Principles Of Protein Structure Research Articles

Using an FPLC to promote active learning of the principles of protein structure and purification.

The concepts of protein purification are often taught in undergraduate biology and biochemistry lectures and reinforced during laboratory exercises; however, very few reported activities allow students to directly gain experience using modern protein purification instruments, such as Fast Protein Liquid Chromatography (FPLC). This laboratory exercise uses size exclusion chromatography (SEC) and ion exchange (IEX) chromatography to separate a mixture of four different proteins. Students use an SEC chromatogram and corresponding SDS-PAGE gel to understand how protein conformations change under different conditions (i.e. native and non-native). Students explore strategies to separate co-eluting proteins by IEX chromatography. Using either cation or anion exchange, one protein is bound to the column while the other is collected in the flow-through. In this exercise, undergraduate students gain hands-on experience with experimental design, buffer and sample preparation, and implementation of instrumentation that is commonly used by experienced researchers while learning and applying the fundamental concepts of protein structure, protein purification, and SDS-PAGE. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(1):60-68, 2017.

The Case Against a Darwinian Origin of Protein Folds

Four decades ago, several scientists suggested that the impossibility of any evolutionary process sampling anything but a miniscule fraction of the possible protein sequences posed a problem for the evolution of new proteins. This potential problem-the sampling problem -was largely ignored, in part because those who raised it had to rely on guesswork to fill some key gaps in their understanding of proteins. The huge advances since that time call for a careful reassessment of the issue they raised. Focusing specifically on the origin of new protein folds, I argue here that the sampling problem remains. The difficulty stems from the fact that new protein functions, when analyzed at the level of new beneficial phenotypes, typically require multiple new protein folds, which in turn require long stretches of new protein sequence. Two conceivable ways for this not to pose an insurmountable barrier to Darwinian searches exist. One is that protein function might generally be largely indifferent to protein sequence. The other is that relatively simple manipulations of existing genes, such as shuffling of genetic modules, might be able to produce the necessary new folds. I argue that these ideas now stand at odds both with known principles of protein structure and with direct experimental evidence. If this is correct, the sampling problem is here to stay, and we should be looking well outside the Darwinian framework for an adequate explanation of fold origins.

Protein Geometry Database: a flexible engine to explore backbone conformations and their relationships to covalent geometry

The backbone bond lengths, bond angles, and planarity of a protein are influenced by the backbone conformation (φ,Ψ), but no tool exists to explore these relationships, leaving this area as a reservoir of untapped information about protein structure and function. The Protein Geometry Database (PGD) enables biologists to easily and flexibly query information about the conformation alone, the backbone geometry alone, and the relationships between them. The capabilities the PGD provides are valuable for assessing the uniqueness of observed conformational or geometric features in protein structure as well as discovering novel features and principles of protein structure. The PGD server is available at http://pgd.science.oregonstate.edu/ and the data and code underlying it are freely available to use and extend.

Textbook of Structural Biology, by Anders Liljas, Lars Liljas, Jure Piskur, Göran Lindblom, Poul Nissen, and Morten Kjeldgaard

Textbook of Structural Biology, by Anders Liljas, Lars Liljas, Jure Piskur, Göran Lindblom, Poul Nissen, and Morten Kjeldgaard

Subunit interfaces of oligomeric hyperthermophilic enzymes display enhanced compactness

Enzymes from thermophilic and, particularly, from hyperthermophilic organisms are surprisingly stable. Understanding the molecular origin of protein thermostability and thermoactivity attracted the interest of many scientists both for the perspective comprehension of the principles of protein structure and for the possible biotechnological applications through protein engineering. Comparative studies at sequence and structure levels were aimed at detecting significant differences of structural parameters related to protein stability between thermophilic and hyperthermophilic proteins and their mesophilic homologs. In a recent work, we focused attention on structural adaptation occurring at the subunit interface of oligomeric hyper- and thermostable enzymes. A set of structural and chemico-physical parameters were compared to those observed at the corresponding interfaces of homologous mesophilic proteins. Among the most significant variations, a general increase of interface apolarity and packing density in hyperthermophilic enzymes were found. This work was therefore aimed at elucidating whether the increased packing observed is reached also through the reduction of interface cavity number and volume. The results indicate that number of cavities tends to be relatively constant while cavity volume tends to decrease in the hyperthermophilic interfaces. The cavity apolarity increases in thermophiles but, apparently, not in hyperthermophiles. Moreover, interface hot spot residues of the mesophilic interfaces tend to be conserved in the extremophilic counterparts.

