Effects of Side Chains in Helix Nucleation Differ from Helix Propagation
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Collagen and Creatine
COLLAGEN AND CREATINE : PROTEIN AND NONPROTEIN NITROGENOUS COMPOUNDS Color index: . Important . Extra explanation “ THERE IS NO ELEVATOR TO SUCCESS. YOU HAVE TO TAKE THE STAIRS ” 435 Biochemistry Team • Amino acid structure. • Proteins. • Level of protein structure. RECALL: 435 Biochemistry Team Amino acid structure 1- hydrogen atom *H* ( which is distictive for each amino 2- side chain *R* acid and gives the amino acid a unique set of characteristic ) - Carboxylic acid group *COOH* 3- two functional groups - Primary amino acid group *NH2* ( except for proline which has a secondary amino acid) .The amino acid with a free amino Group at the end called “N-Terminus” . Alpha carbon that is attached to: to: thatattachedAlpha carbon is .The amino acid with a free carboxylic group At the end called “ C-Terminus” Proteins Proteins structure : - Building blocks , made of small molecules unit called amino acid which attached together in long chain by a peptide bond . Level of protein structure Tertiary Quaternary Primary secondary Single amino acids Region stabilized by Three–dimensional attached by hydrogen bond between Association of covalent bonds atoms of the polypeptide (3D) shape of called peptide backbone. entire polypeptide multi polypeptides chain including forming a bonds to form a Examples : linear sequence of side chain (R functional protein. amino acids. Alpha helix group ) Beta sheet 435 Biochemistry Team Level of protein structure 435 Biochemistry Team Secondary structure Alpha helix: - It is right-handed spiral , which side chain extend outward. - it is stabilized by hydrogen bond , which is formed between the peptide bond carbonyl oxygen and amide hydrogen. - each turn contains 3.6 amino acids. -
Helix Stability of Oligoglycine, Oligoalanine, and Oligoalanine
proteins STRUCTURE O FUNCTION O BIOINFORMATICS Helix stability of oligoglycine, oligoalanine, and oligo-b-alanine dodecamers reflected by hydrogen-bond persistence Chengyu Liu,1 Jay W. Ponder,1 and Garland R. Marshall2* 1 Department of Chemistry, Washington University, St. Louis, Missouri 63130 2 Department of Biochemistry and Molecular Biophysics, Washington University, St. Louis, Missouri 63130 ABSTRACT Helices are important structural/recognition elements in proteins and peptides. Stability and conformational differences between helices composed of a- and b-amino acids as scaffolds for mimicry of helix recognition has become a theme in medicinal chemistry. Furthermore, helices formed by b-amino acids are experimentally more stable than those formed by a-amino acids. This is paradoxical because the larger sizes of the hydrogen-bonding rings required by the extra methylene groups should lead to entropic destabilization. In this study, molecular dynamics simulations using the second-generation force field, AMOEBA (Ponder, J.W., et al., Current status of the AMOEBA polarizable force field. J Phys Chem B, 2010. 114(8): p. 2549–64.) explored the stability and hydrogen-bonding patterns of capped oligo-b-alanine, oligoalanine, and oligo- glycine dodecamers in water. The MD simulations showed that oligo-b-alanine has strong acceptor12 hydrogen bonds, but surprisingly did not contain a large content of 312-helical structures, possibly due to the sparse distribution of the 312-helical structure and other structures with acceptor12 hydrogen bonds. On the other hand, despite its backbone flexibility, the b- alanine dodecamer had more stable and persistent <3.0 A˚ hydrogen bonds. Its structure was dominated more by multicen- tered hydrogen bonds than either oligoglycine or oligoalanine helices. -
Helix Capping'
