Virtual Issues
The following Virtual Issues are available:
- Protein Function Annotation: The next frontier in molecular biology (February, 2012)
- Frontiers in Protein Research: A Joint Virtual Issue of Protein Science and PROTEINS-Structure, Function, and Bioinformatics (July, 2011)
- Focus on The Pacific Rim (May, 2011)
- Protein Folding: Short Question - Long Answer (July, 2010)
- Learning about proteins that live in membranes (November, 2009)
- Celebrating the Structure of Myoglobin and its Impact on the Science of Proteins (May, 2009)
Issue 6, February 2012: protein function annotation: the next frontier in molecular biology
Protein folding has been called the “major unsolved challenge” in understanding proteins. But, one could argue that the real challenge involves understanding, in molecular detail, what those proteins actually do—their detailed molecular function. In 2006, Protein Science published the results from the first Automated Function Prediction meeting, held in Detroit, MI, in 2005. Since then, protein function prediction has become a field in its own right, with researchers trying to make sense of the masses of proteins of unknown function, whose sequences and structures are determined by today’s high-throughput techniques. This virtual issue of Protein Science highlights some of the important articles published at that first AFP meeting, as well as more recently published articles in this relatively young, but exciting, area of protein science.
Introduction to the Virtual Issue
Jacquelyn S. Fetrow
Recent articles-general protein function prediction
Sequence and structure continuity of evolutionary importance improves protein functional site discovery and annotation
A. D. Wilkins, R. Lua, S. Erdin, R. M. Ward and O. Lichtarge
Toward prediction of functional protein pockets using blind docking and pocket search algorithms
Csaba Hetényi and David van der Spoel
Prediction of ligand-binding sites of proteins by molecular docking calculation for a random ligand library
Yoshifumi Fukunishi and Haruki Nakamura
Recent articles- function prediction in a specific protein or protein family
Functional hot spots in human ATP-binding cassette transporter nucleotide binding domains
Libusha Kelly, Hisayo Fukushima, Rachel Karchin, Jason M. Gow, Leslie W. Chinn, Ursula Pieper, Mark R. Segal, Deanna L. Kroetz and Andrej Sali
Fast and automated functional classification with MED-SuMo: An application on purine-binding proteins
Olivia Doppelt-Azeroual, François Delfaud, Fabrice Moriaud and Alexandre G. de Brevern
Analysis and prediction of calcium-binding pockets from apo-protein structures exhibiting calcium-induced localized conformational changes
Xue Wang, Kun Zhao, Michael Kirberger, Hing Wong, Guantao Chen and Jenny J. Yang
Recent articles-examples of why protein function prediction is so hard
Predicting memapsin 2 (β-secretase) hydrolytic activity
Xiaoman Li, Huang Bo, Xuejun C. Zhang, Jean A. Hartsuck and Jordan Tang
Comparison of human solute carriers
Avner Schlessinger, Pär Matsson, James E. Shima, Ursula Pieper, Sook Wah Yee, Libusha Kelly, Leonard Apeltsin, Robert M. Stroud, Thomas E. Ferrin, Kathleen M. Giacomini and Andrej Sali
Analysis of the plasticity of location of the Arg244 positive charge within the active site of the TEM-1 β-lactamase
David C. Marciano, Nicholas G. Brown and Timothy Palzkill
Comparative surface geometry of the protein kinase family
Elaine E. Thompson, Alexandr P. Kornev, Natarajan Kannan, Choel Kim, Lynn F. Ten Eyck and Susan S. Taylor
Future of function prediction is functional site design
Motif-directed flexible backbone design of functional interactions
James J. Havranek and David Baker
From the first Automated Protein Function Prediction (AFP) meeting in 2005
New avenues in protein function prediction
Iddo Friedberg, Martin Jambon and Adam Godzik
Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity
David M. Kristensen, Brian Y. Chen, Viacheslav Y. Fofanov, R. Matthew Ward, Andreas Martin Lisewski, Marek Kimmel, Lydia E. Kavraki and Olivier Lichtarge
Structure-based function inference using protein family-specific fingerprints
Deepak Bandyopadhyay, Jun Huan, Jinze Liu, Jan Prins, Jack Snoeyink, Wei Wang and Alexander Tropsha
A categorization approach to automated ontological function annotation
Karin Verspoor, Judith Cohn, Susan Mniszewski and Cliff Joslyn
Enhanced automated function prediction using distantly related sequences and contextual association by PFP
Troy Hawkins, Stanislav Luban and Daisuke Kihara
Functional annotation prediction: All for one and one for all
Ori Sasson, Noam Kaplan and Michal Linial
Issue 5, July 2011: Frontiers in Protein Research: A Joint Virtual Issue of Protein science and PROTEINS: Structure, Function, and Bioinformatics
This virtual issue is the first joint venture between Protein Science and PROTEINS: STRUCTURE, FUNCTION, AND BIOINFORMATICS. The collection of papers highlights current trends in the field. The issue is organized primarily around relatively new areas of protein research (e.g. unfolded proteins, membrane proteins, amyloids, interactions, design, binding), as represented by some highly cited papers in these journals in recent years. The collection certainly contrasts with the time when PROTEINS and Protein Science first appeared in 1986 and 1992, respectively. At that time few crystal structures were routine, only one high resolution membrane protein structure was available, and the VAX computer was king. Now we see papers on the high resolution structures of seemingly intractable amyloid fibers and giant complexes like the carboxysome, alongside microsecond simulations. Yet proteins continue to challenge us with their complexity and the papers in this virtual issue also underscore the need for continued studies of fundamental structural and physico-chemical properties of proteins.