Development of higher-level cognitive skills in a learner-centered lab on extensions of mendelian inheritance using Drosophila.

Students can have difficulty comprehending complex concepts in science. They can memorize the definition but do not understand the underlying biological principles. In the Fundamentals of Genetics course at Arizona State University at the West campus, students grapple with the topic of "extensions of Mendelism." Additionally, in lab, students are challenged by scoring phenotypes that are not binary. Both of these concepts require that students understand not only inheritance but also the principles of protein structure and function. A genetics laboratory exercise was developed that combines study of some extensions of Mendelian inheritance with practice in manipulating Drosophila melanogaster and scoring subtle and variable phenotypes. Students analyze Drosophila with mutations that demonstrate some extensions of Mendelian inheritance: temperature sensitivity, variable expressivity, incomplete penetrance, multiple alleles, dosage compensation, and gene dosage effect. The phenotypes in some of these mutants differ from individual to individual and are difficult to discern; thus, students also gain experience in investigating challenging phenotypes. Pre- and postlab assessments indicate that performing this exercise increased students' mastery of the molecular basis of extensions of Mendelian inheritance and their abilities in scoring and manipulating flies. This is a discovery-based lab exercise in which students examine some extensions of Mendelian inheritance and gain experience in analyzing complex traits in Drosophila.

Structural trees for proteins containing φ-motifs

In the present study, a novel structural motif of proteins referred to as the phi-motif is considered, and two novel structural trees in which the phi-motif is taken as the root structure have been constructed. The simplest phi-motif is formed by three adjacent beta-strands connected by loops and packed in one beta-sheet so that its overall fold resembles the Greek letter phi. Construction of the structural trees and modeling of folding pathways have shown that all structures of the protein superfamilies can be obtained by stepwise addition of alpha-helices and/or beta-strands to the root phi-motif taking into account a restricted set of rules inferred from known principles of protein structure. The structural trees are a good tool for structure comparison, structural classification of proteins, as well as for searching for all possible protein folds and folding pathways.

SNPs3D: candidate gene and SNP selection for association studies.

BackgroundThe relationship between disease susceptibility and genetic variation is complex, and many different types of data are relevant. We describe a web resource and database that provides and integrates as much information as possible on disease/gene relationships at the molecular level.DescriptionThe resource has three primary modules. One module identifies which genes are candidates for involvement in a specified disease. A second module provides information about the relationships between sets of candidate genes. The third module analyzes the likely impact of non-synonymous SNPs on protein function. Disease/candidate gene relationships and gene-gene relationships are derived from the literature using simple but effective text profiling. SNP/protein function relationships are derived by two methods, one using principles of protein structure and stability, the other based on sequence conservation. Entries for each gene include a number of links to other data, such as expression profiles, pathway context, mouse knockout information and papers. Gene-gene interactions are presented in an interactive graphical interface, providing rapid access to the underlying information, as well as convenient navigation through the network. Use of the resource is illustrated with aspects of the inflammatory response and hypertension.ConclusionThe combination of SNP impact analysis, a knowledge based network of gene relationships and candidate genes, and access to a wide range of data and literature allow a user to quickly assimilate available information, and so develop models of gene-pathway-disease interaction.

3P069 立体構造予測からタンパク質立体構造構築原理を探る(蛋白質 C) 物性 : 安定性、折れたたみなど)

3P069 立体構造予測からタンパク質立体構造構築原理を探る(蛋白質 C) 物性 : 安定性、折れたたみなど)

New Principles of Protein Structure: Nests, Eggs — and What Next?

New Principles of Protein Structure: Nests, Eggs — and What Next?