Prorein Science (1998), 721-38. Cambridge University Press. Printed in the USA. Copyright 0 1998 The Protein Society REVIEW Helix capping' RAJEEV AURORA AND GEORGE D. ROSE Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, Maryland 21205 (RECEIVED June12, 1997; ACCEPTEDJuly 9, 1997) Abstract Helix-capping motifs are specific patterns of hydrogen bonding and hydrophobic interactions found at or near the ends of helices in both proteins and peptides. In an a-helix, the first four >N- H groups and last four >C=O groups necessarily lack intrahelical hydrogen bonds. Instead, such groups are often capped by alternative hydrogen bond partners. This review enlarges our earlier hypothesis (Presta LG, Rose GD. 1988. Helix signals in proteins. Science 240:1632-1641) to include hydrophobic capping. A hydrophobic interaction that straddles the helix terminus is always associated with hydrogen-bonded capping. From a global survey among proteins of known structure, seven distinct capping motifs are identified-three at the helix N-terminus and four at the C-terminus. The consensus sequence patterns of these seven motifs, together with results from simple molecular modeling, are used to formulate useful rules of thumb for helix termination. Finally, we examine the role of helix capping as a bridge linking the conformation of secondary structure to supersecondary structure. Keywords: alpha helix; protein folding; protein secondary structure The a-helixis characterized by consecutive, main-chain, i + i - 4 apolar residues in the a-helix and its flanking turn. This hydro- hydrogen bonds between each amide hydrogen and a carbonyl phobic component of helix capping was unanticipated. -
And Beta-Helical Protein Motifs
Soft Matter Mechanical Unfolding of Alpha- and Beta-helical Protein Motifs Journal: Soft Matter Manuscript ID SM-ART-10-2018-002046.R1 Article Type: Paper Date Submitted by the 28-Nov-2018 Author: Complete List of Authors: DeBenedictis, Elizabeth; Northwestern University Keten, Sinan; Northwestern University, Mechanical Engineering Page 1 of 10 Please doSoft not Matter adjust margins Soft Matter ARTICLE Mechanical Unfolding of Alpha- and Beta-helical Protein Motifs E. P. DeBenedictis and S. Keten* Received 24th September 2018, Alpha helices and beta sheets are the two most common secondary structure motifs in proteins. Beta-helical structures Accepted 00th January 20xx merge features of the two motifs, containing two or three beta-sheet faces connected by loops or turns in a single protein. Beta-helical structures form the basis of proteins with diverse mechanical functions such as bacterial adhesins, phage cell- DOI: 10.1039/x0xx00000x puncture devices, antifreeze proteins, and extracellular matrices. Alpha helices are commonly found in cellular and extracellular matrix components, whereas beta-helices such as curli fibrils are more common as bacterial and biofilm matrix www.rsc.org/ components. It is currently not known whether it may be advantageous to use one helical motif over the other for different structural and mechanical functions. To better understand the mechanical implications of using different helix motifs in networks, here we use Steered Molecular Dynamics (SMD) simulations to mechanically unfold multiple alpha- and beta- helical proteins at constant velocity at the single molecule scale. We focus on the energy dissipated during unfolding as a means of comparison between proteins and work normalized by protein characteristics (initial and final length, # H-bonds, # residues, etc.). -
DNA-Mediated Self-Assembly of Gold Nanoparticles on Protein Superhelix
bioRxiv preprint doi: https://doi.org/10.1101/449561; this version posted October 22, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. DNA-mediated self-assembly of gold nanoparticles on protein superhelix Tao Zhang∗,y,z and Ingemar Andréy yDepartment of Biochemistry and Structural Biology & Center for Molecular Protein Science, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden zCurrent address: Max-Planck-Institute for Intelligent Systems, Heisenbergstraße 3, D-70569 Stuttgart, Germany E-mail: [email protected] Abstract Recent advances in protein engineering have enabled methods to control the self- assembly of protein on various length-scales. One attractive application for designed proteins is to direct the spatial arrangement of nanomaterials of interest. Until now, however, a reliable conjugation method is missing to facilitate site-specific position- ing. In particular, bare inorganic nanoparticles tend to aggregate in the presence of buffer conditions that are often required for the formation of stable proteins. Here, we demonstrated a DNA mediated conjugation method to link gold nanoparticles with protein structures. To achieve this, we constructed de novo designed protein fibers based on previously published uniform alpha-helical units. DNA modification rendered gold nanoparticles with increased stability against ionic solutions and the use of com- plementary strands hybridization guaranteed the site-specific binding to the protein. The combination of high resolution placement of anchor points in designed protein assemblies with the increased control of covalent attachment through DNA binding 1 bioRxiv preprint doi: https://doi.org/10.1101/449561; this version posted October 22, 2018. -
