discussed.
    Acta Crystallographica Section F Structural Biology and Crystallization Communications 02/2015; 71(Pt 2):157-62. DOI:10.1107/S2053230X14027861 · 0.57 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: To enhance the success rate of protein crystallization, many studies were conducted to determine the relationship between amino acid properties and the success rate of protein crystallization. Although those were successful, new efforts should be made to search for the new factors, which affect protein crystallization. In this study, two dynamic amino acid properties were used to correlate with the success rate of crystallization of proteins from Bacteroides vulgatus, because the amino acid properties used in previous studies were steady. As previously done, logistic regression and neural network were used to model that relationship, and the results were compared against those obtained from each of 532 amino acid properties, which severed as benchmark. The results demonstrated that dynamic amino acid properties should be taken into consideration of protein crystallization. (© 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
    Crystal Research and Technology 05/2012; 47(5). DOI:10.1002/crat.201200007 · 1.16 Impact Factor

Full-text (2 Sources)

Download
32 Downloads
Available from
May 28, 2014