Protein Flexibility and Adaptability Seen in 25 Crystal Forms of T4 Lysozyme

Zhang, Xuejun; Wozniak, Joan A.; Matthews, Brian W.

doi:10.1006/jmbi.1995.0396

Cited by 201 publications

(246 citation statements)

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“…Phe 67 has been identified as one of the sidechains that changes conformation in association with interdomain, hinge-bending, motion (Zhang et al, 1995). In the present context, however, the Phe 67 + Ala substitution did not cause a significant hingebending displacement.…”

Section: Phenylalanine 67 To Alaninecontrasting

confidence: 55%

The response of T4 lysozyme to large‐to‐small substitutions within the core and its relation to the hydrophobic effect

et al. 1998

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To further examine the structural and thermodynamic basis of hydrophobic stabilization in proteins, all of the bulky non-polar residues that are buried or largely buried within the core of T4 lysozyme were substituted with alanine. In 25 cases, including eight reported previously, it was possible to determine the crystal structures of the variants. The structures of four variants with double substitutions were also determined. In the majority of cases the "large-to-small" substitutions lead to internal cavities. In other cases declivities or channels open to the surface were formed. In some cases the structural changes were minimal (mainchain shifts 5 0.3 A); in other cases mainchain atoms moved up to 2 A.In the case of Ile 29 -+ Ala the structure col!apsed to such a degree that the volume of the putative cavity was zero. Crystallographic analysis suggests that the occupancy of the engineered cavities by solvent is usually low. The mutants Val 149 4 Ala (V149A) and Met 6 -+ Ala (M6A), however, are exceptions and have, respectively, one and two well-ordered water molecules within the. cavity. The Val 149 -+ Ala substitution allows the solvent molecule to hydrogen bond to polar atoms that are occluded in the wild-type molecule. Similarly, the replacement of Met 6 with alanine allows the two solvent molecules to hydrogen bond to each other and to polar atoms on the protein. Except for Val 149 -+ Ala the loss of stability of all the cavity mutants can be rationalized as a combination of two terms. The first is a constant for a given class of substitution (e.g., -2.1 kcal/mol for all Leu + Ala substitutions) and can be considered as the difference between the free energy of transfer of leucine and alanine from solvent to the core of the protein. The second term can be considered as the energy cost of forming the cavity and is consistent with a numerical value of 22 cal mol" k 3 . Physically, this term is due to the loss of van der Waal's interactions between the bulky sidechain that is removed and the atoms that form the wall of the cavity. The overall results are consistent with the prior rationalization of Leu + Ala mutants in T4 lysozyme by Eriksson et al. (Eriksson et al., 1992, Science 255:178-183).

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Section: Phenylalanine 67 To Alaninecontrasting

confidence: 55%

The response of T4 lysozyme to large‐to‐small substitutions within the core and its relation to the hydrophobic effect

et al. 1998

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“…The accumulation of these minor local effects over large segments of the chain can result in signi®cant displacement of atoms that belong to residues distant in sequence. In fact, the extent of local deviation of structure for most variants is generally no greater than that seen in comparing structures of the same protein solved in different space groups (Zhang et al, 1995).…”

Section: Constructing a Backbone Potentialmentioning

confidence: 88%

Side-chain and backbone flexibility in protein core design 1 1Edited by A. R. Fersht

Desjarlais

Handel

1999

Journal of Molecular Biology

135

105

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We have developed a computational approach for the design and prediction of hydrophobic cores that includes explicit backbone¯exibility. The program consists of a two-stage combination of a genetic algorithm and monte carlo sampling using a torsional model of the protein. Backbone structures are evaluated either by a canonical force-®eld or a constraining potential that emphasizes the preservation of local geometry. The utility of the method for protein design and engineering is explored by designing three novel hydrophobic core variants of the protein 434 cro. We use the new method to evaluate these and previously designed 434 cro variants, as well as a series of phage T4 lysozyme variants. In order to properly evaluate the in¯uence of backbone¯exibility, we have also analyzed the effects of varying amounts of side-chain¯exibility on the performance of ®xed backbone methods. Comparison of results using a ®xed versus¯exible backbone reveals that, surprisingly, the two methods are almost equivalent in their abilities to predict relative experimental stabilities, but only when full side-chain¯exibility is allowed. The prediction of core side-chain structure can vary dramatically between methods. In some, but not all, cases the¯exible backbone method is a better predictor of structure. The development of a¯exible backbone approach to core design is particularly important for attempts at de novo protein design, where there is no prior knowledge of a precise backbone structure.

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“…9 The outlier marked number 1 in Figure 7 is of particular interest. This structure, 179L, is one of many T4 lysozyme mutants published by Matthews et al 10 All of the many hundreds of similar T4 lysozyme structures from Matthews et al have packing scores that are at least average given their resolution, and most are well above average. Comparison of 179L with 177L, which are the same mutation and the same crystal space group, revealed that the placement of secondary structure elements in 179L is stretched along two axes.…”

Section: Packing Analysis Of Structures In the Pdbmentioning

confidence: 99%

RosettaHoles: Rapid assessment of protein core packing for structure prediction, refinement, design, and validation

2008

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We present a novel method called RosettaHoles for visual and quantitative assessment of underpacking in the protein core. RosettaHoles generates a set of spherical cavity balls that fill the empty volume between atoms in the protein interior. For visualization, the cavity balls are aggregated into contiguous overlapping clusters and small cavities are discarded, leaving an uncluttered representation of the unfilled regions of space in a structure. For quantitative analysis, the cavity ball data are used to estimate the probability of observing a given cavity in a high-resolution crystal structure. RosettaHoles provides excellent discrimination between real and computationally generated structures, is predictive of incorrect regions in models, identifies problematic structures in the Protein Data Bank, and promises to be a useful validation tool for newly solved experimental structures.

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Protein Flexibility and Adaptability Seen in 25 Crystal Forms of T4 Lysozyme

Cited by 201 publications

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The response of T4 lysozyme to large‐to‐small substitutions within the core and its relation to the hydrophobic effect

The response of T4 lysozyme to large‐to‐small substitutions within the core and its relation to the hydrophobic effect

Side-chain and backbone flexibility in protein core design 1 1Edited by A. R. Fersht

RosettaHoles: Rapid assessment of protein core packing for structure prediction, refinement, design, and validation

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