Current Protein & Peptide Science[JOURNAL]
Sun
168 papers
Chemical and biological methods to detect post-translational modifications of arginine.
Slade DJ, Subramanian V, Fuhrmann J … +1 more , Thompson PR
Biopolymers · 2014 Feb · PMID 23576281 · Full text
Post-translational modifications (PTMs) of protein embedded arginines are increasingly being recognized as playing an important role in both prokaryotic and eukaryotic biology, and it is now clear that these PTMs modulat...
Post-translational modifications (PTMs) of protein embedded arginines are increasingly being recognized as playing an important role in both prokaryotic and eukaryotic biology, and it is now clear that these PTMs modulate a number of cellular processes including DNA binding, gene transcription, protein-protein interactions, immune system activation, and proteolysis. There are currently four known enzymatic PTMs of arginine (i.e., citrullination, methylation, phosphorylation, and ADP-ribosylation), and two non-enzymatic PTMs [i.e., carbonylation, advanced glycation end-products (AGEs)]. Enzymatic modification of arginine is tightly controlled during normal cellular function, and can be drastically altered in response to various second messengers and in different disease states. Non-enzymatic arginine modifications are associated with a loss of metabolite regulation during normal human aging. This abnormally large number of modifications to a single amino acid creates a diverse set of structural perturbations that can lead to altered biological responses. While the biological role of methylation has been the most extensively characterized of the arginine PTMs, recent advances have shown that the once obscure modification known as citrullination is involved in the onset and progression of inflammatory diseases and cancer. This review will highlight the reported arginine PTMs and their methods of detection, with a focus on new chemical methods to detect protein citrullination.
Peptide design for antimicrobial and immunomodulatory applications.
Haney EF, Hancock RE
Biopolymers · 2013 Nov · PMID 23553602 · Full text
The increasing threat of antibiotic resistance in pathogenic bacteria and the dwindling supply of antibiotics available to combat these infections poses a significant threat to human health throughout the world. Antimicr...
The increasing threat of antibiotic resistance in pathogenic bacteria and the dwindling supply of antibiotics available to combat these infections poses a significant threat to human health throughout the world. Antimicrobial peptides (AMPs) have long been touted as the next generation of antibiotics capable of filling the anti-infective void. Unfortunately, peptide-based antibiotics have yet to realize their potential as novel pharmaceuticals, in spite of the immense number of known AMP sequences and our improved understanding of their antibacterial mechanism of action. Recently, the immunomodulatory properties of certain AMPs have become appreciated. The ability of small synthetic peptides to protect against infection in vivo has demonstrated that modulation of the innate immune response is an effective strategy to further develop peptides as novel anti-infectives. This review focuses on the screening methods that have been used to assess novel peptide sequences for their antibacterial and immunomodulatory properties. It will also examine how we have progressed in our ability to identify and optimize peptides with desired biological characteristics and enhanced therapeutic potential. In addition, the current challenges to the development of peptides as anti-infectives are examined and the strategies being used to overcome these issues are discussed.
Are all regions of folded proteins that undergo ligand-dependent order-disorder transitions targets for allosteric peptide mimetics?
Fenton AW
Biopolymers · 2013 Nov · PMID 23520021 · Full text
Although the classical view of how proteins function relied on well folded structures, it is now recognized that the functions of many proteins are dependent on being intrinsically disordered. The primary consideration i...
Although the classical view of how proteins function relied on well folded structures, it is now recognized that the functions of many proteins are dependent on being intrinsically disordered. The primary consideration in this work is the intermediate group of proteins that are overall well folded, but which contain small regions that undergo order-disorder transitions. In particular, the current focus is on those order-disorder transitions that are energetically coupled to ligand binding. As exemplified by the case of human liver pyruvate kinase (hL-PYK), peptides that mimic the sequence of the order-disorder region can be used as allosteric regulators of the enzyme. On the basis of this example and others reported in the literature, we propose that a similar use of peptides that mimic protein regions that experience ligand-dependent order-disorder transitions can be a generalized initiation point for the development of allosteric drugs.