New principles of protein structure: nests, eggs--and what next?

Protein structure prediction, not only description: A step in this direction is the discovery that many anion and cation binding sites (where ions can be atoms exhibiting a full or partial charge) in proteins are made up of three amino acids of which two exhibit “enantiomeric” main-chain conformations. The combination of torsion angle pairs determines whether an RL or an LR nest is formed (see picture).

Principles of protein structure: an established Internet-based course in structural biology

The Internet is becoming an important medium for the delivery of educational materials. However, relatively few institutions are delivering whole courses using this medium. More often, the technologies are used to complement traditional courses, which may be given face-to-face or at a distance (Farrell, 1999). The Department of Crystallography at Birkbeck College, London, has been in the vanguard of the development of 'virtual education', providing some of the first accredited postgraduate courses in the UK to be offered entirely using the new technologies. For the past four years, we have been running an Advanced Certificate course entitled 'Principles of Protein Structure using the Internet'1 (Sansom, Walshaw and Moss, 1997) (PPS). See http://www.cryst.bbk.aauk/pps for more details. This was one of the first tutor-assisted, accredited, university-level courses to be taught entirely over the Internet, and is certainly the first in biochemistry in the UK.DOI:10.1080/0968776000080204

A structural tree for proteins containing S-like β-sheets

A structural tree for proteins and domains containing S-like β-sheets has been constructed. An S-like β-sheet is taken as a starting structure in modelling or as a root structure of the tree. Larger structures are obtained by a stepwise addition of β-strands and/or α-helices to the root S-like β-sheet in accordance with a restricted set of rules inferred from known principles of protein structure. Applications of the structural tree to structure comparison, protein classification and protein folding are described.

A structural tree for proteins containing 3β-corners

A structural tree for β-proteins with predominantly orthogonal β-sheet packing has been constructed. The 3β-corner, a structural motif that recurs in proteins of this class, is taken as a root structure of the tree. The 3β-corner can be represented as a triple-stranded β-sheet folded on to itself so that its two β-β-hairpins are packed approximately orthogonally in different layers and the central strand bends by ∼90° in a right-handed direction when passing from one layer to the other. The larger protein structures are obtained by stepwise addition of β-strands to the root 3β-corner taking into account a restricted set of rules inferred from known principles of protein structure. The protein structures that can be obtained in this way are grouped into one structural class and those found in branches of the structural tree into subclasses.

A structural tree for α-helical proteins containing α-α-corners and its application to protein classification

A structural tree for α-helical proteins and domains including α-α-corners has been constructed. The α-α-corner is taken as a root structure of the tree. The larger protein structures are obtained by stepwise addition of a-helices to the root α-α-corner taking into account a restricted set of rules inferred from known principles of protein structure. The protein structures that can be obtained in this way are grouped into one structural class and those found in branches of the tree into subclasses.

A molecular model of the inducer binding domain of the galactose repressor of Escherichia coli.

The C-terminal inducer binding domain of the Escherichia coli galactose repressor (GalR) is homologous to several periplasmic chemoreceptor proteins whose three-dimensional structures have been determined at high resolution (Vyas, N. K., Vyas, M. N., and Quiocho, F. A. (1991) J. Biol. Chem. 266, 5226-5237; Mowbray, S. L. and Cole, L. B. (1992) J. Mol. Biol. 225, 155-175). The protein backbone was constructed from the coordinates of glucose/galactose-binding protein using the Homology program (Biosym Technologies, San Diego). Loops were built by searching for substructures in the structure data base, and the side chains were built using a rotamer-base program. A small amount of energy minimization relieved steric strain within the model. The GalR model that has been constructed is consistent with the principles of protein structure; values obtained for the compactness and buried surface area of the model compare favorably with those determined for the chemoreceptor protein structures. The model is consistent with, and provides structural interpretations for, experimental results obtained from physical and biochemical studies. Predictions are made concerning the residues conferring the specificity of galactose induction of GalR and for self-association to dimers. The model provides a first step toward correlating the structure and regulation of GalR and in determining the chemistry of its homologous and heterologous interactions that are critical to its role as a regulator of transcription initiation.

