Exploring amyloid formation by a
            <i>de novo</i>
            design

Kammerer, Richard A.; Kostrewa, Dirk; Zurdo, Jesús; Detken, Andreas; García‐Echeverría, Carlos; Green, Janelle D.; Müller, Shirley A.; Meier, Beat H.; Winkler, Fritz K.; Dobson, Christopher M.; Steinmetz, Michel O.

doi:10.1073/pnas.0306786101

Cited by 164 publications

(217 citation statements)

References 48 publications

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“…7, which is published as supporting information on the PNAS web site, potential interhelical g Arg to eЈ Glu salt bridges are found in many other short (15-50 aa in length) parallel trimeric coiled-coil domains of intracellular, extracellular, transmembrane, viral, and synthetic proteins. Several members of these autonomous coiled coils are well characterized (9,30,31,(33)(34)(35)(36)(37)(38)(39)(40)(41)(42)(43). Based on the alignment, the sequence motif R 1 -h 2 -x 3 -x 4 -h 5 -E 6 can be deduced (R ϭ Arg; E ϭ Glu, L ϭ Leu; h 1 ϭ Ile, Leu, Val, Met; h 2 ϭ Leu, Ile, Val; x ϭ any amino acid residue).…”

Section: The Sequence Motif R-h-x-x-h-e Is Conserved Among Parallel Tmentioning

confidence: 99%

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A conserved trimerization motif controls the topology of short coiled coils

Kammerer

Kostrewa

Progias

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

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108

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In recent years, short coiled coils have been used for applications ranging from biomaterial to medical sciences. For many of these applications knowledge of the factors that control the topology of the engineered protein systems is essential. Here, we demonstrate that trimerization of short coiled coils is determined by a distinct structural motif that encompasses specific networks of surface salt bridges and optimal hydrophobic packing interactions. The motif is conserved among intracellular, extracellular, viral, and synthetic proteins and defines a universal molecular determinant for trimer formation of short coiled coils. In addition to being of particular interest for the biotechnological production of candidate therapeutic proteins, these findings may be of interest for viral drug development strategies.protein engineering ͉ sequence-to-structure rules ͉ protein-protein interaction ͉ salt bridges ͉ x-ray crystallography T he potential of short ␣-helical coiled coils for protein engineering, biotechnological, biomaterial, basic research, and medical applications has recently been recognized (1-12). The wide range of applications underscores the need for topological control of coiled-coil peptides. Although seemingly simple, coiled coils can form a variety of different assemblies ranging from dimers to pentamers (13,14). Furthermore, coiled coils can form homomers or heteromers with their chains arranged in a parallel or antiparallel fashion. To understand how side-chainside-chain interactions determine a particular structure, it is important to discriminate the factors responsible for specific interhelical interactions from those that are common to all coiled coils such as the heptad repeat.It is generally acknowledged that the detailed packing geometry of hydrophobic core residues correlates with the oligomerization state (15,16). In dimers the side chains of the residues at a and d positions pack in a manner termed parallel and perpendicular, respectively. In the four-stranded state the dimer mode is reversed. Trimeric coiled coils are characterized by an intermediate geometry of these residues, termed acute. Previous studies found that these oligomerization states are determined in particular by the distribution of isoleucine and leucine residues that prefer the parallel and acute, and the acute and perpendicular geometries, respectively (15, 16).Buried polar residues in hydrophobic interfaces also play an important role in determining the number and orientation of strands in coiled coils. Many two-stranded leucine zippers of transcription regulators contain at least one conserved polar residue. Frequently an asparagine or a lysine residue occupies heptad position a toward the center of the sequence, suggesting a common mechanism for determining dimer specificity in these molecules (17). Polar residues like glutamine and threonine at positions a and d, respectively, can favor trimer formation (18,19). Interhelical interactions between side chains of residues at the e and g positions as well as the packi...

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Section: The Sequence Motif R-h-x-x-h-e Is Conserved Among Parallel Tmentioning

confidence: 99%

“…T he potential of short ␣-helical coiled coils for protein engineering, biotechnological, biomaterial, basic research, and medical applications has recently been recognized (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12). The wide range of applications underscores the need for topological control of coiled-coil peptides.…”