Investigating proline puckering states in diproline segments in proteins.
Saha I, Shamala N
Biopolymers · 2013 Sep · PMID 23444278 · Publisher ↗
In the current study, the puckering states of the Proline ring occurring in diproline segments ((L) Pro-(L) Pro) in proteins has been investigated with a segregation made on the basis of cis and trans states for the Pro-...
In the current study, the puckering states of the Proline ring occurring in diproline segments ((L) Pro-(L) Pro) in proteins has been investigated with a segregation made on the basis of cis and trans states for the Pro-Pro peptide bond and the conformational states for the diproline segment to investigate the effects of conformation of the diproline segment on the corresponding puckering state of the Proline ring in the segment if any. The value of the endocyclic ring torsional angles of the pyrrolidine ring has been used for calculating and visualizing various puckering states using a proposed new sign convention (+/-) nomenclature. The results have been compared to that obtained in a previous study on peptides from this group. In this study, quite interestingly, the Planar (G) conformation that was present in 14.3% of the cases in peptides, appears to be nearly a rare conformation in the case of proteins (1.9%). The present study indicates that the (C(γ)-exo/C(γ)-exo), (C(γ)-exo/Twisted C(γ)-exo-C(β)-endo) and (Twisted C(γ)-endo-C(β)-exo/Twisted C(γ)-endo-C(β)-exo) categories are the most preferred combinations. For Proline rings in proteins, the states C(γ)-exo, Twisted C(γ)-exo-C(β)-endo and Twisted C(γ)-endo-C(β)-exo are the most preferred states. Within diproline segments, the pyrrolidine ring conformations do not show a strong co-relation to the backbone conformation in which they are observed. It is likely that five-membered rings have a considerable plasticity of structure and are readily deformed to accommodate a variety of energetically preferred backbone conformations.
Review: Pathway analysis for peptide-mediated electronic coupling in the super-exchange mechanism of ET and EET.
Kawatsu T
Biopolymers · 2013 · PMID 23335172 · Publisher ↗
Electron and excitation energy transfers (ET and EET) have an important role in biological energy-exchange processes. Proteins are an inhomogeneous and anisotropic medium for ET and EET. The protein structure influences...
Electron and excitation energy transfers (ET and EET) have an important role in biological energy-exchange processes. Proteins are an inhomogeneous and anisotropic medium for ET and EET. The protein structure influences electronic coupling, an important factor for ET and EET. The structure factor may be predicted by obtaining information about the tunneling pathways. The present paper mainly focuses on tunneling pathway analysis using the tunneling current (flux) of the electron or configuration density. The tunneling pathways for ET and singlet EET through peptides are introduced using tunneling current (flux) analysis. These tunneling pathways differ greatly between ET and singlet EET. This paper also reviews both the theoretical background and other methods for determining electronic tunneling pathways. These pathways are related to the effect of protein coordinates on the electronic coupling between the initial and final states of the ET and EET.
Force modulated conductance of artificial coiled-coil protein monolayers.
Atanassov A, Hendler Z, Berkovich I … +2 more , Ashkenasy G, Ashkenasy N
Biopolymers · 2013 · PMID 23335171 · Publisher ↗
Studies of charge transport through proteins bridged between two electrodes have been the subject of intense research in recent years. However, the complex structure of proteins makes it difficult to elucidate transport...
Studies of charge transport through proteins bridged between two electrodes have been the subject of intense research in recent years. However, the complex structure of proteins makes it difficult to elucidate transport mechanisms, and the use of simple peptide oligomers may be an over simplified model of the proteins. To bridge this structural gap, we present here studies of charge transport through artificial parallel coiled-coil proteins conducted in dry environment. Protein monolayers uniaxially oriented at an angle of ∼ 30° with respect to the surface normal were prepared. Current voltage measurements, obtained using conductive-probe atomic force microscopy, revealed the mechano-electronic behavior of the protein films. It was found that the low voltage conductance of the protein monolayer increases linearly with applied force, mainly due to increase in the tip contact area. Negligible compression of the films for loads below 26 nN allowed estimating a tunneling attenuation factor, β(0) , of 0.5-0.6 Å(-1) , which is akin to charge transfer by tunneling mechanism, despite the comparably large charge transport distance. These studies show that mechano-electronic behavior of proteins can shed light on their complex charge transport mechanisms, and on how these mechanisms depend on the detailed structure of the proteins. Such studies may provide insightful information on charge transfer in biological systems.
