Principles of Protein Structure

Schulz, Georg E.; Schirmer, R. Heiner

doi:10.1007/978-1-4612-6137-7

Cited by 1,071 publications

(434 citation statements)

References 471 publications

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“…Therefore, the chirality of the map was derived from the &barrel because only strands proceeding in a right-handed manner with respect to the barrel axis ( Fig. 2A) allow for the usual twist of P-sheets [35]. The chain direction remains unsafe.…”

Section: Resultsmentioning

confidence: 99%

The three‐dimensional structure of porin from Rhodobacter capsulatus at 3 Å resolution

Weiss

Wacker

Weckesser³

et al. 1990

FEBS Letters

208

117

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The crystal structure of porin from Rhodobacter capsulatus strain 37b4 has been solved at 3.0 A (1 A = 0. I nm) resolution by multiple isomorphous replacement and solvent-flattening. The three pores of the trimer are well defined in the electron density map. Each pore consists of a Hi-stranded B-barrel which traverses the membrane as a tube. Near its center the tube is narrowed by chain segments protruding from the inner wall of the barrel that form an eye-let with an irregular cross-section of about 6 A by 10 A. The eye-let has an axial length of about 10 A; it defines the exclusion limit for diffusing particles.

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Section: Resultsmentioning

confidence: 99%

The three‐dimensional structure of porin from Rhodobacter capsulatus at 3 Å resolution

Weiss

Wacker

Weckesser³

et al. 1990

FEBS Letters

208

117

View full text Add to dashboard Cite

show abstract

“…The free energy change associated with the folding of a protein into the native state can be expressed as (Schulz & Schirmer, 1979): where AHchainr ASchainr and AGsolvent are the changes in intrachain binding energy, chain entropy, and solvation free energy upon protein folding. The change in chain entropy on folding is unfavorable, so any conformational restriction of the polypeptide chain toward the folded structure should reduce the entropic cost of folding and result in a more stable three-dimensional fold.…”

Section: Discussionmentioning

confidence: 99%

Structural engineering of the HIV‐1 protease molecule with a β‐turn mimic of fixed geometry

1993

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An important goal in the de novo design of enzymes is the control of molecular geometry. To this end, an analog of the protease from human immunodeficiency virus 1 (HIV-1 protease) was prepared by total chemical synthesis, containing a constrained, nonpeptidic type 11' 0-turn mimic of predetermined three-dimensional structure.The mimic &turn replaced residues GlyI6,l7 in each subunit of the homodimeric molecule. These residues constitute the central amino acids of two symmetry-related type I' 0-turns in the native, unliganded enzyme. The 0-turn mimic-containing enzyme analog was fully active, possessed the same substrate specificity as the GlyI67l7-containing enzyme, and showed enhanced resistance to thermal inactivation. These results indicate that the precise geometry of the @turn at residues 15-18 in each subunit is not critical for activity, and that replacement of the native sequence with a rigid 0-turn mimic can lead to enhanced protein stability. Finally, the successful incorporation of a fixed element of secondary structure illustrates the potential of a "molecular kit set" approach to protein design and synthesis.

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“…Another possibility for measuring tertiary structure is the fraction of pairs of amino acids which are correctly situated to some accuracy. This measure is related to the distance plots used by crystallographers [64,65]. The similarity measure may also be thought of as a measure of the distance between the two structures, so that similar structures are considered to be close to one another.…”

Section: Quantitative Aspects Of the Statistics And Thermodynamicmentioning

confidence: 99%

Funnels, pathways, and the energy landscape of protein folding: A synthesis

et al. 1995

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The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation, that is, to the energy landscape. The statistical energy landscape approach explains when and why unique behaviors, such as specific folding pathways, occur in some proteins and more generally explains the distinction between folding processes common to all sequences and those peculiar to individual sequences. This approach also gives new, quantitative insights into the interpretation of experiments and simulations of protein folding thermodynamics and kinetics. Specifically, the picture provides simple explanations for folding as a two‐state first‐order phase transition, for the origin of metastable collapsed unfolded states and for the curved Arrhenius plots observed in both laboratory experiments and discrete lattice simulations. The relation of these quantitative ideas to folding pathways, to uniexponential vs. multiexponential behavior in protein folding experiments and to the effect of mutations on folding is also discussed. The success of energy landscape ideas in protein structure prediction is also described. The use of the energy landscape approach for analyzing data is illustrated with a quantitative analysis of some recent simulations, and a qualitative analysis of experiments on the folding of three proteins. The work unifies several previously proposed ideas concerning the mechanism protein folding and delimits the regions of validity of these ideas under different thermodynamic conditions. © 1995 Wiley‐Liss, Inc.

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Principles of Protein Structure

Cited by 1,071 publications

References 471 publications

The three‐dimensional structure of porin from Rhodobacter capsulatus at 3 Å resolution

The three‐dimensional structure of porin from Rhodobacter capsulatus at 3 Å resolution

Structural engineering of the HIV‐1 protease molecule with a β‐turn mimic of fixed geometry

Funnels, pathways, and the energy landscape of protein folding: A synthesis

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