Paramagnetic relaxation enhancements in unfolded proteins: Theory and application to drkN SH3 domain
Yi Xue, Ivan S. Podkorytov, D. Krishna Rao, Nathan Benjamin, Honglei Sun and Nikolai R. Skrynnikov
Order propensity of an intrinsically disordered protein, the cyclin-dependent-kinase inhibitor Sic1
Stefania Brocca, Mária Šamalíková, Vladimir N. Uversky, Marina Lotti, Marco Vanoni, Lilia Alberghina and Rita Grandori
Kazumi Shimono, Mie Goto, Takashi Kikukawa, Seiji Miyauchi, Mikako Shirouzu, Naoki Kamo and Shigeyuki Yokoyama
George Khelashvili, Alan Grossfield, Scott E. Feller, Michael C. Pitman and Harel Weinstein
Selected-fit versus induced-fit protein binding: Kinetic differences and mutational analysis
Thomas R. Weikl and Carola von Deuster
At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?
Shina C. L. Kamerlin and Arieh Warshel
A summary of the measured pK values of the ionizable groups in folded proteins
Gerald R. Grimsley, J. Martin Scholtz and C. Nick Pace
Jed J. W. Wiltzius, Stuart A. Sievers, Michael R. Sawaya and David Eisenberg
Thermodynamics and dynamics of amyloid peptide oligomerization are sequence dependent
Yan Lu, Philippe Derreumaux, Zhi Guo, Normand Mousseau and Guanghong Wei
Improved prediction of protein side-chain conformations with SCWRL4
Georgii G. Krivov, Maxim V. Shapovalov and Roland L. Dunbrack Jr.
Richard H. Kimura, Aron M. Levin, Frank V. Cochran and Jennifer R. Cochran
Will Sheffler and David Baker
Paul C. Whitford, Jeffrey K. Noel, Shachi Gosavi, Alexander Schug, Kevin Y. Sanbonmatsu and José N. Onuchic
Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage miniprotein
Ryan Day, Dietmar Paschek and Angel E. Garcia
Protonate3D: Assignment of ionization states and hydrogen coordinates to macromolecular structures
Paul Labute
Arthur Laganowsky, Justin L. P. Benesch, Meytal Landau, Linlin Ding, Michael R. Sawaya, Duilio Cascio, Qingling Huang, Carol V. Robinson, Joseph Horwitz and David Eisenberg
Small-angle scattering for structural biology—Expanding the frontier while avoiding the pitfalls
David A. Jacques and Jill Trewhella
Insights from multiple structures of the shell proteins from the β-carboxysome
Shiho Tanaka, Michael R. Sawaya, Martin Phillips and Todd O. Yeates
issue 4, May 2011: focus on the Pacific Rim
This issue highlights recent contributions to Protein Science from the nations of the Pacific Rim and the Asian Pacific Protein Association (APPA). Protein science is a vibrant and thriving discipline in all of these countries and, while it is clearly impossible to provide a compressive overview, this issue offers a taste of the exciting and diverse research being undertaken. Three comprehensive, up-to-date, review articles on protein stabilization by small molecules, cryo-electron microscopy, and small angle X-ray scattering are included together with eleven original articles. These papers span the range from protein design, protein folding and stability, enzymology, structural biology, and membrane proteins. This issue is particularly timely since it coincides with the recent 3th international Asian Pacific Protein Association conference held in Shanghai which was jointly sponsored by the APPA and The Protein Society.