Quantification of small cyclic disulfide-rich peptides.
Conibear AC, Daly NL, Craik DJ
Biopolymers · 2012 · PMID 23203757 · Publisher ↗
Cyclic disulfide-rich peptides ranging in size from ∼14 to 29 amino acids have been found in a wide variety of organisms and have exciting biological and medicinal applications due to their stability and structure. Many...
Cyclic disulfide-rich peptides ranging in size from ∼14 to 29 amino acids have been found in a wide variety of organisms and have exciting biological and medicinal applications due to their stability and structure. Many of these peptides can be chemically synthesized, but their small size and limited number of chromophore-containing amino acids make them difficult to quantify by methods routinely used for large proteins. A comparison of the precision and accuracy of gravimetric, UV- and NMR-based methods in current use for the quantification of small peptides is presented for a representative set of cyclic disulfide-rich peptides. The study shows that gravimetric and UV absorbance methods should be used with caution for small peptides and all methods should be carefully validated. For the routine quantification of small disulfide-rich peptides, we recommend comparison of the analytical reverse-phase high-performance liquid chromatography trace or UV absorbance at 214 nm with that of a standard peptide solution quantified by amino acid analysis. An accurate quantification method that is simple and cost effective will assist in comparison of inhibition and activity data between different laboratories and peptides and correct calculation of synthesis yields.
Protease-resistant peptide design-empowering nature's fragile warriors against HIV.
Weinstock MT, Francis JN, Redman JS … +1 more , Kay MS
Biopolymers · 2012 · PMID 23203688 · Full text
Peptides have great potential as therapeutic agents, but their use is often limited by susceptibility to proteolysis and their resulting in vivo fragility. In this review, we focus on peptidomimetic approaches to produce...
Peptides have great potential as therapeutic agents, but their use is often limited by susceptibility to proteolysis and their resulting in vivo fragility. In this review, we focus on peptidomimetic approaches to produce protease-resistant peptides with the potential for greatly improved clinical utility. We focus on the use of mirror-image (D-peptide) and ß-peptides as two leading approaches with distinct design principles and challenges. Application to the important and difficult problem of inhibiting HIV entry illustrates the current state-of-the-art in peptidomimetic technologies. We also summarize future directions for this field and highlight remaining obstacles to widespread use of protease-resistant peptides.
Challenges in mass spectrometry-based quantification of bioactive peptides: a case study exploring the neuropeptide Y family.
Xi L, Jin Y, Parker EA … +4 more , Josh P, Jones A, Wijffels G, Colgrave ML
Biopolymers · 2012 · PMID 23193600 · Publisher ↗
The study of biologically active peptides is critical to the understanding of physiological pathways, especially those involved in the development of disease. Historically, the measurement of biologically active endogeno...
The study of biologically active peptides is critical to the understanding of physiological pathways, especially those involved in the development of disease. Historically, the measurement of biologically active endogenous peptides has been undertaken by radioimmunoassay, a highly sensitive and robust technique that permits the detection of physiological concentrations in different biofluid and tissue extracts. Over recent years, a range of mass spectrometric approaches have been applied to peptide quantification with limited degrees of success. Neuropeptide Y (NPY), peptide YY (PYY), and pancreatic polypeptide (PP) belong to the NPY family exhibiting regulatory effects on appetite and feeding behavior. The physiological significance of these peptides depends on their molecular forms and in vivo concentrations systemically and at local sites within tissues. In this report, we describe an approach for quantification of individual peptides within mixtures using high-performance liquid chromatography electrospray ionization tandem mass spectrometry analysis of the NPY family peptides. Aspects of quantification including sample preparation, the use of matrix-matched calibration curves, and internal standards will be discussed. This method for the simultaneous determination of NPY, PYY, and PP was accurate and reproducible but lacks the sensitivity required for measurement of their endogenous concentration in plasma. The advantages of mass spectrometric quantification will be discussed alongside the current obstacles and challenges.