Folding-TIM Barrel
Protein Folding Practical September 2011 Folding up the TIM barrel Preliminary Examine the parallel beta barrel that you constructed, noting the stagger of the strands that was needed to connect the ends of the 8-stranded parallel beta sheet into the 8-stranded beta barrel. Notice that the stagger dictates which side of the sheet is on the inside and which is on the outside. This will be key information in folding the complete TIM linear peptide into the TIM barrel. Assembling the full linear peptide 1. Make sure the white beta strands are extended correctly, and the 8 yellow helices (with the green loops at each end) are correctly folded into an alpha helix (right handed with H-bonds to the 4th ahead in the chain). 2. starting with a beta strand connect an alpha helix and green loop to make the blue-red connecting peptide bond. Making sure that you connect the carbonyl (red) end of the beta strand to the amino (blue) end of the loop-helix-loop. Secure the just connected peptide bond bond with a twist-tie as shown. 3. complete step 2 for all beta strand/loop-helix-loop pairs, working in parallel with your partners 4. As pairs are completed attach the carboxy end of the strand- loop-helix-loop to the amino end of the next strand-loop-helix-loop module and secure the new peptide bond with a twist-tie as before. Repeat until the full linear TIM polypeptide chain is assembled. Make sure all strands and helices are still in the correct conformations. -
Predicting Protein Secondary and Supersecondary Structure
29 Predicting Protein Secondary and Supersecondary Structure 29.1 Introduction............................................ 29-1 Background • Difficulty of general protein structure prediction • A bottom-up approach 29.2 Secondary structure ................................... 29-5 Early approaches • Incorporating local dependencies • Exploiting evolutionary information • Recent developments and conclusions 29.3 Tight turns ............................................. 29-13 29.4 Beta hairpins........................................... 29-15 29.5 Coiled coils ............................................. 29-16 Early approaches • Incorporating local dependencies • Predicting oligomerization • Structure-based predictions • Predicting coiled-coil protein interactions Mona Singh • Promising future directions Princeton University 29.6 Conclusions ............................................ 29-23 29.1 Introduction Proteins play a key role in almost all biological processes. They take part in, for example, maintaining the structural integrity of the cell, transport and storage of small molecules, catalysis, regulation, signaling and the immune system. Linear protein molecules fold up into specific three-dimensional structures, and their functional properties depend intricately upon their structures. As a result, there has been much effort, both experimental and computational, in determining protein structures. Protein structures are determined experimentally using either x-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. While -
Lecture 7 Protein Secondary Structure Prediction