Introduction to the Virtual issue
Daniel Raleigh
Small-angle scattering for structural biology—Expanding the frontier while avoiding the pitfalls
David A. Jacques and Jill Trewhella
Kwon Joo Yeo, Hye-Yeon Kim, Young Pil Kim, Eunha Hwang, Myung Hee Kim, Chaejoon Cheong, Senyon Choe and Young Ho Jeon
Supachai Sakkhachornphop, Supat Jiranusornkul, Kanchanok Kodchakorn, Sawitree Nangola, Thira Sirisanthana and Chatchai Tayapiwatana
Crystal structure of the human receptor activity-modifying protein 1 extracellular domain
Seisuke Kusano, Mutsuko Kukimoto-Niino, Ryogo Akasaka, Mitsutoshi Toyama, Takaho Terada, Mikako Shirouzu, Takayuki Shindo and Shigeyuki Yokoyama
Structural physiology based on electron crystallography
Yoshinori Fujiyoshi
Structural basis for the negative regulation of bacterial stress response by RseB
Dong Young Kim, Eunju Kwon, JongKeun Choi, Hye-Yeon Hwang and Kyeong Kyu Kim
Structural insight into the catalytic mechanism of gluconate 5-dehydrogenase from Streptococcus suis: Crystal structures of the substrate-free and quaternary complex enzymes
Qiangmin Zhang, Hao Peng, Feng Gao, Yiwei Liu, Hao Cheng, John Thompson and George F. Gao
Solution structure of the ubiquitin-associated domain of human BMSC-UbP and its complex with ubiquitin
Yong-Gang Chang, Ai-Xin Song, Yong-Guang Gao, Yan-Hong Shi, Xiao-Jing Lin, Xue-Tao Cao, Dong-Hai Lin and Hong-Yu Hu
NMR and crystallographic structures of the FK506 binding domain of human malarial parasite Plasmodium vivax FKBP35
Reema Alag, Insaf A. Qureshi, Nagakumar Bharatham, Joon Shin, Julien Lescar and Ho Sup Yoon
Identification of transient hub proteins and the possible structural basis for their multiple interactions
Miho Higurashi, Takashi Ishida and Kengo Kinoshita
Lone pair ··· π interactions between water oxygens and aromatic residues: Quantum chemical studies based on high-resolution protein structures and model compounds
Alok Jain, Venkatnarayan Ramanathan and Ramasubbu Sankararamakrishnan
Stereoelectronic effects on the transition barrier of polyproline conformational interconversion
Yi-Chun Chiang, Yu-Ju Lin and Jia-Cherng Horng
Counting peptide-water hydrogen bonds in unfolded proteins
Haipeng Gong, Lauren L. Porter and George D. Rose
Effect of trehalose on protein structure
Nishant Kumar Jain and Ipsita Roy
Issue 3, July 2010: Protein Folding: Short Question – Long Answer
Arguably, more articles in Protein Science deal with the folding of proteins than any other subject. Solving the protein folding problem also remains as one of the major challenges in biology. This Virtual Issue combines two groups of articles from Protein Science that deal with this subject. The first selections have already established themselves as “citation classics”. The second group of selections includes articles published within the past three years that can be characterized as “up-and-coming citation classics”. Together, these contributions revisit established highlights and provide pointers to future developments.