Aromatic interactions in model peptide β-hairpins: ring current effects on proton chemical shifts.
Rajagopal A, Aravinda S, Raghothama S … +2 more , Shamala N, Balaram P
Biopolymers · 2012 · PMID 22782561 · Publisher ↗
Crystal structures of eight peptide β-hairpins in the sequence Boc-Leu-Phe-Val-Xxx-Yyy-Leu-Phe-Val-OMe revealed that the Phe(2) and Phe(7) aromatic rings are in close spacial proximity, with the centroid-centroid distanc...
Crystal structures of eight peptide β-hairpins in the sequence Boc-Leu-Phe-Val-Xxx-Yyy-Leu-Phe-Val-OMe revealed that the Phe(2) and Phe(7) aromatic rings are in close spacial proximity, with the centroid-centroid distance (R(cen)) of 4.4-5.4 Å between the two phenyl rings. Proton NMR spectra in chloroform and methanol solution reveal a significant upfield shift of the Phe(7) C(δ,δ') H(2) protons (6.65-7.04 ppm). Specific assignments of the aromatic protons have been carried out in the peptide Boc-Leu-Phe-Val-(D)Pro-(L)Pro-Leu-Phe-Val-OMe (6). The anticipated ring current shifts have been estimated from the aromatic ring geometrics observed in crystals for all eight peptides. Only one of the C(δ,δ') H proton lies in the shielding zone with rapid ring flipping, resulting in averaging between the two extreme chemical shifts. An approximate estimate of the population of conformations, which resemble crystal state orientation, may be obtained. Key nuclear Overhauser effects (NOEs) between facing Phe side chains provide support for close similarity between the solid state and solution conformation. Temperature dependence of aromatic ring proton chemical shift and line widths for peptide 6 (Boc-Leu-Phe-Val-(D)Pro-(L)Pro-Leu-Phe-Val-OMe) and the control peptide Boc-Leu-Val-Val-(D)Pro-Gly-Leu-Phe-Val-OMe establish an enhanced barrier to ring flipping when the two Phe rings are in proximity. Modeling studies suggest that small, conformational adjustment about C(α)-C(β) (χ(1) ) and C(β)-C(γ) (χ(2) ) bonds of both the Phe residues may be required in order to permit unhindered, uncorrelated flipping of both the Phe rings. The maintenance of the specific aromatic ring orientation in organic solvents provides evidence for significant stabilizing interaction.
Macromolecular structure modeling from 3D EM using VolRover 2.0.
Zhang Q, Bettadapura R, Bajaj C
Biopolymers · 2012 Sep · PMID 22696407 · Full text
We review tools for structure identification and model-based refinement from three-dimensional electron microscopy implemented in our in-house software package, VOLROVER 2.0. For viral density maps with icosahedral symme...
We review tools for structure identification and model-based refinement from three-dimensional electron microscopy implemented in our in-house software package, VOLROVER 2.0. For viral density maps with icosahedral symmetry, we segment the capsid, polymeric, and monomeric subunits using techniques based on automatic symmetry detection and multidomain fast marching. For large biomolecules without symmetry information, we again use our multidomain fast-marching method with manual or fit-based multiseeding to segment meaningful substructures. In either case, we subject the resulting segmented subunit to secondary structure detection when the EM resolution is sufficiently high, and rigid-body structure fitting when the corresponding X-ray structure is available. Secondary structure elements are identified by three techniques: our earlier volume-based and boundary-based skeletonization methods as well as a new method, currently in development, based on solving the grassfire flow equation. For rigid-body fitting, we adapt our earlier fast Fourier-based correlation scheme F2Dock. Our reported segmentation, secondary structure elements identification, and rigid-body fitting techniques, implemented in VOLROVER 2.0 are applied to the PSB 2011 cryo-EM modeling challenge data, and our results are briefly compared to similar results submitted from other research groups. The comparisons show that our techniques are equally capable of segmenting relatively accurate subunits from a viral or protein assembly, and that high segmentation quality leads in turn to higher-quality results of secondary structure elements identification and correlation-based rigid-body fitting. © 2012 Wiley Periodicals, Inc. Biopolymers 97: 709-731, 2012.