Protein primary structure C Master Course E N DNA/Protein Structure- 20 amino acid types A generic residue Peptide bond T R E function Analysis and F B O I Prediction R O I I N N T F E O G R R M Lecture 7 SARS Protein From Staphylococcus Aureus A A 1 MKYNNHDKIR DFIIIEAYMF RFKKKVKPEV T T 31 DMTIKEFILL TYLFHQQENT LPFKKIVSDL I I 61 CYKQSDLVQH IKVLVKHSYI SKVRSKIDER V C 91 NTYISISEEQ REKIAERVTL FDQIIKQFNL E S 121 ADQSESQMIP KDSKEFLNLM MYTMYFKNII V Protein Secondary 151 KKHLTLSFVE FTILAIITSQ NKNIVLLKDL U 181 IETIHHKYPQ TVRALNNLKK QGYLIKERST 211 EDERKILIHM DDAQQDHAEQ LLAQVNQLLA Structure Prediction 241 DKDHLHLVFE Protein secondary structure Alpha-helix Beta strands/sheet Secondary Structure • An easier question – what is the secondary structure when the 3D structure is known? SARS Protein From Staphylococcus Aureus 1 MKYNNHDKIR DFIIIEAYMF RFKKKVKPEV DMTIKEFILL TYLFHQQENT SHHH HHHHHHHHHH HHHHHHTTT SS HHHHHHH HHHHS S SE 51 LPFKKIVSDL CYKQSDLVQH IKVLVKHSYI SKVRSKIDER NTYISISEEQ EEHHHHHHHS SS GGGTHHH HHHHHHTTS EEEE SSSTT EEEE HHH 101 REKIAERVTL FDQIIKQFNL ADQSESQMIP KDSKEFLNLM MYTMYFKNII HHHHHHHHHH HHHHHHHHHH HTT SS S SHHHHHHHH HHHHHHHHHH 151 KKHLTLSFVE FTILAIITSQ NKNIVLLKDL IETIHHKYPQ TVRALNNLKK HHH SS HHH HHHHHHHHTT TT EEHHHH HHHSSS HHH HHHHHHHHHH 201 QGYLIKERST EDERKILIHM DDAQQDHAEQ LLAQVNQLLA DKDHLHLVFE HTSSEEEE S SSTT EEEE HHHHHHHHH HHHHHHHHTS SS TT SS DSSP • DSSP (Dictionary of Secondary Structure of a Protein) – assigns secondary structure to proteins which have a crystal (x-ray) or NMR (Nuclear Magnetic Resonance) A more challenging task: structure Predicting secondary structure from H = alpha helix primary sequence alone B = beta bridge (isolated residue) DSSP uses hydrogen-bonding E = extended beta strand structure to assign Secondary Structure Elements (SSEs). -
Structures of Proteins and Enzymes
1 xxx-paper name? Biochemistry Enzyme structure Description of Module Subject Name Biochemstry Paper Name 14 Module Name/Title 3 Enzyme Structure Dr. Vijaya Khader Dr. MC Varadaraj 2 xxx-paper name? Biochemistry Enzyme structure 1. Objectives Look at the various components of enzyme structure Understanding the types of enzyme structures in detail 2. Concept Map 3 xxx-paper name? Biochemistry Enzyme structure 3. Description 3.1 Enzymes Enzymes are biological catalysts that increase the rate of reaction without affecting the reaction equilibrium. They work by lowering the activation energy (Ea) for a reaction, which leads to an increase in reaction rate and faster product formation. Enzymatic reactions are also characterized by high substrate and reaction specificity and fewer side reactions. Enzymes have had several applications in areas of research and development, food and feed industry, pharmaceutical industry and other industries like detergent, textile, leather etc. 3.2 Enzyme structure Enzymes have four levels of structures as shown in Fig 1. These are: Primary structure Secondary structure Tertiary structure Quaternary structure The enzyme structure ranges from a basic amino acid sequence to a three dimensional (3D) structure in a folded protein. The amino acid sequence in polypeptide chains in each enzyme is distinct and determines the three-dimensional shape. Further, it is the 3D structure of an enzyme that determines the enzyme activities. We will look at these structures in detail in the sections below. 4 xxx-paper name? Biochemistry Enzyme structure Fig 1 3.3.1 Primary structure • The sequence of amino acids in an enzyme is the primary structure. -
Amino ACIDS PROTEINS
Taras Shevchenko National University of Kyiv The Institute of Biology and Medicine METHODICAL POINTING from the course “Biological and bioorganic chemistry” (part 3. Amino acids and proteins) for the studens of a 1 course with English of educating Compiler – the candidate of biological sciences, the associate professor Synelnyk Tatyana Borysivna Readers: It is ratified to printing by meeting of scientific advice of The Institute of Biology and Medicine (“____”________________ 2018, protocol №____) Kyiv-2018 2 CONTENT 3.1. General information …………………………………………………….. 3 3.2. Nomenclature and classification of α-amino acids ……………. 4 3.3. Amphoteric and stereochemical properties of amino acids. Chiral carbon atom……………………………………………………………… 8 3.4. Isoelectric point of amino acid . Titration curves ……………… 9 3.4.1. The typical titration curve of amino acids with uncharged radical…………………………………………………………. 10 3.4.2. The titration curves of amino acids with charged radical ……………………………………………………………………….. 11 3.5. Chemical properties of amino acids and some methods for amino acids determination and separation…………………………….. 14 3.6. Peptide bond formation. Peptides. …………………………………. 15 3.7. Proteins. The levels of protein molecules organization ……… 16 3.7.1. Primary protein structure ……………………………………. 17 3.7.2. The secondary structure of proteins: types …………….. 18 3.7.3. Super secondary structure …………………………………… 22 3.7.4. Tertiary Structure of proteins ……………………………… 23 3.7.5. Domain structure of proteins ……………………………… 26 3.7.6. Quaternary Structure of proteins ………………………… 26 3.8. Methods of extraction and purification of proteins ………….. 28 3.8.1. Methods of extraction of proteins from cells or tissues in the dissolved state. ………………………………………………….. 28 3.8.2. Methods of separating a mixture of proteins 29 3.9. -