Polymerase Domains of Human Immunodeficiency Virus Type 1 Reverse Transcriptase and Herpes Simplex Virus Type 1 DNA Polymerase: Their Predicted Three-Dimensional Structures and some Putative Functions in Comparison with E. Coli DNA Polymerase I. A Critical Survey

Hypothetical three-dimensional models for the entire polymerase domain of HIV-1 reverse transcriptase (HIV RT) and conserved regions of HSV-1 DNA polymerase (HSV pol) were created, primarily from literature data on mutations and principles of protein structure, and compared with those of E. coli DNA polymerase I (E. coli pol I). The corresponding parts, performing similar functions, were found to be analogous, not homologous, in structure with different β topologies and sequential arrangement. The polymerase domain of HSV pol is shown to form an anti-parallel β-sheet with α-helices, but with a topology different from that of the Klenow fragment of E. coli pol I. The main part of the polymerase domain of HIV RT is made up of a basically parallel β-sheet and α-helices with a topology similar to the nucleotide-binding p21 ras proteins. The putative functions of some conserved or invariant amino acids in the three polymerase families are discussed.

Brave new proteins: what evolution reveals about protein structure.

Synthetic proteins provide important information about the principles of protein structure. They illuminate the processes of natural protein evaluation, but are not limited by these processes. Here, we review studies of several mutant proteins and discuss the general principles that can be derived from them.

The analysis of protein structures: New insights from a growing data base

AbstractWe now know the structures of over 200 proteins to atomic resolution. Despite the impressive extent and quality of the results, crystal‐structure analysis has often been thought of as limited in scope, not only in its restriction to samples that can be crystallized, but in the more important respect that taking ‘snapshots’ of proteins does not directly address the complex spatio‐temporal organization of the processes in which proteins participate. It is suggested here that, as the field has matured, this second limitation is gradually being overcome. As we gain increased access to structures of proteins in different conformational states – for example, in conformations produced by different states of ligation – and to families of homologous proteins, we can proceed from the statics of protein structure to the dynamics of conformational change, function, and evolution.A new scientific speciality has grown up around the solved structures: it has as its goal the elucidation of general principles of protein structure and function, to provide a theoretical framework for understanding the properties of proteins revealed by experiment. In this article we shall discuss some of the activity in this field. It will emerge clearly, I believe, that the increasing number and variety of solved structures is exerting a cumulative force. General principles are emerging from comparisons of related proteins and contrasts of dissimilar ones: the whole corpus of data is greater than the sum of the parts.

Assessment of secondary-structure prediction of proteins comparison of computerized chou-fasman method with others

A method predicting protein secondary structure from sequence information could be assessed for its real efficiency by applying it to a number of proteins which lie completely outside a given data set. This type of test is performed for the three methods of Chou and Fasman (Adv. Enzymol. 47 (1978) 45–148), Robson and co-workers (J. Mol. Biol. 120 (1978) 97–120) and Lim (J. Mol. Biol. 88 (1974) 873–894) by using data of 19 proteins for the former two methods and 11 proteins for the method of Lim. The prediction abilities of these methods turn out to be of almost the same level, but unexpectedly low: their average scores are commonly less than 55% measured by the three-state assessment (α, β and coil) or less than 45% measured by the four-state assessment (α, β, turn and coil). This level of accuracy is more than 20% lower than that of current expectations as summarized by Schulz and Schirmer (Principles of Protein Structure (1979) Ch. 6, Springer, New York). A joint prediction attempted with the simultaneous usage of the three prediction methods did not improve the results. Causes and implications of the unsatisfactory results are discussed. In this study, computer programs were prepared for the methods of Chou and Fasman and of Robson and co-workers. While difficulties arose in the course of the computerization of the Chou-Fasman method, the prediction algorithm was arranged in a fully automatic form with optimization of the original rules as well as introduction of a modified treatment for solving the overlap among initially predicted regions of the secondary structures. Large discrepancies observed between the original results and those obtained by the computerized method are examined.