Invited review nonmulberry silk biopolymers.
Kundu SC, Kundu B, Talukdar S … +9 more , Bano S, Nayak S, Kundu J, Mandal BB, Bhardwaj N, Botlagunta M, Dash BC, Acharya C, Ghosh AK
Biopolymers · 2012 Jun · PMID 22241173 · Publisher ↗
The silk produced by silkworms are biopolymers and can be classified into two types--mulberry and nonmulberry. Mulberry silk of silkworm Bombyx mori has been extensively explored and used for century old textiles and sut...
The silk produced by silkworms are biopolymers and can be classified into two types--mulberry and nonmulberry. Mulberry silk of silkworm Bombyx mori has been extensively explored and used for century old textiles and sutures. But for the last few decades it is being extensively exploited for biomedical applications. However, the transformation of nonmulberry silk from being a textile commodity to biomaterials is relatively new. Within a very short period of time, the combination of load bearing capability and tensile strength of nonmulberry silk has been equally envisioned for bone, cartilage, adipose, and other tissue regeneration. Adding to its advantage is its diverse morphology, including macro to nano architectures with controllable degradation and biocompatibility yields novel natural material systems in vitro. Its follow on applications involve sustained release of model compounds and anticancer drugs. Its 3D cancer models provide compatible microenvironment systems for better understanding of the cancer progression mechanism and screening of anticancer compounds. Diversely designed nonmulberry matrices thus provide an array of new cutting age technologies, which is unattainable with the current synthetic materials that lack biodegradability and biocompatibility. Scientific exploration of nonmulberry silk in tissue engineering, regenerative medicine, and biotechnological applications promises advancement of sericulture industries in India and China, largest nonmulberry silk producers of the world. This review discusses the prospective biomedical applications of nonmulberry silk proteins as natural biomaterials.
Peptoids at the 7th Summit: toward macromolecular systems engineering.
Drexler KE
Biopolymers · 2011 · PMID 22180902 · Publisher ↗
Methods for facile synthesis of extraordinarily diverse peptide-like oligomers have placed peptoids at the center of a broad and vibrant area of foldamer science and technology. The 7th Peptoid Summit offered a perspecti...
Methods for facile synthesis of extraordinarily diverse peptide-like oligomers have placed peptoids at the center of a broad and vibrant area of foldamer science and technology. The 7th Peptoid Summit offered a perspective on the current state of peptoid science and technology and on prospects for engineering supramolecular assemblies that rival the complexity of biomolecular systems. Methods for engineering biomolecular systems based on DNA and protein are advancing rapidly, building a technology platform for engineering increasingly large and complex self-assembled nanosystems. A comparative review of the physical basis for DNA, protein, and peptoid engineering indicates that the characteristics of peptoids suit them for a strong role in developing self-assembled nanosystems. Physical parallels between peptoids and proteins indicate that peptoid engineering, like protein engineering, will require specialized software to support design. Access to novel side-chain functionality will enable peptoid designers to exploit novel binding interactions, including many that have been discovered and exploited in crystal engineering, a field that has extensively explored the self-assembly of small organic molecules to form well-ordered structures. Developments in DNA, protein, and inorganic nanotechnologies are converging to provide a technology platform for the design and fabrication of complex, functional, atomically precise nanosystems. Peptoid-based foldamer technologies, can contribute to this convergence, expanding the scope of the emerging field of atomically precise macromolecular nanosystems.
Invited review current progress and limitations of spider silk for biomedical applications.
Widhe M, Johansson J, Hedhammar M … +1 more , Rising A
Biopolymers · 2012 Jun · PMID 21898363 · Publisher ↗
Spider silk is a fascinating material combining remarkable mechanical properties with low density and biodegradability. Because of these properties and historical descriptions of medical applications, spider silk has bee...