Secondary Structure Assignment and Prediction •Why to Predict Secondary Structures in Proteins
Talk overview •Secondary structure assignment Secondary structure assignment and prediction •Why to predict secondary structures in proteins • Methods to predict secondary structures in proteins • Machine learning approaches • Detailed description of several specific programs (PHD) • Performance and evaluation May 2011 Eran Eyal Automatic assignment of secondary structures to a set of protein coordinates Assignment of secondary structures to known secondary structures is a relatively simple bioinformatics task. Given exact definitions for secondary structures, all we need to do is to see which part of the structure falls within each definition α-helix Why to automatically and routinely assign secondary structures ? •Standardization •Easy visualization •Detection of structural motifs and improved sequence-structure searches •Structural alignment Β-strand •Structural classification What basic structural information is used ? q > 120° and rHO < 2.5 Ǻ •Hydrogen bond patterns •Backbone dihedral angles DSSP algorithm •The helix definition does not include the terminal residue •The so-called “Dictionary of Secondary Structure of Proteins” having the initial and final hydrogen bonds in the helix. (DSSP) by Kabsch and Sander makes its sheet and helix assignments solely on the basis of backbone-backbone •A minimal size helix is set to have two consecutive hydrogen hydrogen bonds. bonds in the helix, leaving out single helix hydrogen bonds, which are assigned as turns (state 'T'). •The DSSP method defines a hydrogen bond when the bond energy is below -0.5 kcal/mol from a Coulomb approximation •beta-sheet residues (state 'E') are defined as either having two of the hydrogen bond energy. hydrogen bonds in the sheet, or being surrounded by two hydrogen bonds in the sheet. -
A Novel Approach for Protein Structure Prediction
A Novel Approach for Protein Structure Prediction The Project Report is submitted in partial fulfillment of the requirements for the award of the degree of BACHELOR OF TECHNOLOGY Submitted By: (Saurabh Sarkar, Prateek Malhotra, Virender Guman) Department of Computer Science & Engineering G.L.Bajaj Institute of Technology & Mgmt. Greater Noida Uttar Pradesh Technical University Lucknow (U. P.) India A Novel Approach for Protein Structure Prediction The Project Report is submitted in partial fulfillment of the requirements for the award of the degree of BACHELOR OF TECHNOLOGY Submitted By: (Saurabh Sarkar, Prateek Malhotra, Virender Guman) Department of Computer Science & Engineering G.L.Bajaj Institute of Technology & Mgmt. Greater Noida Uttar Pradesh Technical University Lucknow (U. P.) India A Novel Approach for Protein Structure Prediction January 1, 2010 CERTIFICATE This is to certify that the project report entitled “A Novel Approach for Protein Structure Prediction” submitted by by Saurabh Sarkar, Prateek Malhortra, Virender Guman in the Department of Computer Science & Engineering, G.L.Bajaj Institute of Technology and Management, Greater Noida for the award of Bachelor of Technology is a record of the bona-fide work carried out by them under my supervision. Details of the student(s) Certified by: Mr. Saurabh Sarkar (0619210099) Prof. K.S. Mehta HOD (CSE Department) Mr. Prateek Malhotra (0619210083) Mr. Virender Guman (0619210118) Department of the Computer Science & Engineering G.L.B.I.T.M. Greater Noida Page I A Novel Approach for Protein Structure Prediction January 1, 2010 ACKNOWLEDGEMENT At the very outset, we are highly indebted to G.L. Bajaj Instt. Of Tech. & Mgmt., Gr.