mentioning

confidence: 99%

A conserved trimerization motif controls the topology of short coiled coils

Kammerer

Kostrewa

Progias

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

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108

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“…From the standpoint of molecular structure, the defining feature of an amyloid fibril is the presence of cross-β supramolecular structure, meaning that the β-sheets within the fibril are formed by β-strand segments that run approximately perpendicular to the long axis of the fibril and are linked by hydrogen bonds that run approximately parallel to this axis (11)(12)(13). Although determination of the molecular structures of amyloid fibrils is made difficult by their inherent noncrystallinity and insolubility, techniques such as solid state nuclear magnetic resonance (NMR) (12,(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33), electron paramagnetic resonance (EPR) (34)(35)(36), electron microscopy (37)(38)(39)(40)(41)(42)(43), hydrogen/deuterium exchange (29,(44)(45)(46)(47), scanning mutagenesis (48), chemical crosslinking (27,49,50), and x-ray diffraction of amyloid-like crystals …”

mentioning

confidence: 99%

Peptide Conformation and Supramolecular Organization in Amylin Fibrils: Constraints from Solid-State NMR

et al. 2007

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The 37-residue amylin peptide, also known as islet amyloid polypeptide, forms fibrils that are the main peptide or protein component of amyloid that develops in the pancreas of type 2 diabetes patients. Amylin also readily forms amyloid fibrils in vitro that are highly polymorphic under typical experimental conditions. We describe a protocol for the preparation of synthetic amylin fibrils that exhibit a single predominant morphology, which we call a striated ribbon, in electron microscope and atomic force microscope images. Solid state nuclear magnetic resonance (NMR) measurements on a series of isotopically labeled samples indicate a single molecular structure within the striated ribbons. We use scanning transmission electron microscopy and several types of one-dimensional and two-dimensional solid state NMR techniques to obtain constraints on the peptide conformation and supramolecular structure in these amylin fibrils, and derive molecular structural models that are consistent with the experimental data. The basic structural unit in amylin striated ribbons, which we call the protofilament, contains four-layers of parallel β-sheets, formed by two symmetric layers of amylin molecules. The molecular structure of amylin protofilaments in striated ribbons closely resembles the protofilament in amyloid fibrils with similar morphology formed by the 40-residue β-amyloid peptide that is associated with Alzheimer's disease. Keywordsislet amyloid polypeptide; type 2 diabetes; amyloid fibril structure; electron microscopy; atomic force microscopy Amylin, also called islet amyloid polypeptide or IAPP, is a 37-residue peptide that is cosecreted with insulin by the β-cells of pancreas. The normal biological effects of amylin secretion include inhibition of glucagon secretion and reduction of the rate of gastric emptying, effects that contribute to the maintenance of postprandial glucose homeostasis (1). Amylin is the major peptide or protein component of the islet amyloid found in the pancreas of approximately 90% of type 2 (or non-insulin-dependent) diabetes patients (2,3). Fibrillar amylin has been shown * Corresponding author: Dr. Robert Tycko, National Institutes of Health, Building 5, Room 112, Bethesda, MD 20892-0520. phone 301-402-8272. fax 301-496-0825. e-mail robertty@mail.nih.gov.Supporting Information Available HPLC chromatograms from the purification of both reduced and oxidized amylin by reverse-phase chromatography ( Figure S1); FPLC chromatograms from the purification of both human and rodent amylin by size-exclusion chromatography ( Figure S2); 1D 13 C spectra of amylin fibrils with various isotopic labeling patterns, in lyophilized and rehydrated conditions ( Figures S3-S5); Table of 13 C NMR chemical shifts in amylin fibrils, TALOS predictions of backbone torsion angles based on these shifts, and torsion angles determined from 15 N fpRFDR-CT measurements (Table S1). This material is freely available on the World Wide Web at http://www.acs.org. to be toxic to cultured β-cells (4), and has been propo...

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“…For example, A␤ 10 -35 gives rise to parallel ␤-strands, whereas A␤ 16 -22 forms antiparallel ␤-strands (20,21). The facile incorporation of selective isotopic labels into cc␤ enabled Kammerer et al (10) to use solid-state NMR methods to determine that its strands are arranged in an antiparallel fashion. The origins of determinants of orientation should be readily explored by rational modification of the cc␤ design.…”

Section: Structural Propertiesmentioning

confidence: 99%

“…In this issue of PNAS, Kammerer et al (10) rigorously characterize an important tool for making these insights. This tool is a 17-residue de novodesigned peptide, cc␤, in which considerations relevant to amyloid formation were overlaid onto a coiled-coil protein design (11).…”

Section: Function and Pathologymentioning

confidence: 99%

Unzipping the mysteries of amyloid fiber formation

Miranker

2004

Proc. Natl. Acad. Sci. U.S.A.

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Exploring amyloid formation by a de novo design

Cited by 164 publications

References 48 publications

A conserved trimerization motif controls the topology of short coiled coils

A conserved trimerization motif controls the topology of short coiled coils

Peptide Conformation and Supramolecular Organization in Amylin Fibrils: Constraints from Solid-State NMR

Unzipping the mysteries of amyloid fiber formation

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