Spider silk is a fascinating material combining remarkable mechanical properties with low density and biodegradability. Because of these properties and historical descriptions of medical applications, spider silk has been proposed to be the ideal biomaterial. However, overcoming the obstacles to produce spider silk in sufficient quantities and in a manner that meets regulatory demands has proven to be a difficult task. Also, there are relatively few studies of spider silk in biomedical applications available, and the methods and materials used vary a lot. Herein we summarize cell culture- and in vivo implantation studies of natural and synthetic spider silk, and also review the current status and future challenges in the quest for a large scale production of spider silk for medical applications.
Investigating diproline segments in proteins: occurrences, conformation and classification.
Saha I, Shamala N
Biopolymers · 2012 Jan · PMID 21898361 · Publisher ↗
The covalent linkage between the side-chain and the backbone nitrogen atom of proline leads to the formation of the five-membered pyrrolidine ring and hence restriction of the backbone torsional angle ϕ to values of -60...
The covalent linkage between the side-chain and the backbone nitrogen atom of proline leads to the formation of the five-membered pyrrolidine ring and hence restriction of the backbone torsional angle ϕ to values of -60 °± 30° for the L-proline. Diproline segments constitute a chain fragment with considerably reduced conformational choices. In the current study, the conformational states for the diproline segment (( L) Pro-( L) Pro) found in proteins has been investigated with an emphasis on the cis and trans states for the Pro-Pro peptide bond. The occurrence of diproline segments in turns and other secondary structures has been studied and compared to that of Xaa-Pro-Yaa segments in proteins which gives us a better understanding on the restriction imposed on other residues by the diproline segment and the single proline residue. The study indicates that P(II) -P(II) and P(II) -α are the most favorable conformational states for the diproline segment. The analysis on Xaa-Pro-Yaa sequences reveals that the Xaa-Pro peptide bond exists preferably as the trans conformer rather than the cis conformer. The present study may lead to a better understanding of the behavior of proline occurring in diproline segments which can facilitate various designed diproline-based synthetic templates for biological and structural studies.
Controlling the dimensions of amyloid fibrils: toward homogenous components for bionanotechnology.
Domigan LJ, Healy JP, Meade SJ … +2 more , Blaikie RJ, Gerrard JA
Biopolymers · 2012 Feb · PMID 21858783 · Publisher ↗
Amyloid fibrils have been recognized as having potential in a variety of bionanotechnological applications. However, realization of these applications is constrained by a lack of control over morphology and alignment, bo...
Amyloid fibrils have been recognized as having potential in a variety of bionanotechnological applications. However, realization of these applications is constrained by a lack of control over morphology and alignment, both crucial for potential end uses. This article focuses on the use of growth and storage conditions to control the length of amyloid fibrils formed from bovine insulin, with length distributions constructed from transmission electron microscopy (TEM) images. Growth temperature, pH, protein concentration, and storage conditions were examined and were seen to offer a range of conditions that favor different length distribution. The use of amyloid fibrils as nanowires is one area where control of fibril dimensions is desirable, for experimental setup and endpoint applications. The conductive properties of fibrils formed from bovine insulin are presented, with these insulin fibrils being shown to have high resistivity in their unmodified state, with current values in the nanoamp range. These low current values can be increased via modification, or the fibrils used in their native state in applications where low current values are desirable. These findings, coupled with the ability to predict and select for various insulin amyloid fibril dimensions, enhances their utility as nanomaterials.
Invited review the coiled coil silk of bees, ants, and hornets.
Sutherland TD, Weisman S, Walker AA … +1 more , Mudie ST
Biopolymers · 2012 Jun · PMID 21830200 · Publisher ↗
In this article, we review current knowledge about the silk produced by the larvae of bees, ants, and hornets [Apoidea and Vespoidea: Hymenoptera]. Different species use the silk either alone or in composites for a varie...