Introduction to the Virtual issue
Brian W. Matthews
Principles of protein folding-A perspective from simple exact models
Ken A. Dill, Sarina Bromberg, Kaizhi Yue, Hue Sun Chan, Klaus M. Ftebig, David P. Yee and Paul D. Thomas
Structure and dynamics of de novo proteins from a designed superfamily of 4-helix bundles
Abigail Go, Seho Kim, Jean Baum and Michael H. Hecht
Molecular dynamics simulations of alanine rich β-sheet oligomers: Insight into amyloid formation
Buyong Ma, Ruth Nussinov
Denaturant m values and heat capacity changes: Relation to changes in accessible surface areas of protein unfolding
Jeffrey K. Myers, C. Nick Pace and J. Martin Scholtz
Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions
Avijit Chakrabartty, Tanja Kortemme and Robert L. Baldwin
Toward quantification of protein backbone-backbone hydrogen bonding energies: An energetic analysis of an amide-to-ester mutation in an α-helix within a protein
Jianmin Gao and Jeffery W. Kelly
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
Hongyi Zhou and Yaoqi Zhou
The effects of macromolecular crowding on the mechanical stability of protein molecules
Jian-Min Yuan, Chia-Lin Chyan, Huan-Xiang Zhou, Tse-Yu Chung, Haibo Peng, Guanghui Ping and Guoliang Yang
Contact order revisited: Influence of protein size on the folding rate
Dmitry N. Ivankov, Sergiy O. Garbuzynskiy, Eric Alm, Kevin W. Plaxco, David Baker, Alexei V. Finkelstein
The topomer search model: A simple, quantitative theory of two-state protein folding kinetics
Dmitrii E. Makarov, Kevin W. Plaxco
Folding thermodynamics and kinetics of the leucine-rich repeat domain of the virulence factor Internalin B
Naomi Courtemanche, Doug Barrick
Structural characterization of partially folded intermediates of apomyoglobin H64F
Stephan Schwarzinger, Ronaldo Mohana-Borges, Gerard J.A. Kroon, H. Jane Dyson, Peter E. Wright
3D domain swapping: A mechanism for oligomer assembly
Melanie J. Bennett, Michael P. Schlunegger, David Eisenberg
RosettaHoles: Rapid assessment of protein core packing for structure prediction, refinement, design, and validation
Will Sheffler, David Baker
GroEL-mediated protein folding
Wayne A. Fenton, Arthur L. Horwich
The Brichos domain of prosurfactant protein C can hold and fold a transmembrane segment
Hanna Johansson, Maria Eriksson, Kerstin Nordling, Jenny Presto, Jan Johansson
Export chaperone SecB uses one surface of interaction for diverse unfolded polypeptide ligands
Angela A. Lilly, Jennine M. Crane, Linda L. Randall
Escherichia coli maltose-binding protein is uncommonly effective at promoting the solubility of polypeptides to which it is fused
Rachel B. Kapust, David S. Waugh
Deamidation destabilizes and triggers aggregation of a lens protein, βA3-crystallin
Takumi Takata, Julie T. Oxford, Borries Demeler, Kirsten J. Lampi
Crystal structures of truncated alphaA and alphaB crystallins reveal structural mechanisms of polydispersity important for eye lens function
Arthur Laganowsky, Justin L. P. Benesch, Meytal Landau, Linlin Ding, Michael R. Sawaya, Duilio Cascio, Qingling Huang, Carol V. Robinson, Joseph Horwitz, David Eisenberg
Issue 2, November 2009: Learning about proteins that live in membranes
Protein Science began publishing in 1992, not long after we were treated to the first high-resolution membrane protein structure. The photosynthetic reaction center structure finally showed that membrane proteins could be investigated at the atomic level, which induced a ratcheting up of membrane protein work that continues to build steam. Protein Science has been a natural place for reporting these efforts and this virtual issue highlights the breadth of membrane protein subjects that have found a home in the journal.
Introduction to the Virtual issue
James U. Bowie
Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms
Erik Wallin, Gunnar Von Heijne
Toward genomic identification of beta-barrel membrane proteins: composition and architecture of known structures
William C. Wimley
The progress of membrane protein structure determination
Stephen H. White
A limited universe of membrane protein families and folds
Amit Oberai, Yungok Ihm, Sanguk Kim, James U. Bowie
Structure of the membrane channel porin from Rhodopseudomonas blastica at 2.0 Å resolution
A. Kreusch, A. Neubüser, E. Schiltz, J. Weckesser, G.E. Schulz
Crystal structure of the antibiotic albomycin in complex with the outer membrane transporter FhuA
Andrew D. Ferguson, James W. Coulton, Kay Diederichs, Wolfram Welte, Volkmar Braun, Hans-Peter Fiedler
Structure and electrostatic property of cytoplasmic domain of ZntB transporter
Kemin Tan, Alicia Sather, Janice L. Robertson, Shiu Moy, Benoît Roux, Andrzej Joachimiak
Simultaneous assignment and structure determination of a membrane protein from NMR orientational restraints
Francesca M. Marassi, Stanley J. Opella
Rationalizing alpha-helical membrane protein crystallization