In this article, we review current knowledge about the silk produced by the larvae of bees, ants, and hornets [Apoidea and Vespoidea: Hymenoptera]. Different species use the silk either alone or in composites for a variety of purposes including mechanical reinforcement, thermal regulation, or humidification. The characteristic molecular structure of this silk is α-helical proteins assembled into tetrameric coiled coils. Gene sequences from seven species are available, and each species possesses a copy of each of four related silk genes that encode proteins predicted to form coiled coils. The proteins are ordered at multiple length scales within the labial gland of the final larval instar before spinning. The insects control the morphology of the silk during spinning to produce either fibers or sheets. The silk proteins are small and non repetitive and have been produced artificially at high levels by fermentation in E. coli. The artificial silk proteins can be fabricated into materials with structural and mechanical properties similar to those of native silks.
Application of ring-closing metathesis to Grb2 SH3 domain-binding peptides.
Liu F, Giubellino A, Simister PC … +5 more , Qian W, Giano MC, Feller SM, Bottaro DP, Burke TR
Biopolymers · 2011 · PMID 21830199 · Full text
Molecular processes depending on protein–protein interactions can use consensus recognition sequences that possess defined secondary structures. Left-handed polyproline II (PPII) helices are a class of secondary structur...
Molecular processes depending on protein–protein interactions can use consensus recognition sequences that possess defined secondary structures. Left-handed polyproline II (PPII) helices are a class of secondary structure commonly involved with cellular signal transduction. However, unlike -helices, for which a substantial body of work exists regarding applications of ring-closing metathesis (RCM), there are few reports on the stabilization of PPII helices by RCM methodologies. The current study examined the effects of RCM macrocyclization on left-handed PPII helices involved with the SH3 domain-mediated binding of Sos1–Grb2. Starting with the Sos1-derived peptide “Ac-V1-P2-P3-P4-V5-P6-P7-R8-R9-R10-amide,” RCM macrocyclizations were conducted using alkenyl chains of varying lengths originating from the pyrrolidine rings of the Pro4 and Pro7 residues. The resulting macrocyclic peptides showed increased helicity as indicated by circular dichroism and enhanced abilities to block Grb2–Sos1 interactions in cell lysate pull-down assays. The synthetic approach may be useful in RCM macrocyclizations, where maintenance of proline integrity at both ring junctures is desired.
Minireview: structural insights into early folding events using continuous-flow time-resolved small-angle X-ray scattering.
Kathuria SV, Guo L, Graceffa R … +5 more , Barrea R, Nobrega RP, Matthews CR, Irving TC, Bilsel O
Biopolymers · 2011 Aug · PMID 21442608 · Full text
Small-angle X-ray scattering (SAXS) is a powerful method for obtaining quantitative structural information on the size and shape of proteins, and it is increasingly used in kinetic studies of folding and association reac...
Small-angle X-ray scattering (SAXS) is a powerful method for obtaining quantitative structural information on the size and shape of proteins, and it is increasingly used in kinetic studies of folding and association reactions. In this minireview, we discuss recent developments in using SAXS to obtain structural information on the unfolded ensemble and early folding intermediates of proteins using continuous-flow mixing devices. Interfacing of these micromachined devices to SAXS beamlines has allowed access to the microsecond time regime. The experimental constraints in implementation of turbulence and laminar flow-based mixers with SAXS detection and a comparison of the two approaches are presented. Current improvements and future prospects of microsecond time-resolved SAXS and the synergy with ab initio structure prediction and molecular dynamics simulations are discussed.
Sortase transpeptidases: insights into mechanism, substrate specificity, and inhibition.
Clancy KW, Melvin JA, McCafferty DG
Biopolymers · 2010 · PMID 20593474 · Full text
Gram-positive bacteria pose a serious healthcare threat. The growing antibiotic resistance epidemic creates a dire need for new antibiotic targets. The sortase family of enzymes is a promising target for antimicrobial th...
Gram-positive bacteria pose a serious healthcare threat. The growing antibiotic resistance epidemic creates a dire need for new antibiotic targets. The sortase family of enzymes is a promising target for antimicrobial therapy. This review covers the current knowledge of the mechanism, substrate specificity, and inhibitory studies of the Gram-positive bacterial [corrected] enzyme sortase.
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