Simon Newstead, Sébastien Ferrandon, So Iwata
Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information
Håkan Viklund, Arne Elofsson
Experimentally based topology models for E. coli inner membrane proteins
Mikaela Rapp, David Drew, Daniel O. Daley, Johan Nilsson, Tiago Carvalho, Karin Melén, Jan-Willem De Gier, Gunnar Von Heijne
How do helix-helix interactions help determine the folds of membrane proteins? Perspectives from the study of homo-oligomeric helical bundles
William F. DeGrado, Holly Gratkowski, James D. Lear
Determination of membrane protein stability via thermodynamic coupling of folding to thiol-disulfide interchange
Lidia Cristian, James D. Lear, William F. DeGrado
Interaction and conformational dynamics of membrane-spanning protein helices
Dieter Langosch, Isaiah T. Arkin
An improved tripod amphiphile for membrane protein solubilization
Seungju M. Yu, D. Tyler McQuade, Mariah A. Quinn, Christian P.R. Hackenberger, Samuel H. Gellman, Mark P. Krebs, Arthur S. Polans
Self-assembly of single integral membrane proteins into soluble nanoscale phospholipid bilayers
Timothy H. Bayburt, Stephen G. Sligar
Engineering a G protein-coupled receptor for structural studies: stabilization of the BLT1 receptor ground state
Aimée Martin, Marjorie Damian, Michel Laguerre, Joseph Parello, Bernard Pucci, Laurence Serre, Sophie Mary, Jacky Marie, Jean-Louis Banères
Expression of human peripheral cannabinoid receptor for structural studies
Alexei A. Yeliseev, Karen K. Wong, Olivier Soubias, Klaus Gawrisch
Efficient production of membrane-integrated and detergent-soluble G protein-coupled receptors in Escherichia coli
A. James Link, Georgios Skretas, Eva-Maria Strauch, Nandini S. Chari, George Georgiou
Genetic selection system for improving recombinant membrane protein expression in E. coli
Elizabeth Massey-Gendel, Anni Zhao, Gabriella Boulting, Hye-Yeon Kim, Michael A. Balamotis, Len M. Seligman, Robert K. Nakamoto, James U. Bowie
Issue 1, May 2009: Celebrating the Structure of Myoglobin and its Impact on the Science of Proteins
This virtual issue of Protein Science is intended to commemorate the 50th anniversary of the myoglobin structure determination. It is made up of articles selected exclusively from the first six years of the journal’s publication (1992-1997). As such, the coverage is not all-inclusive. Nevertheless, it does provide a remarkable historical overview not only of the myoglobin structure determination, per se, but other pioneers who have shaped the field of protein science as we now understand it. Against all odds, Perutz and Kendrew established the field of protein crystallography. The structure of myoglobin, now 50 years ago, vindicated their efforts. More important, however, was the revolution in structural biology that they made possible. This volume celebrates their achievement.
A message from the editor
Brian W. Matthews
A little ancient history
Richard E. Dickerson
The beginnings of structural biology
Michael G. Rossmann
Max Perutz's achievements: How did he do it?
David Eisenberg
Obituary: Sir John Kendrew (1917-1997)
M.F. Perutz
Linderstrøm-Lang and the Carlsberg Laboratory: The view of a postdoctoral fellow in 1954
Frederic M. Richards
How my interest in proteins developed
Linus Pauling
Memories of early days in protein science, 1926-1940
John T. Edsall
Macromolecules
Charles Tanford
Poly-α-amino acids as the simplest protein models: Recollections of a retired state president
Ephraim Katchalski-Katzir
The contributions of Stein and Moore to protein science
James M. Manning
Christian B. Anfinsen (1916-1995) Remembering His Life and His Science
Michael Young
Some early tracer experiments with stable isotopes
Mildred Cohn
ATP and inorganic pyro- and polyphosphate
Arthur Kornberg
The joys and vicissitudes of protein science
Daniel E. Koshland Jr.
The chemical synthesis of proteins
Bruce Merrifield
Reconstructing history with amino acid sequences
Russell F. Doolittle
A database of protein structure families with common folding motifs
Liisa Holm, Christos Ouzounis, Chris Sander, Georg Tuparev, Gert Vriend
The molten globule intermediate of apomyoglobin and the process of protein folding
Doug Barrick, Robert L. Baldwin
Principles of protein folding - A perspective from simple exact models
Ken A. Dill, Sarina Bromberg, Kaizhi Yue, Hue Sun Chan, Klaus M. Ftebig, David P. Yee, Paul D. Thomas
Buried waters and internal cavities in monomeric proteins
Mark A. Williams, Julia M. Goodfellow, Janet M. Thornton
Sequence determinants of the capping box, a stabilizing motif at the N-termini of α-helices
Jeffrey W. Seale, Rajgopal Srinivasan, George D. Rose
De novo design of the hydrophobic cores of proteins
John R. Desjarlais, Tracy M. Handel
3D domain swapping: A mechanism for oligomer assembly
Melanie J. Bennett, Michael P. Schlunegger, David Eisenberg
Influenza virus neuraminidase: Structure, antibodies, and inhibitors
P.M. Colman
